Rule 15: (6, lift 20.5) [ss( A ,c),nss( A , B ,a),len_lteq( B ,10)] = 1 [hom( A ),species( A ,halobacterium_halobium),mol_wt_gt( A ,32892)] = 1 [hom( A ),mol_wt_lteq( A ,43194),classification( A ,bacillaceae)] = 0 -> class 'Extrachromosomal' [0.875] Evaluation on test data (712 items): ecoli1989 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_7' 'IS5 protein' ecoli680 - 1,5,30 Cell processes Transport/binding proteins P-type ATPase family 'kdpB' 'P-type ATPase familyATPase of high-affinity potassium transport system B chain' ecoli1953 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_6' 'IS5 protein' Test Accuracy: 2/3 (66.67%) Test Frequency class 'Extrachromosomal': 25/712 (3.51%) Test Significance: dev(5.94) ; prob(3.612055E-03) Application to new data (2167 items): ecoli162 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaeG' 'orf' ecoli1940 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1978' 'paral putative factor(2nd module)' ecoli4232 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4343' 'orf joins former yjiU and yjiV' ecoli2079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2120' 'orf' ecoli1945 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1983' 'orf' Frequency rule on new data: 5/2167 (0.23%) Evaluation on training data (939 items): ecoli251 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_1' 'IS5 protein 1' ecoli3428 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_11' 'IS5 protein 11' ecoli2150 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_8' 'IS5 protein' ecoli542 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_2' 'IS 5 protein' ecoli1341 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_5' 'IS5 protein' ecoli2916 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_9' 'IS5 protein' Training Accuracy: 6/6 (100.00%) Training Frequency class 'Extrachromosomal': 40/939 (4.26%) Training Significance: dev(11.61) ; prob(5.975392E-09) Evaluation on validation data (471 items): ecoli1302 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_4' 'IS5 protein' ecoli3148 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_10' 'IS5 protein 10' Validation Accuracy: 2/2 (100.00%) Validation Frequency class 'Extrachromosomal': 26/471 (5.52%) Validation Significance: dev(5.85) ; prob(3.047228E-03) ------------------ Rule 30: (5, lift 10.1) [ss_beta( A ,lteq,3),nss_beta( A , B ,lteq,6)] = 0 [hom( A ),species( A ,acanthamoeba_castellanii__amoeba_),mol_wt_lteq( A ,77359)] = 1 [hom( A ),mol_wt_gt( A ,55220),classification( A ,ciliophora)] = 0 [hom( A ),keyword( A ,transmembrane),classification( A ,clostridiaceae)] = 0 -> class 'Structural elements' [0.857] Evaluation on test data (712 items): ecoli3228 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplF' '50S ribosomal subunit protein L6' ecoli3264 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsG' '30S ribosomal subunit protein S7 initiates assembly' ecoli1089 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1116' 'ABC superfamily (membrane) paral putative membrane component of ABC transport system' ecoli1249 - 2,2,7 Macromolecule metabolism Macromolecule synthesis, modification Phospholipids 'pgpB' 'non-essential phosphatidylglycerophosphate phosphatase membrane bound' ecoli3229 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsH' '30S ribosomal subunit protein S8 and regulator' ecoli424 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'cyoA' 'cytochrome o ubiquinol oxidase subunit II' Test Accuracy: 3/6 (50.00%) Test Frequency class 'Structural elements': 64/712 (8.99%) Test Significance: dev(3.51) ; prob(1.179371E-02) Application to new data (2167 items): ecoli2634 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2689' 'orf' ecoli1766 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1798' 'paral putative transport protein' ecoli2993 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiH' 'orf' ecoli2018 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2059' 'putative glycosyl transferase in colanic acid biosynthesis (1st module)' ecoli3124 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbE' 'orf' Frequency rule on new data: 5/2167 (0.23%) Evaluation on training data (939 items): ecoli3881 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplK' '50S ribosomal subunit protein L11' ecoli3220 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsK' '30S ribosomal subunit protein S11' ecoli3230 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsN' '30S ribosomal subunit protein S14' ecoli3265 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsL' '30S ribosomal subunit protein S12' ecoli3233 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplN' '50S ribosomal subunit protein L14' Training Accuracy: 5/5 (100.00%) Training Frequency class 'Structural elements': 80/939 (8.52%) Training Significance: dev(7.33) ; prob(4.488714E-06) Evaluation on validation data (471 items): ecoli3237 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsC' '30S ribosomal subunit protein S3' ecoli3239 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsS' '30S ribosomal subunit protein S19' ecoli1915 4,1,5 Structural elements Cell envelop Surface structures 'fliR' 'paral putative transport protein for flagellar biosynthesis' ecoli3221 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsM' '30S ribosomal subunit protein S13' Validation Accuracy: 4/4 (100.00%) Validation Frequency class 'Structural elements': 45/471 (9.55%) Validation Significance: dev(6.15) ; prob(8.332329E-05) ------------------ Rule 1: (111/1, lift 3.5) [hom( A ),classification( A ,salmonella)] = 1 [hom( A ),e_val_gt( A ,0.0006),mol_wt_gt( A ,55220)] = 1 [hom( A ),e_val_lteq( A ,0.0006),classification( A ,actinobacteria)] = 1 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,methanobacteriales)] = 0 [hom( A ),mol_wt_lteq( A ,55220),classification( A ,streptococcaceae)] = 1 [hom( A ),mol_wt_lteq( A ,32892),classification( A ,zea)] = 0 [hom( A ),keyword( A ,inner_membrane),classification( A ,epsilon_subdivision)] = 1 -> class 'Cell processes' [0.982] Evaluation on test data (712 items): ecoli3646 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'pstB' 'ABC superfamily (atp_bind) ATP-binding component of high-affinity phosphate-specific ABC transport system' ecoli924 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0949' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli335 1,5,21 Cell processes Transport/binding proteins MFS family 'lacY' 'MFS family of transport protein galactoside permease (M protein)(1st module)' ecoli151 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fhuC' 'ABC superfamily (atp_bind) ATP-binding component of hydroxymate-dependent iron transport' ecoli3338 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntT' 'high-affinity gluconate permease in GNT-I system' ecoli3967 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'nrfD' 'putative nitrate reductase formate dependent also paral putative STP family of transport protein' ecoli2711 1,5,21 Cell processes Transport/binding proteins MFS family 'b2771' 'MFS family of transport protein (3rd module (function unknown)' ecoli2240 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoH' 'NADH dehydrogenase I chain H' ecoli1485 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1514' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system' ecoli889 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'msbA' 'ABC superfamily (atp&memb) paral putative ATP-binding component of transport system' ecoli1307 1,5,43 Cell processes Transport/binding proteins ArAAP family 'ydaH' 'ArAAP family p-aminobenzoyl-glutamate utilization paral putative pump protein (transport)(1st module)' ecoli470 1,5,21 Cell processes Transport/binding proteins MFS family 'fsr' 'MFS family of transport protein fosmidomycin resistance protein(2nd module)' ecoli2374 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysW' 'ABC superfamily (membrane) membrane component of sulfate ABC transport system; permease W protein' ecoli3275 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yheS' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli746 1,5,11 Cell processes Transport/binding proteins DASS family 'b0770' 'DASS family of transport protein' ecoli1400 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'tehA' 'tellurite resistance; K+-tellurite ethidium and proflavin transport; membrane protein' ecoli3374 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpE' 'ABC superfamily (membrane)sn-glycerol 3-phosphate transport system integral membrane protein(1st module)' ecoli175 - 3,6,1 Metabolism of small molecules Fatty acid biosynthesis Fatty acid and phosphatidic acid biosynth 'cdsA' 'CDP-diglyceride synthase(2nd module)' ecoli112 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'aroP' 'APC family of transport protein aromatic amino acid transport protein' ecoli818 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b0842' 'transmembrane multidrug/chloramphenicol efflux transporter (2nd module)' ecoli333 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'cynX' 'cyanate transport' ecoli1499 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ydeA' 'ABC superfamily (membrane)putative membrane component of ABC transport system appears to facilitate arabinose export contributes to control of arabinose regulon' ecoli785 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'glnQ' 'ABC superfamily (atp_bind) ATP-binding component of glutamine high-affinity ABC transport system(2nd module)' ecoli3462 1,5,36 Cell processes Transport/binding proteins STP family 'yhjV' 'STP family of transport protein' ecoli47 1,5,9 Cell processes Transport/binding proteins CPA2 family 'kefC' 'CPA2 family k+ efflux antiporter glutathione-regulated (2nd module)' ecoli3409 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b3486' 'ABC superfamily (membrance) paral putative membrane component of transport system (3rd module)' ecoli2921 1,5,32 Cell processes Transport/binding proteins PiT family 'pitB' 'PiT family low-affinity phosphate transport(1st module)' ecoli3525 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'lldP' 'L-lactate permease(1st module)' ecoli581 1,5,31 Cell processes Transport/binding proteins POT family 'ybdA' 'paral putative POT family of transport protein (1st module)' ecoli3980 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjcV' 'ABC superfamily (membrane) membrane component of allose ABC transport system(1st module)' ecoli4176 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fecE' 'ABC superfamily (atp_bind) ATP-binding component of citrate-dependent iron(III) transport protein' ecoli1467 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yddA' 'ABC superfamily (atp_bind) paral putative ATP-binding module (2nd module)' ecoli3200 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli252 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'ykfD' 'APC family of transport protein S-methylmethionine permease' ecoli2622 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'proV' 'ABC superfamily (atp_bind) ATP-binding component of transport system for glycine betaine and proline(1st module)' ecoli3961 1,5,35 Cell processes Transport/binding proteins SSS family 'yjcG' 'SSS family transport protein' ecoli1380 - 3,3,11 Metabolism of small molecules Central intermediary metabolism Nucleotide interconversions 'b1409' 'putative phosphatidate cytidiltransferase(2nd module)' ecoli3125 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b3195' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2324 1,5,21 Cell processes Transport/binding proteins MFS family 'emrY' 'MFS family of transport protein multidrug resistance protein y (2nd module)' ecoli662 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'nagE' 'Sugar Specific PTS family n-acetylglucosamine-specific enzyme IIABC (3rd module)' ecoli796 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0820' 'paral putative ATP-binding component of transport system' ecoli3587 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpT' 'MFS family of transport protein hexose phosphate transport protein (2nd module)' ecoli644 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltJ' 'ABC superfamily (membrane) glutamate/aspartate transport system permease' ecoli1089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1116' 'ABC superfamily (membrane) paral putative membrane component of ABC transport system' ecoli3293 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'yhfM' 'APC family paral putative amino-acid transport protein (2nd module)' ecoli3998 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'phnE' 'membrane channel protein component of Pn transporter' ecoli4017 1,5,12 Cell processes Transport/binding proteins Dcu family 'dcuB' 'Dcu family anaerobic C4-dicarboxylate transporter' ecoli602 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b0612' 'citrate carrier transport citrate trading for succinate export' ecoli3380 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livH' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system(2nd module)' ecoli2662 - 3,5,4 Metabolism of small molecules Energy metabolism, carbon Fermentation 'hycD' 'membrane-spanning protein of hydrogenase 3 (part of FHL complex)' ecoli486 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ybbA' 'ABC superfamily (atp_bind) putative' ecoli2538 1,5,21 Cell processes Transport/binding proteins MFS family 'kgtP' 'MFS family of transport protein alpha-ketoglutarate permease(1st module)' ecoli3580 1,5,21 Cell processes Transport/binding proteins MFS family 'yicK' 'MFS family of transport protein two-module paral putative transport protein (2nd module)' ecoli2198 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glpT' 'sn-glycerol-3-phosphate permease' ecoli566 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pheP' 'phenylalanine-specific transport system' ecoli4041 1,5,34 Cell processes Transport/binding proteins SMR family 'sugE' 'SMR family of transport protein' ecoli3201 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yhdZ' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli3579 1,5,16 Cell processes Transport/binding proteins GPH family 'yicJ' 'GPH family paral putative transport protein' ecoli1827 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'yebI' 'inner memrane component of a high affininty Zn transport system' ecoli2264 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'hisP' 'ABC superfamily (atp_bind) ATP-binding component of histidine ABC transport system' ecoli578 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fepC' 'ABC superfamily (atp_bind) ATP-binding component of ferric enterobactin transport(2nd module)' ecoli786 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glnP' 'glutamine high-affinity transport system; membrane component(1st module)' ecoli3043 1,5,36 Cell processes Transport/binding proteins STP family 'yhaO' 'STP family of transport protein (1st module)' ecoli1164 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1191' 'PUTATIVE NA(+)/H(+) EXCHANGER according to SwissProt version 38 the orf starts at a methionine 42 aa upstream of b 1191 start' ecoli1514 1,5,21 Cell processes Transport/binding proteins MFS family 'b1543' 'MFS family of transport protein (1st module)' ecoli3188 1,5,35 Cell processes Transport/binding proteins SSS family 'panF' 'SSS family transport protein sodium/pantothenate symporter(1st module)' ecoli1633 1,5,20 Cell processes Transport/binding proteins MATE family 'ydhE' 'MATE family of transport protein(2nd module)' ecoli2357 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'xapB' 'xanthosine permease' ecoli2421 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'acrD' 'sensitivity to acriflavine integral membrane protein possible efflux pump' ecoli1261 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'sapF' 'ABC superfamily (atp_bind) ATP-binding protein of peptide ABC transport system(2nd module)' ecoli358 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0366' 'ABC superfamily (atp_bind) ATP-binding component of a taurine transport system' ecoli1097 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potC' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli67 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yabK' 'ABC superfamily (membrane) membrane component of thiamine ABC transport system(1st module)' ecoli3981 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yjcW' 'ABC superfamily (atp_bind) ATP-binding component of allose transport system (2nd module)' ecoli2497 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b2546' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system (2nd module)' ecoli3594 1,5,21 Cell processes Transport/binding proteins MFS family 'emrD' 'MFS family of transport protein 2-module integral membrane pump; multidrug resistance (2nd module)' ecoli4277 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yjjK' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system (2nd module)' ecoli2034 1,5,33 Cell processes Transport/binding proteins RNDfamily 'b2075' 'RND family of transport protein paral putative outer membrane receptor' ecoli45 1,5,21 Cell processes Transport/binding proteins MFS family 'yaaU' 'MFS family transport protein' ecoli1826 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1858' 'ABC superfamily (atp_bind) ATP-binding component of a high affinity Zn transport system(1st module)' ecoli840 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'artP' 'ABC superfamily (atp&memb) ATP-binding component of 3rd arginine transport system(2nd module)' ecoli4155 1,5,19 Cell processes Transport/binding proteins GntP family 'yjgT' 'GntP family l-idonate transporter (2nd module)' ecoli2373 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'cysA' 'ABC superfamily (atp_bind) ATP-binding component of sulfate permease A protein of ABC transport; chromate resistance (1st module)' ecoli2137 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejB' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3026 1,5,21 Cell processes Transport/binding proteins MFS family 'exuT' 'MFS family of transport protein transport of hexuronates (2nd module)' ecoli1875 1,5,43 Cell processes Transport/binding proteins ArAAP family 'tyrP' 'ArAAP family tyrosine-specific transport system' ecoli3971 1,5,10 Cell processes Transport/binding proteins DAACS family 'gltP' 'DAACS family of transport protein glutamate-aspartate symport protein' ecoli3131 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yhbG' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli1022 1,6,2 Cell processes Adaptation Osmotic adaptation 'mdoH' 'membrane glycosyltransferase; synthesis of membrane-derived oligosaccharide (MDO)/synthesis of OPGs (osmoregulated periplasmic glucans)(2nd module)' ecoli2141 1,5,21 Cell processes Transport/binding proteins MFS family 'bcr' 'MFS family of transport protein bicyclomycin resistance protein; transmembrane protein (2nd module)' ecoli127 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yadG' 'ABC superfamily (atp_bind) ATP-binding component of transport protein (1st module)' ecoli2487 1,5,21 Cell processes Transport/binding proteins MFS family 'b2536' 'MFS family of transport protein (1st module)' ecoli3959 1,5,8 Cell processes Transport/binding proteins CPA1 family 'yjcE' 'CPA1 family PUTATIVE NA(+)/H(+) EXCHANGER YJCE(1st module)' ecoli1455 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1484' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli420 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'cyoE' 'protohaeme IX farnesyltransferase (haeme O biosynthesis)' ecoli3952 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'uvrA' 'excision nuclease subunit (3rd module prob. DNA binding)' ecoli770 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0794' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli807 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0831' 'paral putative membrane component of transport system' ecoli254 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yagC' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' Test Accuracy: 91/99 (91.92%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(13.77) ; prob(1.711207E-39) Application to new data (2167 items): ecoli1604 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1634' 'orf' ecoli2625 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2680' 'orf' ecoli3170 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcP' 'orf' ecoli487 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0496' 'putative oxidoreductase' ecoli2634 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2689' 'orf' ecoli821 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0845' 'paral putative transport protein (2nd module bind phosphorylated sugar? )' ecoli3606 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidE' 'paral putative transport protein(1st module)' ecoli3581 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yicL' 'putative permease transporter' ecoli3028 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3095' 'orf' ecoli1404 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1433' 'putative membrane transport protein' ecoli4009 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4115' 'putative amino acid/amine transport protein cryptic' ecoli1575 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1605' 'putative arginine/ornithine antiporter' ecoli1562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1592' 'orf' ecoli4034 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjeH' 'putative transport' ecoli3437 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiV' 'paral putative membrane component of transport system (3rd module)' ecoli3849 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yijE' 'orf (2nd module)' ecoli3780 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihN' 'orf' ecoli155 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yadQ' 'putative channel transporter' ecoli2095 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohD' 'orf' ecoli3419 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhiP' 'orf' ecoli3357 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3434' 'orf' ecoli2821 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2885' 'orf' ecoli1766 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1798' 'paral putative transport protein' ecoli3739 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigM' 'paral putative transport protein (2nd module)' ecoli980 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1006' 'putative transport protein(2nd module)' ecoli2943 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yghB' 'orf' ecoli2997 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygjE' 'paral putative DASS family of transport protein' ecoli3585 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yicO' 'orf (2nd module)' ecoli1658 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1690' 'paral putative MFS family of transport protein' ecoli1720 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1752' 'orf' ecoli3114 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhbE' 'orf' ecoli1923 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yedA' 'orf (1st module)' ecoli2558 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2611' 'orf' ecoli1042 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'mviN' 'putative virulence factor' ecoli1504 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeD' 'orf' ecoli4221 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiJ' 'paral putative transport protein (2nd module)' ecoli2250 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2292' 'putative transport protein' ecoli3600 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidK' 'putative cotransporter' ecoli3731 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rarD' 'chloramphenicol resistance' ecoli1505 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ydeF' 'paral putative transport protein (1st module)' ecoli502 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0511' 'orf' ecoli1743 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1775' 'paral putative transport protein (1st module)' ecoli3706 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yifJ' 'putative cytochrome' ecoli1718 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1750' 'orf' ecoli3083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yraQ' 'orf' ecoli2715 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2775' 'orf' ecoli2858 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yggA' 'orf' ecoli4083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfS' 'orf' ecoli789 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybiF' 'orf' ecoli2088 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehX' 'paral putative ATP-binding component of transport system' ecoli3576 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yicE' 'putative transport protein' ecoli2204 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2246' 'putative transport protein' ecoli3126 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbG' 'orf' ecoli320 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0328' 'paral putative transport protein' ecoli2285 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfcA' 'putative structural protein' ecoli1569 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1599' 'orf' ecoli2349 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2392' 'putative transport system permease(1st module)' ecoli2498 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2547' 'paral putative ATP-binding component of transport system' ecoli7 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yaaJ' 'putative inner membrane transport protein' ecoli504 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0513' 'putative transport(2nd module)' ecoli4243 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiY' 'putative carbon starvation protein' ecoli1943 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1981' 'shikimate and dehydroshikimate permease (2nd module)' ecoli1697 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1729' 'part of a kinase(1st module paral putative tdomain shared with transporter)' ecoli1454 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1483' 'paral putative ATP-binding component of transport system' ecoli2322 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'dsdX' 'transport system permease (serine?)' ecoli1753 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1785' 'orf(2nd module)' ecoli2275 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'dedA' 'orf' ecoli3500 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yiaN' 'putative membrane protein' ecoli873 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycaD' 'paral putative transport protein (1st module)' ecoli3635 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yieG' 'orf (2nd module)' ecoli4245 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4356' 'paral putative transport protein cryptic orf joins former yjiZ and yjjL' ecoli1038 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1065' 'orf' ecoli2361 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfeH' 'putative cytochrome oxidase' ecoli1759 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1791' 'putative amino acid/amine transport protein (3rd module)' ecoli4049 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjeM' 'paral putative amino-acid transport protein' ecoli262 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagG' 'paral putative transport protein' ecoli2729 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2789' 'paral putative membrane component of transport system (2nd module)' ecoli2256 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2298' 'putative S-transferase' ecoli794 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0818' 'orf' ecoli3751 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigU' 'integral membrane protein part of sec-independent protein export' ecoli3958 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcD' 'orf (2nd module)' Frequency rule on new data: 81/2167 (3.74%) Evaluation on training data (939 items): ecoli4024 1,5,31 Cell processes Transport/binding proteins POT family 'b4130' 'POT family of transport protein paral putative transport protein (3rd module)' ecoli2057 1,5,21 Cell processes Transport/binding proteins MFS family 'b2098' 'MFS family of transport protein (2nd module)' ecoli3359 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntU_1' 'split gene low-affinity gluconate transport permease protein in GNT-I system first part of fragment 1(1st module)' ecoli855 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0879' 'ABC superfamily (atp&memb) paral putative ATP-binding component of transport system' ecoli3425 1,5,4 Cell processes Transport/binding proteins Ars family 'arsB' 'Ars family arsenical pump membrane protein(2nd module)' ecoli1099 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'potA' 'ABC superfamily (atp_bind) ATP-binding component of spermidine/putrescine ABC transport system (1st module)' ecoli3489 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'xylG' 'ABC superfamily (atp_bind) ATP-binding component of D-xylose ABC transport system(2nd module)' ecoli1723 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1755' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3647 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstA' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli2265 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisM' 'ABC superfamily (membrane)histidine transport membrane protein m (2nd module transport function )' ecoli3991 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'phnK' 'ABC superfamily (atp_bind) ATP-binding component of phosphonate ABC transportbelieved to be part of carbon-phosphorus (C-P) lyase in phosphonate metabolism' ecoli87 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'mraY' 'phospho-N-acetylmuramoyl-pentapeptide transferase essential in cell wall growth' ecoli153 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fhuB' 'ABC superfamily (membrane) split gene C-term module hydroxamate-dependent iron uptake (2nd module iron uptake )' ecoli1659 1,5,21 Cell processes Transport/binding proteins MFS family 'b1691' 'MFS family of transport protein' ecoli3396 1,5,21 Cell processes Transport/binding proteins MFS family 'yhhS' 'MFS family of transport protein (2nd module)' ecoli1566 1,5,21 Cell processes Transport/binding proteins MFS family 'b1596' 'MFS familty transport protein (2nd module)' ecoli3154 1,5,21 Cell processes Transport/binding proteins MFS family 'nanT' 'MFS family of transport protein sialic acid transporter cryptic in K12?(1st module)' ecoli3386 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ftsE' 'ABC superfamily (atp_bind) ATP-binding component of a membrane-associated complex involved in cell division' ecoli66 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yabJ' 'ABC superfamily (atp_bind) ATP-binding component of thiamine ABC transport system' ecoli2736 1,5,36 Cell processes Transport/binding proteins STP family 'sdaC' 'STP family of transport protein serine transporter' ecoli3403 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'nikE' 'ABC superfamily (stp_bind) ATP-binding component of nickel ABC transport system probably couples energy to transport system' ecoli3783 1,5,16 Cell processes Transport/binding proteins GPH family 'yihP' 'GPH family paral putative transport protein' ecoli1650 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1682' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2680 1,5,19 Cell processes Transport/binding proteins GntP family 'b2740' 'GntP family of transport protein function unknown (3rd module)' ecoli3782 1,5,16 Cell processes Transport/binding proteins GPH family 'b3876' 'GPH family paral putative transport protein (2nd module)' ecoli1267 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b1296' 'APC family paral putative amino-acid transport protein' ecoli2631 1,5,21 Cell processes Transport/binding proteins MFS family 'emrB' 'MFS family of transport protein multidrug resistance; probably membrane translocase(1st module)' ecoli400 1,2,1 Cell processes Chromosome replication Chromosome replication 'secD' 'protein secretion; membrane protein part of the channel' ecoli3049 1,5,36 Cell processes Transport/binding proteins STP family 'tdcC' 'STP family of transport protein anaerobically inducible L-threonine/ L-serine permease' ecoli3373 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ugpC' 'ABC superfamily (atp_bind) ATP-binding component of sn-glycerol 3-phosphate ABC transport system (1st module)' ecoli1264 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapB' 'ABC superfamily (membrane) membrane component of peptide ABC transport system' ecoli3670 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'rbsA' 'ABC superfamily (atp_bind) ATP-binding component of d-ribose high-affinity transport system (2nd module)' ecoli1026 1,5,21 Cell processes Transport/binding proteins MFS family 'yceE' 'MFS family of transport protein (2nd module)' ecoli1586 1,5,16 Cell processes Transport/binding proteins GPH family 'uidB' 'GPH family glucuronide permease' ecoli425 1,5,21 Cell processes Transport/binding proteins MFS family 'ampG' 'MFS family of transport protein ampicillin resistance (1st module)' ecoli2115 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'lysP' 'APC family lysine-specific permease (2nd module)' ecoli1090 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1117' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli4226 1,5,21 Cell processes Transport/binding proteins MFS family 'yjiO' 'MFS family of transport protein (1st module)' ecoli1179 1,5,38 Cell processes Transport/binding proteins SulP family 'ychM' 'SulP family transport protein (1st module)' ecoli2036 1,5,21 Cell processes Transport/binding proteins MFS family 'b2077' 'MFS family of transport protein (1st module)' ecoli89 1,7,1 Cell processes Cell division Cell division 'ftsW' 'cytoplasmic membrane required for PBP2 expression' ecoli675 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'potE' 'APC family putrescine-lyase antiporter' ecoli2608 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gabP' 'transport permease protein of gamma-aminobutyrate' ecoli3157 1,5,13 Cell processes Transport/binding proteins DcuC 'yhcL' 'DcuC family of transport protein (2nd module)' ecoli643 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltK' 'ABC superfamily (membrane) glutamate/aspartate transport (1st module)' ecoli369 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sbmA' 'ABC superfamily (atp&memb) sensitivity to microcin B17; methylmalonyl-CoA mutase (mcm); ATP-binding and membrane component' ecoli1159 1,5,27 Cell processes Transport/binding proteins NhaA family 'nhaB' 'NhaB family of transport protein Na+/H+ antiporter regulator of intracellular pH(1st module)' ecoli3675 1,5,21 Cell processes Transport/binding proteins MFS family 'yieO' 'MFS family of tranport protein (1st mdule)' ecoli908 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ycbE' 'paral putative ATP-binding component of transport system' ecoli3466 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'dppB' 'ABC superfamily (membrane) membrane component of dipeptide ABC transport system; permease protein 1(2nd module)' ecoli1262 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'sapD' 'ABC superfamily (atp_bind) ATP-binding protein of peptide transport system(2nd module) affects potassium transport;' ecoli1705 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'celB' 'PTS family sugar specific enzyme II for cellobiose arbutin and salicin' ecoli453 1,5,33 Cell processes Transport/binding proteins RNDfamily 'acrB' 'RND family of transport protein acridine efflux pump(2nd module)' ecoli345 1,5,21 Cell processes Transport/binding proteins MFS family 'b0353' 'MFS family transport protein (2nd module function unknown)' ecoli394 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b0402' 'APC family of transport protein proline permease transport protein' ecoli3059 1,5,21 Cell processes Transport/binding proteins MFS family 'yhaU' 'MFS family of transport protein (D)-glucarate or galactarate transporter (1st module)' ecoli3463 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'dppF' 'ABC superfamily (atp_bind) ATP-binding component of a dipeptide transport system(1st module)' ecoli2129 1,5,21 Cell processes Transport/binding proteins MFS family 'yeiO' 'MFS family proton-coupled sugar efflux pump transport selective monosaccharides and disaccharides narrower substr. specificity than SetA(2nd module)' ecoli4026 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'cadB' 'APC family transport of lysine/cadaverine(1st module)' ecoli989 1,5,35 Cell processes Transport/binding proteins SSS family 'putP' 'SSS family transport protein major sodium/proline symporter' ecoli2139 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yejF' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2448 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'uraA' 'uracil transport' ecoli861 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cydC' 'ABC superfamily (atp&memb) ATP-binding and membrane components of cytochrome-related ABC transport(2nd module)' ecoli2899 1,5,21 Cell processes Transport/binding proteins MFS family 'nupG' 'MFS family of transport protein transport of nucleosides (2nd module)' ecoli3273 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'kefB' 'K+ efflux; NEM-activable K+/H+ antiporter' ecoli3022 1,5,10 Cell processes Transport/binding proteins DAACS family 'ygjU' 'DAACS family Na+/serine (threonine) symporter' ecoli3011 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'ygjI' 'APC family paral putative amino-acid transport protein' ecoli2035 1,5,33 Cell processes Transport/binding proteins RNDfamily 'b2076' 'RND family of transport protein paral putative outer membrane receptor' ecoli3630 1,5,43 Cell processes Transport/binding proteins ArAAP family 'tnaB' 'ArAAP family low affinity tryptophan permease' ecoli3378 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'livG' 'ABC superfamily (atp_bind) ATP-binding component of high-affinity branched-chain amino acid ABC transport system' ecoli3668 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'kup' 'low affinity potassium transport system' ecoli4121 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjfF' 'ABC superfamily (membrane) ABC superfamily of transport protein (1st module membrance component)' ecoli3648 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstC' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli393 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'brnQ' 'branched chain; mutants valine and o-methylthreonine resistant glyclyvaline sensitive; transport system I for Ile Leu and Val' ecoli1218 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'oppF' 'ABC superfamily (atp_bind) ATP-binding protein of oligopeptide ABC transport system' ecoli1414 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1443' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli862 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cydD' 'ABC superfamily (atp&memb) ATP-binding and membrane components of cytochrome-related ABC transport Zn sensitive(2nd module)' ecoli388 1,5,21 Cell processes Transport/binding proteins MFS family 'araJ' 'MFS family of transport protein involved in either transport or processing of arabinose polymers (2nd module function unknown)' ecoli1098 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potB' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli4178 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fecC' 'ABC superfamily (membrane) citrate-dependent iron(III) transport protein (2nd module)' ecoli1463 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'xasA' 'APC family acid sensitivity protein putative glutamate:gamma-aminobutyric acid antiporter (GadC)(2nd module)' ecoli2138 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli469 1,5,9 Cell processes Transport/binding proteins CPA2 family 'ybaL' 'CPA2 family transport protein' ecoli3287 1,5,21 Cell processes Transport/binding proteins MFS family 'yhfC' 'MFS family of transport protein paral putative transport protein' ecoli2375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysU' 'ABC superfamily (membrane) membrane component of sulfate thiosulfate ABC transport system (2nd module)' ecoli874 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b0899' 'APC family paral putative amino-acid transport protein' ecoli2878 1,5,21 Cell processes Transport/binding proteins MFS family 'galP' 'MFS family of transport protein galactose-proton symport of transport system (2nd module)' ecoli2005 1,2,1 Cell processes Chromosome replication Chromosome replication 'b2046' 'probable export protein /export to periplasm in colanic acid gene cluster' ecoli2159 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ccmA' 'ABC superfamily (atp_bind) ATP-binding component of heme exporter A heme exporter protein A cytochrome c-type biogenesis protein' ecoli2108 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'mglA' 'ABC superfamily (atp_bind) ATP-binding component of methyl-galactoside transport and galactose taxis (2nd module)' ecoli2741 1,5,21 Cell processes Transport/binding proteins MFS family 'fucP' 'MFS family of transport protein fucose permease(1st module)' ecoli3711 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'yifK' 'APC family paral putative amino-acid transport protein' ecoli3402 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'nikD' 'ABC superfamily (atp_bind) ATP-binding component of nickel ABC transport system probably couples energy to transport system(2nd module)' ecoli1283 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1312' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1882 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1917' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli3408 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhhJ' 'ABC superfamily (membrane)paral putative transport system membrane (2nd module)' ecoli481 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0490' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli3469 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'yhjX' 'putative resistance protein' ecoli401 1,2,1 Cell processes Chromosome replication Chromosome replication 'secF' 'protein secretion membrane protein' ecoli19 1,5,27 Cell processes Transport/binding proteins NhaA family 'nhaA' 'NhaA family of transport protein Na+/H antiporter pH dependent(1st module)' ecoli3583 1,5,21 Cell processes Transport/binding proteins MFS family 'yicM' 'MFS family of tranport protein (1st mdule)' ecoli3855 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'frwC' 'PTS system fructose-like IIC component first module overlaps second(2nd module)' ecoli736 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'modF' 'ABC superfamily (atp_bind) ATP-binding component of molybdenum transport system (2nd module)' ecoli1215 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppB' 'ABC superfamily (membrane) membrane component of oligopeptide ABC transport system(2nd module)' ecoli1440 1,5,21 Cell processes Transport/binding proteins MFS family 'narU' 'MFS family of transport protein nitrate sensor-transmitter protein anaerobic respiratory path(1st module)' ecoli1334 1,5,39 Cell processes Transport/binding proteins Trk system 'trkG' 'Trk system potassium uptake' ecoli2107 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'mglC' 'ABC superfamily (membrane) membrane component of methyl-galactoside ABC transport system and galactose taxis(1st module)' ecoli1679 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'btuC' 'ABC superfamily (membrane) membrane component of vitamin B12 ABC transport system' ecoli440 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'mdlA' 'ATP-binding component of a transport system (2nd module)' ecoli477 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b0486' 'APC family of transport protein amino-acid transport protein' ecoli4185 1,5,19 Cell processes Transport/binding proteins GntP family 'yjhF' 'GntP family of transport protein (1st module)' Training Accuracy: 110/111 (99.10%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(16.81) ; prob(3.629743E-60) Evaluation on validation data (471 items): ecoli4014 1,5,16 Cell processes Transport/binding proteins GPH family 'melB' 'GPH family melibiose permease II' ecoli3929 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'malK' 'ABC superfamily (atp_bind) ATP-binding component of transport system for maltose phenotypic repressor of mal operon(1st module)' ecoli837 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'artM' 'arginine 3rd transport system permease protein' ecoli1883 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yecC' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli441 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'mdlB' 'ABC superfamily (atp&memb) paral putative ATP-binding component of transport system' ecoli419 1,5,21 Cell processes Transport/binding proteins MFS family 'b0427' 'MFS family transport protein' ecoli4119 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ytfS' 'ABC superfamily (atp_bind) putative ATP-binding component of a transport system' ecoli3990 - 3,3,13 Metabolism of small molecules Central intermediary metabolism Phosphorus compounds 'phnL' 'ABC superfamily (atp_bind) ATP-binding component of phosphonate ABC transport believed to be part of carbon-phosphorus (C-P) lyase in phosphonate metabolism' ecoli1216 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppC' 'ABC superfamily (membrane)homolog of Salmonella oligopeptide transport permease protein(2nd module)' ecoli3926 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'malG' 'ABC superfamily (membrane) membrane component of maltose ABC transport system (2nd module)' ecoli3375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpA' 'ABC superfamily (membrane) sn-glycerol 3-phosphate integral membrane protein ABC transport system' ecoli2778 1,5,21 Cell processes Transport/binding proteins MFS family 'araE' 'MFS family of transport protein low-affinity L-arabinose transport system proton symport protein(1st module)' ecoli1289 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1318' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli4098 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'cycA' 'APC family transport of D-alanine D-serine and glycine (2nd module)' ecoli2623 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'proW' 'ABC superfamily (membrane) membrane component of high-affinity ABC transport system for glycine betaine and proline (2nd module)' ecoli1196 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'narK' 'nitrite extrusion protein(2nd module)' ecoli2089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yehY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1627 1,5,21 Cell processes Transport/binding proteins MFS family 'b1657' 'MFS family of transport protein (2nd module)' ecoli2772 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'ygeD' 'putative resistance proteins' ecoli3196 1,5,33 Cell processes Transport/binding proteins RNDfamily 'acrF' 'RND family of transport protein acriflavin resistance protein F multidrug efflux (?encodes lipoprotein with signal peptide; osmotcially remedial envelope defect)' ecoli1630 1,5,21 Cell processes Transport/binding proteins MFS family 'ydhC' 'MFS family transport protein (2nd module)' ecoli70 1,5,21 Cell processes Transport/binding proteins MFS family 'yabM' 'MFS family of transport protein proton-coupled beta-galactosidase/sugar efflux pump ? role in lactose metabolism (2nd module)' ecoli3446 1,5,21 Cell processes Transport/binding proteins MFS family 'yhjE' 'MFS family of transport protein (2nd module)' ecoli4168 1,5,21 Cell processes Transport/binding proteins MFS family 'yjhB' 'MFS family of tranport protein (1st module)' ecoli1973 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'yeeF' 'APC family paral putative amino-acid transport protein' ecoli2929 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hybB' 'probable cytochrome Ni/Fe component of hydrogenase-2(1st module)' ecoli3938 1,5,20 Cell processes Transport/binding proteins MATE family 'dinF' 'MATE family of transport protein; also DNA-damage-inducible protein F;induced by UV and mitomycin C; SOS lexA regulon(2nd module)' ecoli1282 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1311' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3464 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'dppD' 'ABC superfamily (atp_bind) ATP-binding component of dipeptide tABCransport system(2nd module)' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' ecoli1796 1,5,21 Cell processes Transport/binding proteins MFS family 'b1828' 'MFS family of transport protein (2nd module)' ecoli642 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'gltL' 'ABC superfamily (atp_bind) ATP-binding protein of glutamate/aspartate transport system' ecoli1424 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1453' 'L-asparagine permease (2nd module)' ecoli3377 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'livF' 'ABC superfamily (atp_bind) ATP-binding component of leucine ABC transport system' ecoli1677 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'btuD' 'ABC superfamily (atp_bind) ATP-binding component of vitamin B12 ABC transport system(2nd module)' ecoli3465 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'dppC' 'ABC superfamily (membrane) membrane component of dipeptide ABC transport system; permease protein 2 (2nd module)' ecoli2782 1,5,36 Cell processes Transport/binding proteins STP family 'b2845' 'STP family of transport protein' ecoli3223 1,2,1 Cell processes Chromosome replication Chromosome replication 'prlA' 'protein secretion inner membrane preprotein translocase SecY subunit interacts with SecE (1st module)' ecoli3925 1,5,21 Cell processes Transport/binding proteins MFS family 'xylE' 'MFS family of tranport protein xylose-proton symport (2nd module)' ecoli3612 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'yidT' 'D-galactonate transport' ecoli2909 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b2975' 'LctP transporter L-lactate permease homologue' ecoli199 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'abc' 'ABC superfamily (atp_bind) ATP-binding component of ABC transport system(1st module)' ecoli3588 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpC' 'regulator of uhpT (1st module)' ecoli4177 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fecD' 'ABC superfamily (membrane) membrane component of citrate-dependent ABC transport system of iron' ecoli1868 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'araG' 'ABC superfamily (atp_bind) ATP-binding component of high-affinity l-arabinose transport system (2nd module)' ecoli1867 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1899' 'split high-affinity L-arabinose transport system; membrane protein fragment 1' ecoli1996 - 4,1,4 Structural elements Cell envelop Surface polysaccharides & antigens 'rfbX' 'hydroponic protein o-antigen (3rd module)' ecoli4005 1,5,21 Cell processes Transport/binding proteins MFS family 'proP' 'MFS family of tranport protein low-affinity constitutive transport system; proline permease II transports proline and betaine under conditions of hyperosmolarity(2nd module)' ecoli741 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'modC' 'ABC superfamily (atp_bind) ATP-binding component of molybdate ABC transport (1st module)' ecoli1591 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'malX' 'Sugar Specific PTS family maltose and glucose-specific ii abc (2nd module hydrophilic second phosphorylation domain)' ecoli3631 1,5,21 Cell processes Transport/binding proteins MFS family 'yidY' 'MFS family of tranport protein (1st mdule)' ecoli3093 1,5,43 Cell processes Transport/binding proteins ArAAP family 'mtr' 'ArAAP family tryptophan-specific transport protein' ecoli1724 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1756' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli831 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'potG' 'ABC superfamily (atp_bind) ATP-binding component of putrescine ABC transport system(1st module)' ecoli2280 1,5,21 Cell processes Transport/binding proteins MFS family 'b2322' 'MFS family of transport protein paral putative (2nd module)' ecoli4000 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'phnC' 'ABC superfamily (atp_bind) ATP-binding component of phosphonate ABC transport system' ecoli1412 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1441' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2380 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2429' 'Sugar Specific paral putative PTS system enzyme II' ecoli4031 1,5,12 Cell processes Transport/binding proteins Dcu family 'dcuA' 'Dcu family anaerobic dicarboxylate transport' ecoli2169 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yojI' 'ABC superfamily (atp&memb) paral putative ATP-binding component of transport system' ecoli2818 1,5,13 Cell processes Transport/binding proteins DcuC 'b2882' 'DcuC family paral putative transport protein' ecoli1217 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'oppD' 'ABC superfamily (atp_bind) ATP-binding protein of oligopeptide ABC transport system' ecoli1189 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'chaA' 'sodium-calcium/proton antiporter' ecoli692 1,5,31 Cell processes Transport/binding proteins POT family 'b0709' 'POT family of transport protein (1st module)' ecoli3385 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ftsX' 'ABC superfamily (membrane) cell division membrane protein (2nd module)' ecoli3451 1,5,10 Cell processes Transport/binding proteins DAACS family 'dctA' 'DAACS family of transport protein uptake of C4-dicarboxylic acids' ecoli2824 1,5,26 Cell processes Transport/binding proteins NCS2 family 'b2888' 'NCS2 family paral putative transport protein' ecoli1737 1,5,21 Cell processes Transport/binding proteins MFS family 'ydjE' 'MFS family of transport protein (1st module)' Validation Accuracy: 65/68 (95.59%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(12.20) ; prob(9.666461E-32) ------------------ Rule 5: (11, lift 3.3) [ss_alpha( A ,gt,1),nss_alpha( A , B ,lteq,830),nss_alpha( B , C ,gt,1)] = 1 [hom( A ),classification( A ,shigella)] = 0 [hom( A ),species( A ,oenothera_bertiana__bertero_s_evening_primrose_),mol_wt_gt( A ,55220)] = 0 [hom( A ),keyword( A ,transmembrane),classification( A ,clostridiaceae)] = 1 -> class 'Cell processes' [0.923] Evaluation on test data (712 items): ecoli3927 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'malF' 'ABC superfamily (membrane) membrane component of maltose ABC transport system (2nd module)' ecoli808 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0832' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3620 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'gyrB' 'DNA gyrase subunit B type II topoisomerase ATPase activity(1st module)' ecoli4248 1,6,2 Cell processes Adaptation Osmotic adaptation 'mdoB' 'phosphoglycerol transferase I add phosphoglycerols to OPG backbone' ecoli1457 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1486' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2246 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoA' 'NADH dehydrogenase I chain A' ecoli1097 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potC' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli3641 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'yieC' '(bglH) cryptic carbohydrate-specific outer membrane porin(2nd module)' ecoli2266 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisQ' 'ABC superfamily (membrane)histidine transport system' ecoli3805 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'frvB' 'PTS family fructose-like enzyme IIBC component(2nd module)' ecoli3026 1,5,21 Cell processes Transport/binding proteins MFS family 'exuT' 'MFS family of transport protein transport of hexuronates (2nd module)' ecoli139 - 4,1,5 Structural elements Cell envelop Surface structures 'htrE' 'probable outer membrane porin protein involved in fimbrial assembly (2nd module)' Test Accuracy: 9/12 (75.00%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(3.50) ; prob(1.319132E-03) Application to new data (2167 items): ecoli2859 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yggB' 'involved in stability of MscS mechanosensitive channel paral putative transport protein' ecoli3250 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofF' 'orf' ecoli2296 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2338' 'paral putative outer membrane protein (2nd module)' ecoli1213 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ychE' 'orf' ecoli6 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaaA' 'orf' ecoli3076 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yraJ' 'paral putative outer membrane protein (2nd module)' ecoli2858 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yggA' 'orf' ecoli1466 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yddB' 'orf' ecoli4110 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfM' 'orf' ecoli283 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagX' 'paral putative enzyme' ecoli1171 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycgC' 'paral putative phosphotransferase' ecoli4197 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjhR' 'putative frameshift suppressor' ecoli2087 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehW' 'paral putative membrane component of transport system' ecoli1569 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1599' 'orf' ecoli2309 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2352' 'paral putative ligase(1st module)' ecoli2769 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2832' 'putative transport protein' ecoli3500 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yiaN' 'putative membrane protein' ecoli3635 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yieG' 'orf (2nd module)' ecoli4147 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4257' 'orf joins former yjgN and yjgO' ecoli2072 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'mrp' 'putative ATPase' ecoli255 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0263' 'paral putative membrane component of transport system' Frequency rule on new data: 21/2167 (0.97%) Evaluation on training data (939 items): ecoli740 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'modB' 'ABC superfamily (membrane) membrane component of molybdate ABC transport system (2nd module)' ecoli1456 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1485' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli643 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltK' 'ABC superfamily (membrane) glutamate/aspartate transport (1st module)' ecoli3199 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdX' 'ABC superfamily (membrane)paral putative membrane component of transport system' ecoli54 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'imp' 'organic solvent tolerance' ecoli2035 1,5,33 Cell processes Transport/binding proteins RNDfamily 'b2076' 'RND family of transport protein paral putative outer membrane receptor' ecoli3401 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'nikC' 'ABC superfamily (membrane) membrane component in nickel transport system probably forms heterodimeric pore with NikB(1st module)' ecoli1413 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1442' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli533 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b0543' 'multidrug transporter methylviologen and ethidium resistance' ecoli4180 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fecA' 'outer membrane receptor; citrate-dependent iron transport outer membrane receptor(1st module)' ecoli1769 1,5,5 Cell processes Transport/binding proteins BCCT superfamily 'b1801' 'BCCT superfamily paral putative transporter' Training Accuracy: 11/11 (100.00%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(5.36) ; prob(7.334750E-07) Evaluation on validation data (471 items): ecoli1883 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yecC' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3446 1,5,21 Cell processes Transport/binding proteins MFS family 'yhjE' 'MFS family of transport protein (2nd module)' ecoli1148 1,7,1 Cell processes Cell division Cell division 'minD' 'cell division inhibitor a membrane ATPase activates minC' ecoli1282 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1311' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' ecoli751 - 3,2,2 Metabolism of small molecules Biosynthesis of cofactors, carriers Biotin 'bioB' 'biotin synthetase dethiobiotin to biotin pathway(2nd module)' ecoli4177 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fecD' 'ABC superfamily (membrane) membrane component of citrate-dependent ABC transport system of iron' ecoli3214 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'mscL' 'mechanosensitive channel' ecoli832 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potH' 'ABC superfamily (membrane) membrane component of putrescine ABC transport system(2nd module)' ecoli3821 1,5,6 Cell processes Transport/binding proteins CDF family 'yiiP' 'CDF family of transport protein (1st module)' Validation Accuracy: 9/10 (90.00%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(4.29) ; prob(9.313955E-05) ------------------ Rule 2: (26, lift 3.5) [ss_beta( A ,gt,3)] = 0 [hom( A ),e_val_lteq( A ,0.0006),classification( A ,actinobacteria)] = 1 [hom( A ),keyword( A ,inner_membrane),classification( A ,epsilon_subdivision)] = 1 -> class 'Cell processes' [0.964] Evaluation on test data (712 items): ecoli3338 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntT' 'high-affinity gluconate permease in GNT-I system' ecoli3967 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'nrfD' 'putative nitrate reductase formate dependent also paral putative STP family of transport protein' ecoli1485 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1514' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system' ecoli2374 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysW' 'ABC superfamily (membrane) membrane component of sulfate ABC transport system; permease W protein' ecoli1400 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'tehA' 'tellurite resistance; K+-tellurite ethidium and proflavin transport; membrane protein' ecoli3374 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpE' 'ABC superfamily (membrane)sn-glycerol 3-phosphate transport system integral membrane protein(1st module)' ecoli4120 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ytfT' 'ABC superfamily (membrane)paral putative membrane component' ecoli581 1,5,31 Cell processes Transport/binding proteins POT family 'ybdA' 'paral putative POT family of transport protein (1st module)' ecoli3980 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjcV' 'ABC superfamily (membrane) membrane component of allose ABC transport system(1st module)' ecoli3200 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli644 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltJ' 'ABC superfamily (membrane) glutamate/aspartate transport system permease' ecoli3998 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'phnE' 'membrane channel protein component of Pn transporter' ecoli3380 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livH' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system(2nd module)' ecoli566 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pheP' 'phenylalanine-specific transport system' ecoli1827 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'yebI' 'inner memrane component of a high affininty Zn transport system' ecoli786 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glnP' 'glutamine high-affinity transport system; membrane component(1st module)' ecoli1633 1,5,20 Cell processes Transport/binding proteins MATE family 'ydhE' 'MATE family of transport protein(2nd module)' ecoli1097 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potC' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli67 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yabK' 'ABC superfamily (membrane) membrane component of thiamine ABC transport system(1st module)' ecoli2497 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b2546' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system (2nd module)' ecoli4155 1,5,19 Cell processes Transport/binding proteins GntP family 'yjgT' 'GntP family l-idonate transporter (2nd module)' ecoli2137 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejB' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli328 1,5,25 Cell processes Transport/binding proteins NCS1 family 'codB' 'NCS1 family transport protein cytosine permease/transport(2nd module)' ecoli807 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0831' 'paral putative membrane component of transport system' Test Accuracy: 23/24 (95.83%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(7.20) ; prob(7.918729E-12) Application to new data (2167 items): ecoli2625 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2680' 'orf' ecoli3170 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcP' 'orf' ecoli2634 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2689' 'orf' ecoli3028 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3095' 'orf' ecoli2529 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfiK' 'paral putative transport protein' ecoli1766 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1798' 'paral putative transport protein' ecoli3739 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigM' 'paral putative transport protein (2nd module)' ecoli2585 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2639' 'putative pump protein' ecoli4100 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfF' 'orf (1st module)' ecoli1720 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1752' 'orf' ecoli2558 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2611' 'orf' ecoli3083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yraQ' 'orf' ecoli2858 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yggA' 'orf' ecoli789 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybiF' 'orf' ecoli2346 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2389' 'orf' ecoli320 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0328' 'paral putative transport protein' ecoli1726 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1758' 'putative cytochrome oxidase' ecoli1486 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1515' 'paral putative membrane component of ABC transport system' ecoli1569 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1599' 'orf' ecoli2349 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2392' 'putative transport system permease(1st module)' ecoli1444 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yddG' 'orf' ecoli762 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0786' 'orf' ecoli2322 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'dsdX' 'transport system permease (serine?)' Frequency rule on new data: 23/2167 (1.06%) Evaluation on training data (939 items): ecoli3359 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntU_1' 'split gene low-affinity gluconate transport permease protein in GNT-I system first part of fragment 1(1st module)' ecoli128 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yadH' 'ABC superfamily (membrane) paral putative ABC superfamily (membrane)' ecoli1723 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1755' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3647 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstA' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli2265 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisM' 'ABC superfamily (membrane)histidine transport membrane protein m (2nd module transport function )' ecoli2680 1,5,19 Cell processes Transport/binding proteins GntP family 'b2740' 'GntP family of transport protein function unknown (3rd module)' ecoli1264 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapB' 'ABC superfamily (membrane) membrane component of peptide ABC transport system' ecoli643 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltK' 'ABC superfamily (membrane) glutamate/aspartate transport (1st module)' ecoli3466 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'dppB' 'ABC superfamily (membrane) membrane component of dipeptide ABC transport system; permease protein 1(2nd module)' ecoli3671 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'rbsC' 'ABC superfamily (membrane) ABC superfamily of transport protein D-ribose high-affinity ABC transport system(1st module ATP-binding subunit)' ecoli3379 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livM' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system (2nd module)' ecoli4121 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjfF' 'ABC superfamily (membrane) ABC superfamily of transport protein (1st module membrance component)' ecoli3648 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstC' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli1570 1,5,34 Cell processes Transport/binding proteins SMR family 'b1600' 'SMR family of transport protein' ecoli1414 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1443' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1098 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potB' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli4178 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fecC' 'ABC superfamily (membrane) citrate-dependent iron(III) transport protein (2nd module)' ecoli2343 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2386' 'Sugar Specific paral putative membrane component of transport system' ecoli1786 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'manY' 'Sugar Specific PTS Sugar specific-family of transport protein; enzyme IIC mannose-specific(1st module)' ecoli2138 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysU' 'ABC superfamily (membrane) membrane component of sulfate thiosulfate ABC transport system (2nd module)' ecoli1283 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1312' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1215 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppB' 'ABC superfamily (membrane) membrane component of oligopeptide ABC transport system(2nd module)' ecoli2107 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'mglC' 'ABC superfamily (membrane) membrane component of methyl-galactoside ABC transport system and galactose taxis(1st module)' ecoli1679 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'btuC' 'ABC superfamily (membrane) membrane component of vitamin B12 ABC transport system' ecoli4185 1,5,19 Cell processes Transport/binding proteins GntP family 'yjhF' 'GntP family of transport protein (1st module)' Training Accuracy: 26/26 (100.00%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(8.24) ; prob(3.162290E-15) Evaluation on validation data (471 items): ecoli837 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'artM' 'arginine 3rd transport system permease protein' ecoli1883 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yecC' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2237 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoK' 'NADH dehydrogenase I chain K' ecoli1216 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppC' 'ABC superfamily (membrane)homolog of Salmonella oligopeptide transport permease protein(2nd module)' ecoli3926 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'malG' 'ABC superfamily (membrane) membrane component of maltose ABC transport system (2nd module)' ecoli3375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpA' 'ABC superfamily (membrane) sn-glycerol 3-phosphate integral membrane protein ABC transport system' ecoli2089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yehY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2158 1,2,1 Cell processes Chromosome replication Chromosome replication 'ccmB' 'heme exporter protein B cytochrome c-type biogenesis protein' ecoli2929 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hybB' 'probable cytochrome Ni/Fe component of hydrogenase-2(1st module)' ecoli1282 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1311' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' ecoli3815 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'kdgT' '2-keto-3-deoxy-D-gluconate transport system' ecoli3659 1,5,24 Cell processes Transport/binding proteins Membrane-bound ATP synthase 'atpB' 'membrane-bound ATP synthase F0 sector subunit a' ecoli3490 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'xylH' 'ABC superfamily (membrane)d-xylose transport permease (2nd module might interact with atp hydrolysing subunit )' ecoli4177 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fecD' 'ABC superfamily (membrane) membrane component of citrate-dependent ABC transport system of iron' ecoli1189 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'chaA' 'sodium-calcium/proton antiporter' ecoli692 1,5,31 Cell processes Transport/binding proteins POT family 'b0709' 'POT family of transport protein (1st module)' Validation Accuracy: 15/17 (88.24%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(5.43) ; prob(5.010356E-07) ------------------ Rule 3: (21, lift 3.5) [ss_beta( A ,lteq,5),nss_beta( A , B ,gt,6)] = 0 [ss_coil( A ,lteq,10),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,6)] = 1 [ss_alpha( A ,lteq,5),nss_alpha( A , B ,gt,10),nss_alpha( B , C ,lteq,3)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,10),nss_coil( C , D ,gt,10),nss_coil( D , E ,gt,6)] = 0 [hom( A ),e_val_lteq( A ,0.0006),keyword( A ,repeat)] = 1 [hom( A ),e_val_lteq( A ,3e-06),classification( A ,asteraceae)] = 0 [hom( A ),species( A ,halobacterium_halobium),mol_wt_gt( A ,32892)] = 1 -> class 'Cell processes' [0.957] Evaluation on test data (712 items): ecoli581 1,5,31 Cell processes Transport/binding proteins POT family 'ybdA' 'paral putative POT family of transport protein (1st module)' ecoli3980 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjcV' 'ABC superfamily (membrane) membrane component of allose ABC transport system(1st module)' ecoli3200 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3341 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'malT' 'transcriptional activator of the mal genes binds inducer (maltotriose) and ATP subject to catabolite repression' ecoli644 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltJ' 'ABC superfamily (membrane) glutamate/aspartate transport system permease' ecoli3101 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'nusA' 'transcription pausing; L factor' ecoli3998 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'phnE' 'membrane channel protein component of Pn transporter' ecoli2655 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'ascF' 'PTS family enzyme II ABC (asc) cryptic transports specific beta-glucosides' ecoli3645 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'phoU' 'regulatory gene for high affinity phosphate uptake under phosphate excess PhoU downregulates the PHO regulon' ecoli1853 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tap' 'methyl-accepting chemotaxis protein IV peptide sensor receptor (2nd module)' ecoli3380 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livH' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system(2nd module)' ecoli566 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pheP' 'phenylalanine-specific transport system' ecoli786 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glnP' 'glutamine high-affinity transport system; membrane component(1st module)' ecoli4287 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'arcA' 'negative response regulator of genes in aerobic pathways (sensors ArcB and CpxA)(1st module)' ecoli1097 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potC' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli198 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yaeE' 'ABC superfamily (membrane) paral putative membrane component of transport system' Test Accuracy: 12/16 (75.00%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(4.05) ; prob(1.911066E-04) Application to new data (2167 items): ecoli1339 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1368' 'putative alpha helix protein' ecoli3028 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3095' 'orf' ecoli1562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1592' 'orf' ecoli2959 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3025' 'paral putative regulator protein' ecoli155 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yadQ' 'putative channel transporter' ecoli3914 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjbB' 'putative alpha helix protein' ecoli2943 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yghB' 'orf' ecoli4052 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjeP' 'putative periplasmic binding protein (2nd module)' ecoli1599 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1629' 'paral putative membrane protein (3rd module)' ecoli2084 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehT' 'paral putative regulator protein' ecoli3113 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhbZ' 'paral putative GTP-binding factor' ecoli3410 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiI' 'paral putative membrane protein' ecoli2578 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2632' '2nd module of a paral GTP-binding factor (2nd module)' ecoli320 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0328' 'paral putative transport protein' ecoli1486 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1515' 'paral putative membrane component of ABC transport system' ecoli3869 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yijC' 'orf' ecoli610 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'criR' 'part of two component regulatory system with DpiB transcriptional regulation of citrate fermentation (?transport) genes and of plasmid inheritance genes(1st module)' Frequency rule on new data: 17/2167 (0.78%) Evaluation on training data (939 items): ecoli1263 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapC' 'ABC superfamily (membrane) membrane component of peptide ABC transport system(2nd module)' ecoli3647 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstA' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli1392 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'trg' 'methyl-accepting chemotaxis protein III ribose and galactose sensor receptor(2nd module)' ecoli3627 1,4,2 Cell processes Protection responses Detoxification 'thdF' 'GTP-binding protein in thiophene and furan oxidation' ecoli675 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'potE' 'APC family putrescine-lyase antiporter' ecoli4244 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tsr' 'methyl-accepting chemotaxis protein I serine sensor receptor(2nd module)' ecoli1854 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tar' 'methyl-accepting chemotaxis protein II aspartate sensor receptor (2nd module)' ecoli3379 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livM' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system (2nd module)' ecoli1851 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'cheB' 'response regulator for chemotaxis (cheA sensor); protein methylesterase(1st module)' ecoli4121 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjfF' 'ABC superfamily (membrane) ABC superfamily of transport protein (1st module membrance component)' ecoli3648 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstC' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli1414 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1443' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1098 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potB' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli2138 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysU' 'ABC superfamily (membrane) membrane component of sulfate thiosulfate ABC transport system (2nd module)' ecoli3387 1,7,1 Cell processes Cell division Cell division 'ftsY' 'cell division membrane protein (2nd module)' ecoli899 1,7,1 Cell processes Cell division Cell division 'mukB' 'kinesin-line cell division protein involved in sister chromosome partitioning (3rd module DNA binding ?)' ecoli19 1,5,27 Cell processes Transport/binding proteins NhaA family 'nhaA' 'NhaA family of transport protein Na+/H antiporter pH dependent(1st module)' ecoli3332 1,5,15 Cell processes Transport/binding proteins FeoB family 'feoB' 'FeoB family ferrous iron transport protein B(1st module)' ecoli2969 1,7,1 Cell processes Cell division Cell division 'tolC' 'outer membrane channel; specific tolerance to colicin E1; segregation of daughter chromosomes' ecoli359 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0367' 'ABC superfamily (membrane) membrane component of taurine ABC transport system' Training Accuracy: 21/21 (100.00%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(7.41) ; prob(1.942956E-12) Evaluation on validation data (471 items): ecoli837 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'artM' 'arginine 3rd transport system permease protein' ecoli1074 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'ptsG' 'Sugar Specific PTS family glucose-specific IIBCcomponent (3rd module hydrophilic second phosphorylation domain) mutant form transports D-ribose' ecoli3734 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'recQ' 'ATP-dependent DNA helicase (helicase) (2nd module) BIFUNCT: initiate homol recomb disrupt aberrant recombination interacts with TopB' ecoli1216 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppC' 'ABC superfamily (membrane)homolog of Salmonella oligopeptide transport permease protein(2nd module)' ecoli2987 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'glnE' 'adenylyl transferase for glutamine synthetase regulates P-II (GlnB) and GlnK' ecoli3416 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pitA' 'low-affinity phosphate transport' ecoli3375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpA' 'ABC superfamily (membrane) sn-glycerol 3-phosphate integral membrane protein ABC transport system' ecoli2623 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'proW' 'ABC superfamily (membrane) membrane component of high-affinity ABC transport system for glycine betaine and proline (2nd module)' ecoli2089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yehY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' ecoli3490 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'xylH' 'ABC superfamily (membrane)d-xylose transport permease (2nd module might interact with atp hydrolysing subunit )' ecoli4239 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'hsdR' 'host restriction; endonuclease R (2nd module)' ecoli692 1,5,31 Cell processes Transport/binding proteins POT family 'b0709' 'POT family of transport protein (1st module)' ecoli909 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0934' 'ABC superfamily (membrane) probable membrane component of transport system' Validation Accuracy: 11/14 (78.57%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(4.13) ; prob(1.417418E-04) ------------------ Rule 4: (14, lift 3.4) [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,gt,5)] = 1 [ss_beta( A ,gt,1),nss_beta( A , B ,gt,3),nss_beta( B , C ,gt,5)] = 0 [hom( A ),e_val_lteq( A ,2e-37),keyword( A ,inner_membrane)] = 1 [hom( A ),psi_iter_gt( A ,5),classification( A ,apocrita)] = 0 [hom( A ),keyword( A ,inner_membrane),classification( A ,epsilon_subdivision)] = 0 -> class 'Cell processes' [0.938] Evaluation on test data (712 items): ecoli3927 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'malF' 'ABC superfamily (membrane) membrane component of maltose ABC transport system (2nd module)' ecoli3833 1,5,22 Cell processes Transport/binding proteins MIP family 'glpF' 'MIP family facilitated diffusion of glycerol' ecoli808 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0832' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3669 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'rbsD' 'D-ribose high-affinity transport system; membrane-associated protein' ecoli3575 1,5,18 Cell processes Transport/binding proteins GltS family 'gltS' 'GltS family glutamate transport (2nd module)' ecoli1457 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1486' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli879 1,5,14 Cell processes Transport/binding proteins FNT family 'focA' 'FNT family membrane protein (formate channel 1)(2nd module)' ecoli4191 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'yjhL' 'Sugar Specific paral putative sugar specific-family of transport protein' ecoli3072 - 3,3,2 Metabolism of small molecules Central intermediary metabolism Amino sugars 'agaD' 'PTS system N-acetylglucosamine enzyme IID component 1' ecoli580 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fepD' 'ABC superfamily (membrane) membrane component of ferric enterobactin (enterochelin) ABC transport' ecoli2266 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisQ' 'ABC superfamily (membrane)histidine transport system' ecoli681 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'kdpA' 'ATPase of high-affinity potassium transport system A chain(2nd module)' ecoli3805 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'frvB' 'PTS family fructose-like enzyme IIBC component(2nd module)' ecoli83 1,7,1 Cell processes Cell division Cell division 'ftsL' 'cell division protein; ingrowth of wall at septum' ecoli3258 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'hofD' 'leader peptidase integral membrane protein cryptic gene integral membrane protein' ecoli720 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'tolQ' 'inner membrane protein membrane-spanning maintains integrity of cell envelope; tolerance to group A colicins' ecoli410 - 2,2,7 Macromolecule metabolism Macromolecule synthesis, modification Phospholipids 'b0418' 'phosphatidylglycerophosphatase' ecoli1904 - 4,1,5 Structural elements Cell envelop Surface structures 'fliG' 'flagellar biosynthesis component of motor switching and energizing enabling rotation and determining its direction' ecoli3603 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'glvB' 'Sugar Specific family of transport protein PTS system arbutin-like IIB component' ecoli1560 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1590' 'putative DMSO reductase anchor subunit' Test Accuracy: 14/20 (70.00%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(4.03) ; prob(1.805578E-04) Application to new data (2167 items): ecoli2445 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2494' 'orf(1st module)' ecoli2507 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2556' 'paral putative sensor/kinase in regulatory system' ecoli1615 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1645' 'orf' ecoli1469 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1498' 'orf' ecoli935 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0960' 'paral putative transport protein (1st module)' ecoli1243 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'sohB' 'paral putative peptide peptidase (2nd module)' ecoli1638 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1670' 'orf' ecoli2974 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiE' 'orf' ecoli2903 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2969' 'orf (2nd module)' ecoli2853 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygfD' 'membrane-bound ATP-binding transport protein phosphorylates AO and LAO periplasmic proteins' ecoli2087 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehW' 'paral putative membrane component of transport system' ecoli55 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yabH' 'DnaJ like protein chaperone' ecoli4164 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgX' 'orf' ecoli106 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofC' 'orf' ecoli3281 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfK' 'orf' Frequency rule on new data: 15/2167 (0.69%) Evaluation on training data (939 items): ecoli679 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'kdpC' 'high-affinity potassium transport system' ecoli1456 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1485' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1797 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'htpX' 'heat shock protein integral membrane protein' ecoli306 1,5,5 Cell processes Transport/binding proteins BCCT superfamily 'betT' 'BCCT superfamily transport protein high-affinity choline transport' ecoli3199 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdX' 'ABC superfamily (membrane)paral putative membrane component of transport system' ecoli2940 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'exbB' 'uptake of enterochelin; tonB-dependent uptake of B colicins' ecoli647 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'lnt' 'apolipoprotein N-acyltransferase copper homeostasis protein inner membrane(1st module)' ecoli3358 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntU_2' 'split gene low-affinity gluconate transport permease protein in GNT-I system fragment 2' ecoli3401 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'nikC' 'ABC superfamily (membrane) membrane component in nickel transport system probably forms heterodimeric pore with NikB(1st module)' ecoli933 1,7,1 Cell processes Cell division Cell division 'sulA' 'suppressor of lon; inhibits cell division and ftsZ ring formation when DNA damage/inhibition HslVU and Lon involved in its turnover' ecoli1413 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1442' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli111 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'ampE' 'ampicillin resistance; membrane protein' ecoli624 1,7,1 Cell processes Cell division Cell division 'mrdB' 'rod shape-determining membrane protein; cell elongation in e phase(1st module)' ecoli851 1,5,22 Cell processes Transport/binding proteins MIP family 'aqpZ' 'MIP family transmembrane water channel; aquaporin Z' Training Accuracy: 14/14 (100.00%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(6.05) ; prob(1.557072E-08) Evaluation on validation data (471 items): ecoli1148 1,7,1 Cell processes Cell division Cell division 'minD' 'cell division inhibitor a membrane ATPase activates minC' ecoli2436 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2485' 'hydrogenase 4 membrane subunit(1st module)' ecoli579 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fepG' 'ABC superfamily (membrane) ferric enterobactin transport protein' ecoli3071 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'agaC' 'Sugar specific-family of transport protein; PTS system N-acetylgalactosamine-specific IIC component 1(1st module)' ecoli2325 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'emrK' 'multidrug resistance protein K' ecoli2160 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'napC' 'cytochrome c-type protein' ecoli3214 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'mscL' 'mechanosensitive channel' ecoli832 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potH' 'ABC superfamily (membrane) membrane component of putrescine ABC transport system(2nd module)' ecoli3066 - 3,3,2 Metabolism of small molecules Central intermediary metabolism Amino sugars 'agaW' 'PTS system N-acetylgalactosameine-specific IIC component 2' Validation Accuracy: 6/9 (66.67%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(2.52) ; prob(1.690875E-02) ------------------ Rule 20: (12/1, lift 5.6) [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,6),nss_coil( C , D ,gt,6),nss_coil( D , E ,gt,1)] = 1 [hom( A ),e_val_lteq( A ,3e-06),classification( A ,euryarchaeota)] = 1 [hom( A ),species( A ,oenothera_bertiana__bertero_s_evening_primrose_),mol_wt_gt( A ,55220)] = 1 [hom( A ),species( A ,halobacterium_halobium),mol_wt_gt( A ,32892)] = 0 [hom( A ),keyword( A ,inner_membrane),classification( A ,epsilon_subdivision)] = 0 -> class 'Macromolecule metabolism' [0.857] Evaluation on test data (712 items): ecoli937 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'helD' 'DNA helicase IV(2nd module)' ecoli1384 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'hrpA' 'helicase ATP-dependent(1st module)' ecoli26 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'ileS' 'isoleucine tRNA synthetase' ecoli886 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsA' '30S ribosomal subunit protein S1' ecoli4148 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'valS' 'valine tRNA synthetase' ecoli1844 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'argS' 'arginine tRNA synthetase' ecoli2477 - 1,3,1 Cell processes Folding and ushering proteins Chaperones 'hscA' 'heat shock protein chaperone member of Hsp70 protein family(2nd module)' ecoli4069 2,1,2 Macromolecule metabolism Macromolecule degradation Degradation of RNA 'vacB' 'RNase R(3rd module RNA binding domain )' ecoli3574 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'recG' 'DNA helicase resolution of Holliday junctions branch migration(2nd module)' ecoli4023 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'lysU' 'lysine tRNA synthetase inducible; heat shock protein(2nd module)' ecoli2826 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'lysS' 'lysine tRNA synthetase constitutive; suppressor of ColE1 mutation in primer RNA(2nd module)' ecoli32 - 3,7,2 Metabolism of small molecules Nucleotide biosynthesis Pyrimidine ribonucleotide biosynthesis 'carA' 'carbamoyl-phosphate synthetase glutamine-hydrolysing small subunit(2nd module)' ecoli464 - 1,3,1 Cell processes Folding and ushering proteins Chaperones 'htpG' 'chaperone Hsp90 heat shock protein C 62.5' ecoli3345 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'yhgB' 'sigma54-dependent regulator of rtcBA expression 3 functional domains(2nd module)' Test Accuracy: 10/14 (71.43%) Test Frequency class 'Macromolecule metabolism': 97/712 (13.62%) Test Significance: dev(6.31) ; prob(1.300478E-06) Application to new data (2167 items): ecoli107 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'hofB' 'putative integral membrane protein involved in biogenesis of fimbriae protein transport DNA uptake(2nd module)' ecoli3519 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yibH' 'paral putative membrane protein' ecoli2442 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2491' 'paral putative regulator protein' ecoli1803 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1835' 'paral putative rRNA methyltransferase (2nd module)' ecoli3680 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yifB' 'paral putative regulator protein' ecoli2885 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2950' 'putative protein transport(2nd module)' ecoli3456 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3533' 'putative cellulose synthase' ecoli2573 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2627' 'orf' ecoli2486 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'csiE' 'stationary phase inducible protein' ecoli2174 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yojN' 'paral putative sensor/kinase in regulatory system' ecoli415 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0423' 'thiozole biosynthesis protein and 4-thiouridine synthesis in tRNA (paral putative oxidoreductase)(2nd module)' ecoli322 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0330' 'regulator for prp operon(2nd module)' ecoli923 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0948' 'orf' ecoli3803 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'frvR' 'putative frv operon regulatory protein' ecoli3666 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3745' 'orf' ecoli1174 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1201' 'putative 2-component regulator (2nd module)' ecoli2805 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2869' 'paral putative regulator protein' Frequency rule on new data: 17/2167 (0.78%) Evaluation on training data (939 items): ecoli955 2,2,10 Macromolecule metabolism Macromolecule synthesis, modification Proteins - translation and modification 'yccC' 'Tyrosine-protein kinase ETK appears to be expressed only by pathogenic strains can autophosphorylate' ecoli3330 2,1,2 Macromolecule metabolism Macromolecule degradation Degradation of RNA 'yhgF' 'paral putative RNase R(3rd module RNA binding domain )' ecoli2757 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'recB' 'DNA helicase ATP-dependent dsDNA/ssDNA exonuclease V subunit ssDNA endonuclease chi sequence recognition (1st module)' ecoli4237 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'hsdS' 'specificity determinant for hsdM and hsdR' ecoli2073 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'metG' 'methionine tRNA synthetase (3rd module substrate recognition/ dimerisation/proof reading )' ecoli2539 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'clpB' 'ClpB protease ATP dependent part of novel multi-chaperone system with DnaK DnaJ and GrpE (2nd module)' ecoli1681 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'pheT' 'phenylalanine tRNA synthetase beta-subunit' ecoli3249 - 1,2,1 Cell processes Chromosome replication Chromosome replication 'yheG' 'putative general secretion pathway for protein export (GSP) (TYPE II TRAFFIC WARDEN ATPASE)(2nd module)' ecoli755 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'uvrB' 'DNA repair; excision nuclease subunit B(2nd module)' ecoli868 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'serS' 'serine tRNA synthetase ; also charges selenocystein tRNA with serine' ecoli3108 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'hflB' 'ATP-dependent zinc-metallo protease (integral membrane protein) modulated by HflKC cleaves sigma32 CII lamda protein SecY ATP-dependent zinc-metallo protease (integral membrane protein) modulat(2nd module)' ecoli2756 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'recD' 'DNA helicase ATP-dependent dsDNA/ssDNA exonuclease V subunit ssDNA endonuclease chi sequence recognition' Training Accuracy: 11/12 (91.67%) Training Frequency class 'Macromolecule metabolism': 145/939 (15.44%) Training Significance: dev(7.31) ; prob(1.226372E-08) Evaluation on validation data (471 items): ecoli2637 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'alaS' 'alanyl-tRNA synthetase' ecoli4097 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'fklB' 'FKBP-type 22KD peptidyl-prolyl cis-trans isomerase (rotamase)' ecoli3000 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'dnaG' 'DNA biosynthesis; DNA primase' ecoli1878 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'uvrC' 'excinuclease ABC subunit C; repair of UV damage to DNA(1st module)' ecoli1087 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'mfd' 'transcription-repair coupling factor; mutation frequency decline(2nd module)' ecoli431 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'lon' 'DNA-binding ATP-dependent protease la; heat shock k-protein (3rd module DNA-binding)' ecoli3270 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'fkpA' 'FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase)' ecoli3837 - 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'hslU' 'heat shock protein hslVU ATPase subunit homologous to chaperones (1st module)' ecoli2433 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2482' 'hydrogenase 4 membrane subunit(1st module)' Validation Accuracy: 6/9 (66.67%) Validation Frequency class 'Macromolecule metabolism': 71/471 (15.07%) Validation Significance: dev(4.33) ; prob(6.037000E-04) ------------------ Rule 12: (8/1, lift 2.9) [ss_coil( A ,gt,5),nss_coil( A , B ,gt,10),nss_coil( B , C ,lteq,3)] = 0 [hom( A ),psi_iter_gt( A ,7),classification( A ,rhodospirillum)] = 0 [hom( A ),species( A ,halobacterium_halobium),mol_wt_gt( A ,32892)] = 0 [hom( A ),mol_wt_lteq( A ,43194),classification( A ,protacanthopterygii)] = 1 [hom( A ),keyword( A ,inner_membrane),classification( A ,epsilon_subdivision)] = 0 -> class 'Cell processes' [0.800] Evaluation on test data (712 items): ecoli3607 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'hslS' 'heat shock protein' ecoli3833 1,5,22 Cell processes Transport/binding proteins MIP family 'glpF' 'MIP family facilitated diffusion of glycerol' ecoli4069 - 2,1,2 Macromolecule metabolism Macromolecule degradation Degradation of RNA 'vacB' 'RNase R(3rd module RNA binding domain )' ecoli115 - 3,5,7 Metabolism of small molecules Energy metabolism, carbon Pyruvate dehydrogenase 'aceF' 'pyruvate dehydrogenase (dihydrolipoyltransacetylase component)(2nd module)' ecoli2246 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoA' 'NADH dehydrogenase I chain A' ecoli572 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi81_2' 'IS186 protein' ecoli3259 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'bfr' 'bacterioferrin an iron storage homoprotein' ecoli2503 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'hmpA' 'dihydropteridine reductase ferrisiderophore reductase activity(2nd module)' ecoli4167 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi41' 'IS4 protein' ecoli424 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'cyoA' 'cytochrome o ubiquinol oxidase subunit II' Test Accuracy: 3/10 (30.00%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(0.06) ; prob(5.921104E-01) Application to new data (2167 items): ecoli1873 - 1 Cell processes 'ftn' 'cytoplasmic ferritin (an iron storage protein)' ecoli2791 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2854' 'orf' ecoli3750 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3838' 'transmembrane protein part of sec-independent protein export' ecoli2431 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'bcp' 'bacterioferritin comigratory protein' ecoli4111 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfN' 'orf' ecoli1567 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'asr' 'acid shock protein' ecoli2272 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'dedD' 'paral putative lipoprotein(1st module)' ecoli1870 - 1 Cell processes 'yecI' 'ferritin-like protein' Frequency rule on new data: 8/2167 (0.37%) Evaluation on training data (939 items): ecoli1295 1,4,2 Cell processes Protection responses Detoxification 'tpx' 'thiol peroxidase' ecoli16 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi81_1' 'homolog IS186 transposase' ecoli68 1,5,16 Cell processes Transport/binding proteins GPH family 'tbpA' 'ABC superfamily (periplasmic) periplasmic thiamine binding component of thiamine transport protein' ecoli2376 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'cysP' 'thiosulfate binding protein' ecoli1096 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'potD' 'ABC superfamily (peri_perm) spermidine/putrescine binding periplasmic ABC transport protein' ecoli1678 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'btuE' 'not required for vitamin B12 transport perhaps periplasmic protein' ecoli3608 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'hslT' 'heat shock protein' ecoli851 1,5,22 Cell processes Transport/binding proteins MIP family 'aqpZ' 'MIP family transmembrane water channel; aquaporin Z' Training Accuracy: 7/8 (87.50%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(3.78) ; prob(7.564036E-04) Evaluation on validation data (471 items): ecoli2112 - 3,2,5 Metabolism of small molecules Biosynthesis of cofactors, carriers Folic acid 'folE' 'GTP cyclohydrolase I' ecoli2126 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'fruA' 'Sugar Specific PTS system fructose-specific transport protein(2nd module)' ecoli3311 1,7,1 Cell processes Cell division Cell division 'damX' 'membrane protein(2nd module)' ecoli3884 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplL' '50S ribosomal subunit protein L7/L12' ecoli4042 - 2,2,6 Macromolecule metabolism Macromolecule synthesis, modification Lipoprotein 'blc' 'outer membrane lipoprotein (lipocalin)' ecoli3823 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'sbp' 'periplasmic sulfate-binding protein' ecoli1223 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'tonB' 'energy transducer; uptake of iron cyanocobalimin; sensitivity to phages colicins(1st module)' ecoli3181 1,7,1 Cell processes Cell division Cell division 'mreB' 'split gene mecillinam resistance; cell shape affects division versus elongation; fragment 1 (2nd module)' Validation Accuracy: 5/8 (62.50%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(2.12) ; prob(3.932851E-02) ------------------ Rule 6: (17/1, lift 3.2) [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,lteq,3),nss_coil( C , D ,lteq,830),nss_coil( D , E ,gt,5)] = 1 [hom( A ),e_val_gt( A ,2e-37),classification( A ,alcaligenaceae)] = 0 [hom( A ),psi_iter_lteq( A ,13),classification( A ,neurospora)] = 0 [hom( A ),species( A ,methanococcus_jannaschii),mol_wt_lteq( A ,32892)] = 0 [hom( A ),mol_wt_gt( A ,77359),classification( A ,mollicutes)] = 1 [hom( A ),mol_wt_gt( A ,55220),classification( A ,ciliophora)] = 0 -> class 'Cell processes' [0.895] Evaluation on test data (712 items): ecoli2620 - 3,3,11 Metabolism of small molecules Central intermediary metabolism Nucleotide interconversions 'nrdE' 'ribonucleoside diphosphate reductase 2 alpha subunit' ecoli2759 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'recC' 'DNA helicase ATP-dependent dsDNA/ssDNA exonuclease V subunit ssDNA endonuclease chi sequence recognition' ecoli806 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b0830' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' ecoli3094 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'deaD' 'cysteine sulfinate desulfinase(1st module)' ecoli3575 1,5,18 Cell processes Transport/binding proteins GltS family 'gltS' 'GltS family glutamate transport (2nd module)' ecoli140 - 4,1,5 Structural elements Cell envelop Surface structures 'ecpD' 'probable pilin chaperone similar to PapD' ecoli2992 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'ygiG' 'dihydroneopterin aldolase' ecoli578 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fepC' 'ABC superfamily (atp_bind) ATP-binding component of ferric enterobactin transport(2nd module)' ecoli2954 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b3020' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' ecoli437 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'ybaE' 'paral putative periplasmic binding protein of ABC transport system' ecoli3805 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'frvB' 'PTS family fructose-like enzyme IIBC component(2nd module)' ecoli2527 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'srmB' 'ATP-dependent RNA helicase (2nd module)' ecoli2192 - 3,3,1 Metabolism of small molecules Central intermediary metabolism 2'-Deoxyribonucleotide metabolism 'nrdA' 'ribonucleoside diphosphate reductase 1 alpha subunit B1(2nd module)' Test Accuracy: 6/13 (46.15%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(1.36) ; prob(1.468945E-01) Application to new data (2167 items): ecoli1751 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1783' 'orf' ecoli3694 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rhlB' 'paral putative helicase' ecoli1876 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yecA' 'orf' ecoli2574 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2628' 'orf' ecoli1078 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1105' 'orf' ecoli379 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaiI' 'orf' ecoli773 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rhlE' 'paral putative helicase' ecoli3322 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrfG' 'orf' ecoli1942 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1980' 'orf' ecoli3540 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3618' 'involved in lipopolysaccharide biosynthesis' ecoli3255 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yheJ' 'putative export protein J for general secretion pathway (GSP)' ecoli4197 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjhR' 'putative frameshift suppressor' ecoli1300 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1329' 'murein peptide binding periplasmic protein also a negative regulator of mulitple antibiotic resistance' ecoli1313 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1342' 'orf' ecoli55 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yabH' 'DnaJ like protein chaperone' ecoli1584 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1614' 'orf' ecoli1330 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1359' 'orf' ecoli3636 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3715' 'orf' ecoli809 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0833' 'orf(2nd module)' Frequency rule on new data: 19/2167 (0.88%) Evaluation on training data (939 items): ecoli2136 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'yejA' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' ecoli98 1,2,1 Cell processes Chromosome replication Chromosome replication 'secA' 'preprotein translocase; secretion protein' ecoli1214 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'oppA' 'ABC superfamily (peri_perm) oligopeptide binding periplasmic protein of transport system with chaperone properties' ecoli15 1,3,1 Cell processes Folding and ushering proteins Chaperones 'dnaJ' 'chaperone (with DnaK); heat shock protein' ecoli1265 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'sapA' 'ABC superfamily (peri_perm) peptide binding periplasmic protein of ABC transport system' ecoli974 1,3,1 Cell processes Folding and ushering proteins Chaperones 'cbpA' 'curved DNA-binding protein; functions closely related to DnaJ' ecoli907 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'pepN' 'aminopeptidase N' ecoli1281 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1310' 'ABC superfamily (peri_perm) ABC super family transport protein peri_perm subunit' ecoli564 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b0574' 'putative resistance protein(2nd module)' ecoli69 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'yabN' 'paral putative periplasmic binding protein of transport system' ecoli1294 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'tyrR' 'transcriptional regulation of aroF aroG tyrA and aromatic amino acid transport(2nd module)' ecoli3399 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'nikA' 'ABC superfamily (peri_perm) nickel-binding perimplasmic protein precursor in nickel ABC transport system(1st module)' ecoli1155 1,4,1 Cell processes Protection responses Cell killing 'b1182' 'hemolysin E' ecoli736 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'modF' 'ABC superfamily (atp_bind) ATP-binding component of molybdenum transport system (2nd module)' ecoli2367 1,5,17 Cell processes Transport/binding proteins General PTS family 'ptsI' 'General PTS family enzyme i (2nd module necessary for autophosphorylation and dimerization)' ecoli3728 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'corA' 'Mg2+ transport system I' ecoli1458 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1487' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' Training Accuracy: 16/17 (94.12%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(6.12) ; prob(1.500552E-08) Evaluation on validation data (471 items): ecoli1687 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'thrS' 'threonine tRNA synthetase(2nd module)' ecoli3009 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'ebgA' 'evolved beta-D-galactosidase alpha subunit; cryptic gene(1st module)' ecoli3376 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'ugpB' 'ABC superfamily (peri_perm) ABC super family transport protein peri_perm subunit sn-glycerol 3-phosphate periplasmic binding protein of ABC transport system(2nd module)' ecoli1274 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'pspF' 'psp operon transcriptional activator (sigma 54 transcription activator)' ecoli642 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'gltL' 'ABC superfamily (atp_bind) ATP-binding protein of glutamate/aspartate transport system' ecoli3467 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'dppA' 'ABC superfamily (peri_perm) dipeptide binding periplasmic protein of ABC transport system (1st module)' ecoli1411 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1440' 'ABC superfamily (peri_perm) ABC superfamily of transport protein peri_perm subunit' ecoli741 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'modC' 'ABC superfamily (atp_bind) ATP-binding component of molybdate ABC transport (1st module)' Validation Accuracy: 5/8 (62.50%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(2.12) ; prob(3.932851E-02) ------------------ Rule 17: (8, lift 5.8) [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,6),nss_coil( B , C ,gt,1)] = 1 [ss_coil( A ,gt,3),nss_coil( A , B ,gt,6),nss_coil( B , C ,gt,5)] = 1 [hom( A ),psi_iter_gt( A ,7),classification( A ,rhodospirillum)] = 0 [hom( A ),mol_wt_gt( A ,77359),classification( A ,amphibia)] = 1 [hom( A ),mol_wt_gt( A ,77359),classification( A ,mollicutes)] = 0 [hom( A ),mol_wt_lteq( A ,32892),keyword( A ,membrane)] = 0 -> class 'Macromolecule metabolism' [0.900] Evaluation on test data (712 items): ecoli3480 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi5B' 'IS150 transposase' ecoli2182 - 3,4,4 Metabolism of small molecules Degradation of small molecules Fatty acids 'b2224' 'acetyl-CoA acetyltransferase' ecoli3329 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'greB' 'transcription elongation factor and transcript cleavage' ecoli3747 - 3,2,8 Metabolism of small molecules Biosynthesis of cofactors, carriers Menaquinone, ubiquinone 'b3835' 'ubiquinone biosynthesis protein regulator of 2-N-acetyltransferase' ecoli3164 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'hhoA' 'serine endoprotease' ecoli2738 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'exo' '5-3 exonuclease' ecoli4036 - 1,7,1 Cell processes Cell division Cell division 'mopA' 'GroEL chaperone Hsp60 peptide-dependent ATPase heat shock protein; affects cell division' Test Accuracy: 3/7 (42.86%) Test Frequency class 'Macromolecule metabolism': 97/712 (13.62%) Test Significance: dev(2.25) ; prob(5.780815E-02) Application to new data (2167 items): ecoli2257 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2299' 'orf' ecoli2879 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'sprT' 'orf' ecoli3162 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcM' 'orf' ecoli1954 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1995' 'orf' ecoli2471 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2520' 'orf' ecoli4232 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4343' 'orf joins former yjiU and yjiV' ecoli991 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1017' 'putative cytochrome' ecoli176 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaeL' 'orf' ecoli2750 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2810' 'orf(1st module)' ecoli2228 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2270' 'orf' ecoli992 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1018' 'orf' ecoli766 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0790' 'orf' ecoli3766 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihE' 'orf' ecoli250 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ykfC' 'orf' ecoli310 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0318' 'putative transcription factor' Frequency rule on new data: 15/2167 (0.69%) Evaluation on training data (939 items): ecoli1686 2,2,10 Macromolecule metabolism Macromolecule synthesis, modification Proteins - translation and modification 'infC' 'protein chain initiation factor IF-3' ecoli2639 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'recA' 'DNA strand exchange and renaturation DNA-dependent ATPase DNA- and ATP-dependent coprotease(1st module)' ecoli3552 2,2,5 Macromolecule metabolism Macromolecule synthesis, modification Lipopolysaccharide 'rfaP' 'lipopolysaccharide core biosynthesis; phosphorylation of core heptose; attaches phosphate-containing substrate to LPS core' ecoli1813 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'ptrB' 'protease II' ecoli2532 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'yfiF' 'hypothetical tRNA/rRNA methyltransferase (2nd module)' ecoli3543 2,2,5 Macromolecule metabolism Macromolecule synthesis, modification Lipopolysaccharide 'rfaC' 'lipopolysaccharide core biosynthesis; heptosyl transferase I' ecoli172 2,2,10 Macromolecule metabolism Macromolecule synthesis, modification Proteins - translation and modification 'frr' 'ribosome releasing factor' ecoli1717 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'xthA' 'exonuclease III' Training Accuracy: 8/8 (100.00%) Training Frequency class 'Macromolecule metabolism': 145/939 (15.44%) Training Significance: dev(6.62) ; prob(3.233101E-07) Evaluation on validation data (471 items): ecoli2112 - 3,2,5 Metabolism of small molecules Biosynthesis of cofactors, carriers Folic acid 'folE' 'GTP cyclohydrolase I' ecoli4097 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'fklB' 'FKBP-type 22KD peptidyl-prolyl cis-trans isomerase (rotamase)' ecoli4261 2,2,10 Macromolecule metabolism Macromolecule synthesis, modification Proteins - translation and modification 'prfC' 'peptide chain release factor RF-3(1st module)' ecoli1670 - 3,3,4 Metabolism of small molecules Central intermediary metabolism Gluconeogenesis 'ppsA' 'phosphoenolpyruvate synthase (3rd module autophosphorylation and dimerization ?)' ecoli2362 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'lig' 'DNA ligase' Validation Accuracy: 3/5 (60.00%) Validation Frequency class 'Macromolecule metabolism': 71/471 (15.07%) Validation Significance: dev(2.81) ; prob(2.470532E-02) ------------------