Rule 1: (120/5, lift 3.4) ecoli_hydro > 0.214 amino_acid_ratio_g > 4.4 amino_acids_e > 1 amino_acid_pair_ratio_ec <= 1.9 amino_acid_pair_ratio_em <= 7.5 amino_acid_pair_ratio_gy <= 7.6 amino_acid_pair_ratio_ih <= 3.8 amino_acid_pair_ratio_mx <= 3.1 amino_acid_pair_ratio_rt <= 9.5 amino_acid_pair_ratio_wc <= 2.3 amino_acid_pair_ratio_xn <= 3.2 amino_acid_pairs_dp <= 2 amino_acid_pairs_px <= 1 -> class 'Cell processes' [0.951] Evaluation on test data (712 items): ecoli716 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'cydA' 'cytochrome d terminal oxidase polypeptide subunit I' ecoli335 1,5,21 Cell processes Transport/binding proteins MFS family 'lacY' 'MFS family of transport protein galactoside permease (M protein)(1st module)' ecoli1913 - 4,1,5 Structural elements Cell envelop Surface structures 'fliP' 'flagellar biosynthesis' ecoli3879 1,2,1 Cell processes Chromosome replication Chromosome replication 'secE' 'protein secretion inner membrane protein' ecoli3338 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntT' 'high-affinity gluconate permease in GNT-I system' ecoli2670 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hypE' 'plays structural role in maturation of all 3 hydrogenases' 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)' ecoli3798 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'fdoI' 'formate dehydrogenase cytochrome B556 (FDO) subunit' 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)' 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' ecoli470 1,5,21 Cell processes Transport/binding proteins MFS family 'fsr' 'MFS family of transport protein fosmidomycin resistance protein(2nd module)' ecoli3833 1,5,22 Cell processes Transport/binding proteins MIP family 'glpF' 'MIP family facilitated diffusion of glycerol' 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' 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' ecoli953 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'appB' 'probable third cytochrome oxidase subunit II' 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' ecoli4210 1,5,19 Cell processes Transport/binding proteins GntP family 'gntP' 'GntP family of transport protein high affinity gluconate transporter/gluconate permease in gnt-iii system (2nd module)' ecoli818 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b0842' 'transmembrane multidrug/chloramphenicol efflux transporter (2nd module)' ecoli4120 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ytfT' 'ABC superfamily (membrane)paral putative membrane component' ecoli333 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'cynX' 'cyanate transport' ecoli728 1,5,6 Cell processes Transport/binding proteins CDF family 'b0752' 'CDF family of transport protein (1st module)' 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' ecoli808 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0832' 'ABC superfamily (membrane) paral putative membrane component of transport system' 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)' ecoli769 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0793' 'putative membrane component of ABC transport system(2nd 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' ecoli614 1,7,1 Cell processes Cell division Cell division 'ybeI' 'high-copy crc-csp restores normal chromosome condensation in presence of camphor or mukB mutations' ecoli3961 1,5,35 Cell processes Transport/binding proteins SSS family 'yjcG' 'SSS family transport protein' ecoli565 1,5,33 Cell processes Transport/binding proteins RNDfamily 'ybdE' 'RND family of transport protein paral putative transport system (2nd module)' ecoli3643 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'bglF' 'Sugar Specific PTS family beta-glucosides enzyme II cryptic (2nd module eiia (ei interaction)?)' ecoli2364 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'cysZ' 'required for sulfate transport' ecoli1787 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'manZ' 'Sugar Specific PTS Sugar specific-family of transport protein; enzyme IID mannose-specific' 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' ecoli2182 - 3,4,4 Metabolism of small molecules Degradation of small molecules Fatty acids 'b2224' 'acetyl-CoA acetyltransferase' 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)' 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)' ecoli3575 1,5,18 Cell processes Transport/binding proteins GltS family 'gltS' 'GltS family glutamate transport (2nd module)' 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' ecoli4017 1,5,12 Cell processes Transport/binding proteins Dcu family 'dcuB' 'Dcu family anaerobic C4-dicarboxylate transporter' ecoli2404 - 3,4,1 Metabolism of small molecules Degradation of small molecules Amines 'eutG' 'ethanolamine utilization; homolog of salmonella enzyme similar to iron-containing alcohol dehydrogenase (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)' ecoli2662 - 3,5,4 Metabolism of small molecules Energy metabolism, carbon Fermentation 'hycD' 'membrane-spanning protein of hydrogenase 3 (part of FHL complex)' ecoli2538 1,5,21 Cell processes Transport/binding proteins MFS family 'kgtP' 'MFS family of transport protein alpha-ketoglutarate permease(1st module)' ecoli2246 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoA' 'NADH dehydrogenase I chain A' 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)' ecoli879 1,5,14 Cell processes Transport/binding proteins FNT family 'focA' 'FNT family membrane protein (formate channel 1)(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' ecoli407 - 3,2,13 Metabolism of small molecules Biosynthesis of cofactors, carriers Riboflavin 'ribH' 'riboflavin synthase beta chain' ecoli4041 1,5,34 Cell processes Transport/binding proteins SMR family 'sugE' 'SMR family of transport protein' ecoli2120 1,5,7 Cell processes Transport/binding proteins CNT family 'yeiJ' 'CNT family of transport protein' ecoli3579 1,5,16 Cell processes Transport/binding proteins GPH family 'yicJ' 'GPH family paral putative transport protein' ecoli3589 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpB' 'sensor histidine protein kinase phosphorylates UhpA(2nd module)' ecoli2063 - 3,2,14 Metabolism of small molecules Biosynthesis of cofactors, carriers Thiamin 'b2104' 'hydoxyethylthiazole kinase (TH kinase) (EC 2 7 1 50)' 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' ecoli2435 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2484' 'hydrogenase 4 membrane subunit(1st module)' ecoli3072 - 3,3,2 Metabolism of small molecules Central intermediary metabolism Amino sugars 'agaD' 'PTS system N-acetylglucosamine enzyme IID component 1' ecoli1447 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'fdnI' 'formate dehydrogenase-N nitrate-inducible cytochrome B556(Fdn) gamma subunit' 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)' 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)' ecoli378 - 3,1,16 Metabolism of small molecules Amino acid biosynthesis Proline 'proC' 'pyrroline-5-carboxylate reductase' 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' ecoli3604 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'glvC' 'PTS family arbutin-like IIC component' 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)' ecoli681 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'kdpA' 'ATPase of high-affinity potassium transport system A chain(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)' ecoli2015 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b2056' 'putative colanic acid polymerase' 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)' ecoli3805 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'frvB' 'PTS family fructose-like enzyme IIBC component(2nd module)' ecoli3836 - 3,2,8 Metabolism of small molecules Biosynthesis of cofactors, carriers Menaquinone, ubiquinone 'menA' '14-dihydroxy-2-naphthoate --> dimethylmenaquinone' ecoli2034 1,5,33 Cell processes Transport/binding proteins RNDfamily 'b2075' 'RND family of transport protein paral putative outer membrane receptor' ecoli2137 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejB' 'ABC superfamily (membrane) paral putative membrane component of transport system' 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' ecoli2358 - 3,3,11 Metabolism of small molecules Central intermediary metabolism Nucleotide interconversions 'xapA' 'xanthosine phosphorylase' ecoli328 1,5,25 Cell processes Transport/binding proteins NCS1 family 'codB' 'NCS1 family transport protein cytosine permease/transport(2nd module)' ecoli3971 1,5,10 Cell processes Transport/binding proteins DAACS family 'gltP' 'DAACS family of transport protein glutamate-aspartate symport protein' ecoli3813 1,5,19 Cell processes Transport/binding proteins GntP family 'rhaT' 'GntP family rhamnose permease; L-rhamnose-H+ symporter membrane protein(1st 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)' ecoli2123 1,5,7 Cell processes Transport/binding proteins CNT family 'yeiM' 'CNT family of transport protein' ecoli3392 1,5,30 Cell processes Transport/binding proteins P-type ATPase family 'b3469' 'P-type ATPase familyzinc-transporting ATPase(2nd module)' ecoli1560 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1590' 'putative DMSO reductase anchor subunit' ecoli2051 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'gatC' 'PTS family galactitol-specific enzyme IIC' Test Accuracy: 71/93 (76.34%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(10.04) ; prob(5.835645E-21) Application to new data (2167 items): ecoli1604 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1634' 'orf' ecoli3434 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hdeD' 'orf' ecoli479 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0488' 'orf' ecoli1602 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1632' 'orf(1st module)' ecoli211 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0218' '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' ecoli1303 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1332' 'orf' ecoli2117 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yeiH' 'orf' ecoli2850 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2915' '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? )' ecoli314 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0322' 'orf' ecoli2613 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2668' 'orf(1st module)' ecoli4015 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjdF' 'orf' ecoli3606 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidE' 'paral putative transport protein(1st module)' ecoli2215 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2257' 'orf(2nd module)' ecoli1597 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1627' 'orf' ecoli3042 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhaN' 'orf' ecoli1404 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1433' 'putative membrane transport protein' ecoli2835 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2899' 'putative oxidoreductase' 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' ecoli2329 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2372' 'putative receptor protein' ecoli850 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0874' 'putative surface protein' ecoli1801 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1833' 'orf' ecoli279 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yagU' 'orf' 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)' ecoli763 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0787' 'orf' ecoli1221 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'kch' 'putative potassium channel protein' ecoli1213 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ychE' 'orf' ecoli2196 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yfaH' 'orf' 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' ecoli2559 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2612' 'orf' ecoli4253 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjjP' 'paral putative membrane protein' 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' ecoli764 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0788' 'orf (2nd module)' ecoli1596 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1626' 'orf' ecoli823 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0847' 'putative transport protein' ecoli980 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1006' 'putative transport protein(2nd module)' ecoli3962 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcH' 'orf' ecoli3730 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yigG' 'orf' ecoli1250 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1279' 'orf' ecoli1226 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciC' 'orf' ecoli698 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0715' 'putative transport protein(1st module)' ecoli2943 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yghB' 'orf' ecoli1600 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1630' 'orf' ecoli3585 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yicO' 'orf (2nd module)' ecoli3037 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhaI' 'orf' ecoli2585 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2639' 'putative pump protein' ecoli3128 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbI' 'orf formerly yrbI and yrbJ' ecoli1788 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1820' 'orf' ecoli1638 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1670' 'orf' ecoli2689 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygbE' 'putative cytochrome oxidase subunit' ecoli3036 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhaH' 'orf' ecoli3729 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yigF' 'orf' ecoli371 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0379' 'orf' ecoli1658 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1690' 'paral putative MFS family of transport 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' 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)' ecoli2628 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygaH' 'orf' ecoli984 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1010' 'orf' ecoli4219 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiH' 'orf' ecoli2627 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2682' 'orf' ecoli1694 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1726' 'orf' ecoli1094 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1121' 'homolog of virulence factor' ecoli1500 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeB' 'orf' ecoli2820 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2884' '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' ecoli2454 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2503' 'orf' ecoli2917 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2983' 'orf' ecoli4221 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiJ' 'paral putative transport protein (2nd module)' 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' ecoli4218 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiG' 'orf' ecoli309 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0317' 'orf' ecoli1301 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1330' 'orf(2nd module)' ecoli2352 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yfeA' 'orf(2nd module)' ecoli3731 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rarD' 'chloramphenicol resistance' ecoli2598 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2653' 'orf' ecoli1505 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ydeF' 'paral putative transport protein (1st module)' ecoli3706 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yifJ' 'putative cytochrome' ecoli784 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0808' 'pral putative transport protein (2nd module)' 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' ecoli817 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0841' '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' ecoli3267 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3344' 'orf' ecoli738 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0762' 'orf' ecoli372 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0380' 'orf' ecoli518 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybcI' 'orf' ecoli3870 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yijD' 'orf' ecoli1696 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1728' 'orf' ecoli1577 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1607' 'orf' ecoli3484 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiaA' 'orf' ecoli3576 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yicE' 'putative transport protein' ecoli888 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycaI' 'orf' ecoli2133 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2174' 'orf' ecoli1784 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1816' 'orf (2nd module)' ecoli1789 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1821' 'orf' ecoli4151 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgP' 'orf(1st module)' ecoli2204 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2246' 'putative transport protein' ecoli1972 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yeeE' 'paral putative membrane component of transport system' ecoli3126 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbG' 'orf' ecoli2993 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiH' 'orf' ecoli3788 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yihU' 'paral putative oxidoreductase(1st module)' ecoli1946 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1985' 'paral putative transport protein (3rd module)' ecoli65 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yabI' 'orf(1st module)' ecoli2285 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfcA' 'putative structural protein' ecoli1799 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yebJ' 'possible structural element which influences activation of ProP (?posttranslationally)' ecoli3389 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3466' 'orf' ecoli3431 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiD' 'putative transport ATPase' ecoli2087 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehW' 'paral putative membrane component of transport system' ecoli567 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ybdG' 'putative transport(2nd module)' ecoli2901 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2966' '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' ecoli3568 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yicG' 'orf' ecoli1569 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1599' 'orf' ecoli1030 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1057' 'putative cytochrome' ecoli2269 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ubiX' '3-octaprenyl-4-hydroxybenzoate carboxy-lyase' ecoli4193 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjhN' 'paral putative PTS system enzyme IIC component' ecoli1571 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1601' 'paral putative transport protein (2nd module)' ecoli2349 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2392' 'putative transport system permease(1st module)' ecoli1382 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1411' 'putative enzymes' ecoli1444 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yddG' 'orf' ecoli1145 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1172' 'orf' ecoli2399 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2448' 'orf' ecoli504 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0513' 'putative transport(2nd module)' ecoli762 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0786' 'orf' ecoli3975 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcQ' 'orf(2nd module)' ecoli1943 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1981' 'shikimate and dehydroshikimate permease (2nd module)' ecoli4152 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgQ' 'orf(1st module)' ecoli3325 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhgE' 'putative transport' ecoli1894 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yedE' 'paral putative membrane component of transport system' ecoli3720 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'o161' 'orf' 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)' ecoli3152 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhcI' 'ManNAc kinase' ecoli4074 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfL' 'orf' ecoli2322 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'dsdX' 'transport system permease (serine?)' ecoli2216 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2258' 'paral putative ABC superfamily transport protein' ecoli2275 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'dedA' 'orf' ecoli4108 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfL' 'orf (2nd module)' 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)' ecoli1038 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1065' 'orf' ecoli4147 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4257' 'orf joins former yjgN and yjgO' ecoli3499 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiaM' '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' ecoli2104 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2145' 'orf' ecoli2676 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2736' 'paral putative oxidoreductase' ecoli801 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0825' 'putative transaldolase' 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)' ecoli3034 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yqjF' 'orf' ecoli10 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaaH' 'orf' ecoli3300 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfT' 'orf (2nd module)' ecoli2256 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2298' 'putative S-transferase' ecoli1532 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'rem' 'orf' ecoli3417 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiO' 'universal stress protein B involved in stationary-phase resistance to ethanol (integral membr prot sigmaS related)' ecoli2906 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2972' 'paral putative peptidase' ecoli3958 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcD' 'orf (2nd module)' Frequency rule on new data: 172/2167 (7.94%) Evaluation on training data (939 items): ecoli4029 - 3,3,19 Metabolism of small molecules Central intermediary metabolism Sulfur metabolism 'dsbD' 'thiol:disulfide interchange protein N-term.(1st module)' 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)' ecoli3425 1,5,4 Cell processes Transport/binding proteins Ars family 'arsB' 'Ars family arsenical pump membrane protein(2nd module)' 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)' 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)' 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)' ecoli1456 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1485' 'ABC superfamily (membrane) paral putative membrane component of transport system' 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 )' 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 )' 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)' ecoli2736 1,5,36 Cell processes Transport/binding proteins STP family 'sdaC' 'STP family of transport protein serine transporter' ecoli3783 1,5,16 Cell processes Transport/binding proteins GPH family 'yihP' 'GPH family paral putative transport protein' ecoli3105 1,2,1 Cell processes Chromosome replication Chromosome replication 'secG' 'protein export - membrane protein' 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)' ecoli3049 1,5,36 Cell processes Transport/binding proteins STP family 'tdcC' 'STP family of transport protein anaerobically inducible L-threonine/ L-serine permease' ecoli1264 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapB' 'ABC superfamily (membrane) membrane component of peptide ABC transport system' ecoli1295 1,4,2 Cell processes Protection responses Detoxification 'tpx' 'thiol peroxidase' ecoli1797 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'htpX' 'heat shock protein integral membrane protein' ecoli1950 - 3,2,3 Metabolism of small molecules Biosynthesis of cofactors, carriers Cobalamin 'cobT' 'nicotinate-nucleotide dimethylbenzimidazole-P phophoribosyl transferase' ecoli1091 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1118' 'ABC superfamily (membrane) paral putative membrane component of ABC transport system' 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)' ecoli306 1,5,5 Cell processes Transport/binding proteins BCCT superfamily 'betT' 'BCCT superfamily transport protein high-affinity choline transport' 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)' ecoli3199 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdX' 'ABC superfamily (membrane)paral putative membrane component of transport system' 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)' ecoli3400 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'nikB' 'ABC superfamily (membrane) membrane component in nickel transport system probably forms heterodimeric pore with NikC(2nd 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)' 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)' 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)' ecoli1855 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'cheW' 'purine-binding chemotaxis protein; regulation' ecoli2940 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'exbB' 'uptake of enterochelin; tonB-dependent uptake of B colicins' 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' ecoli2448 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'uraA' 'uracil transport' ecoli3761 1,5,39 Cell processes Transport/binding proteins Trk system 'trkH' 'Trk system potassium uptake requires TrkE' 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)' ecoli647 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'lnt' 'apolipoprotein N-acyltransferase copper homeostasis protein inner membrane(1st 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' 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)' 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' 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' 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' ecoli833 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potI' 'ABC superfamily (membrane) membrane component of putrescine 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' 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)' 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)' 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)' ecoli2343 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2386' 'Sugar Specific paral putative membrane component of transport system' ecoli2437 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2486' 'hydrogenase 4 membrane subunit(2nd module)' 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' 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' 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' 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' ecoli1413 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1442' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2181 - 3,4,4 Metabolism of small molecules Degradation of small molecules Fatty acids 'atoB' 'short chain fatty acids transporter' ecoli533 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b0543' 'multidrug transporter methylviologen and ethidium resistance' ecoli3408 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhhJ' 'ABC superfamily (membrane)paral putative transport system membrane (2nd module)' ecoli611 1,5,13 Cell processes Transport/binding proteins DcuC 'b0621' 'DcuC family of tranport protein transport of dicarboxylates succinate efflux during glucose fermentation(2nd module)' ecoli3469 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'yhjX' 'putative resistance protein' ecoli2642 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'srlA_1' 'PTS family glucitol/sorbitol-specific IIC component one of two' 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)' ecoli3332 1,5,15 Cell processes Transport/binding proteins FeoB family 'feoB' 'FeoB family ferrous iron transport protein B(1st module)' ecoli2643 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'srlA_2' 'PTS family glucitol/sorbitol-specific IIB component and second of two IIC components' ecoli111 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'ampE' 'ampicillin resistance; membrane protein' 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)' ecoli2443 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b2492' 'membrane protein formate transporter of hyf operon (formate channel 2)' 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' ecoli477 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b0486' 'APC family of transport protein amino-acid transport protein' ecoli1769 1,5,5 Cell processes Transport/binding proteins BCCT superfamily 'b1801' 'BCCT superfamily paral putative transporter' ecoli4185 1,5,19 Cell processes Transport/binding proteins GntP family 'yjhF' 'GntP family of transport protein (1st module)' 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: 115/120 (95.83%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(16.68) ; prob(2.809884E-57) Evaluation on validation data (471 items): ecoli4014 1,5,16 Cell processes Transport/binding proteins GPH family 'melB' 'GPH family melibiose permease II' 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' ecoli3521 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'mtlA' 'Sugar Specific PTS family mannitol-specific enzyme IIABC components (3rd module eii a domain phosphoryl by p-hpr 491-637)' ecoli419 1,5,21 Cell processes Transport/binding proteins MFS family 'b0427' 'MFS family transport 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' ecoli3416 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pitA' 'low-affinity phosphate transport' 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)' 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)' 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)' ecoli2126 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'fruA' 'Sugar Specific PTS system fructose-specific transport protein(2nd module)' ecoli1196 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'narK' 'nitrite extrusion protein(2nd module)' ecoli482 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b0491' 'putative metal resistance protein' ecoli443 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'amtB' 'probable ammonium transporter' ecoli1627 1,5,21 Cell processes Transport/binding proteins MFS family 'b1657' 'MFS family of transport protein (2nd module)' 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)' ecoli3057 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'yhaE' 'tartronate semialdehyde reductase (TSAR) in glucarate/galactarate catabolic pathway (1st 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)' ecoli4130 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'treB' 'PTS family enzyme II trehalose specific (maltose may be transported)' ecoli2052 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'gatB' 'PTS family galactitol-specific enzyme IIB' 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' ecoli2271 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'cvpA' 'membrane protein required for colicin V production' ecoli2436 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2485' 'hydrogenase 4 membrane subunit(1st module)' ecoli952 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'appC' 'probable third cytochrome oxidase subunit I' 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' ecoli1424 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1453' 'L-asparagine permease (2nd module)' ecoli2046 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'gatR_1' 'split galactitol utilization operon repressor fragment 1' ecoli3884 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplL' '50S ribosomal subunit protein L7/L12' ecoli579 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fepG' 'ABC superfamily (membrane) ferric enterobactin transport protein' 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 )' ecoli2350 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'nupC' 'permease of transport system for 3 nucleosides' 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)' 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)' 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' 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' ecoli1867 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1899' 'split high-affinity L-arabinose transport system; membrane protein fragment 1' 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)' 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)' ecoli159 - 3,3,11 Metabolism of small molecules Central intermediary metabolism Nucleotide interconversions 'pfs' '5-methylthioadenosine/S-adenosylhomocysteine nucleosidase' ecoli3214 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'mscL' 'mechanosensitive channel' ecoli3093 1,5,43 Cell processes Transport/binding proteins ArAAP family 'mtr' 'ArAAP family tryptophan-specific transport protein' ecoli4031 1,5,12 Cell processes Transport/binding proteins Dcu family 'dcuA' 'Dcu family anaerobic dicarboxylate transport' ecoli1915 - 4,1,5 Structural elements Cell envelop Surface structures 'fliR' 'paral putative transport protein for flagellar biosynthesis' ecoli727 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pnuC' 'required for NMN transport' ecoli2818 1,5,13 Cell processes Transport/binding proteins DcuC 'b2882' 'DcuC family paral putative transport protein' 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)' ecoli714 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'hrsA' 'protein modification enzyme induction of ompc (2nd module eiibc? )' ecoli423 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'cyoB' 'cytochrome o ubiquinol oxidase subunit I' ecoli3709 - 3,3,18 Metabolism of small molecules Central intermediary metabolism Sugar-nucleotide biosynthesis, conversions 'rffT' 'synthesis of enterobacterial common antigen (ECA): TDP-Fuc4NAc:lipidII transferase(1st module)' ecoli3066 - 3,3,2 Metabolism of small molecules Central intermediary metabolism Amino sugars 'agaW' 'PTS system N-acetylgalactosameine-specific IIC component 2' ecoli692 1,5,31 Cell processes Transport/binding proteins POT family 'b0709' 'POT family of transport protein (1st module)' ecoli1948 - 3,3,0 Metabolism of small molecules Central intermediary metabolism other 'nac' 'nitrogen assimilation control protein represses gdhA transcription under nitrogen limiting conditions(1st 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' ecoli909 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0934' 'ABC superfamily (membrane) probable membrane component of transport system' ecoli2433 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2482' 'hydrogenase 4 membrane subunit(1st module)' Validation Accuracy: 47/62 (75.81%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(8.21) ; prob(1.828981E-14) ------------------ Rule 16: (4, lift 19.6) ecoli_theo_pI > 9.25 amino_acid_pair_ratio_ty > 9.5 -> class 'Extrachromosomal' [0.833] Evaluation on test data (712 items): ecoli545 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0555' 'bacteriophage lambda lysozyme homolog' ecoli22 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_1' 'IS1 protein InsA' Test Accuracy: 2/2 (100.00%) Test Frequency class 'Extrachromosomal': 25/712 (3.51%) Test Significance: dev(7.41) ; prob(1.232878E-03) Application to new data (2167 items): ecoli3691 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3777' 'orf' ecoli365 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0373' 'orf' ecoli3690 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3776' 'orf' ecoli290 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0298' 'orf' ecoli1527 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1556' 'orf' ecoli2047 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2088' 'orf' ecoli2572 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2626' 'orf' ecoli244 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yafZ' 'orf' ecoli2579 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2633' 'orf' ecoli530 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0540' 'orf' ecoli241 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0249' 'orf' ecoli1083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycfJ' 'orf' ecoli1151 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1178' 'orf' ecoli2071 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yehE' 'orf' ecoli3062 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhaV' 'orf' ecoli4113 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfA' 'orf' ecoli3435 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhiE' 'orf' ecoli1001 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1027' 'orf' ecoli682 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybfA' 'orf' ecoli1938 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1974' 'putative cytochrome' ecoli288 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0296' 'putative ribosomal protein' ecoli324 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0332' 'orf' ecoli1536 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1565' 'orf' Frequency rule on new data: 23/2167 (1.06%) Evaluation on training data (939 items): ecoli267 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_3' 'IS1 protein InsA' ecoli1323 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'ydaD' 'prophage protein inhibitor of ftsZ' ecoli544 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0554' 'homolog of Rz of phage PA-2' ecoli1862 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_5' 'IS1 protein InsA' Training Accuracy: 4/4 (100.00%) Training Frequency class 'Extrachromosomal': 40/939 (4.26%) Training Significance: dev(9.48) ; prob(3.292893E-06) Evaluation on validation data (471 items): ecoli257 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_2' 'IS1 protein InsA 2' ecoli3239 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsS' '30S ribosomal subunit protein S19' ecoli4183 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_7' 'IS1 protein InsA' ecoli3367 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_6' 'IS1 protein InsA' Validation Accuracy: 3/4 (75.00%) Validation Frequency class 'Extrachromosomal': 26/471 (5.52%) Validation Significance: dev(6.08) ; prob(6.357062E-04) ------------------ Rule 13: (39/13, lift 2.4) amino_acid_pair_ratio_xi > 1.8 amino_acid_pairs_kw <= 1 -> class 'Cell processes' [0.659] Evaluation on test data (712 items): ecoli335 1,5,21 Cell processes Transport/binding proteins MFS family 'lacY' 'MFS family of transport protein galactoside permease (M protein)(1st module)' ecoli3228 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplF' '50S ribosomal subunit protein L6' ecoli1772 - 2,1,2 Macromolecule metabolism Macromolecule degradation Degradation of RNA 'rnd' 'RNase D processes tRNA precursor' ecoli154 - 3,2,6 Metabolism of small molecules Biosynthesis of cofactors, carriers Heme, porphyrin 'hemL' 'glutamate-1-semialdehyde aminotransferase (aminomutase)' ecoli3070 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'agaB' 'Sugar Specific PTS system cytoplasmic N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA)' ecoli3555 - 4,1,4 Structural elements Cell envelop Surface polysaccharides & antigens 'kdtA' '3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)' 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' ecoli3462 1,5,36 Cell processes Transport/binding proteins STP family 'yhjV' 'STP family of transport protein' ecoli769 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0793' 'putative membrane component of ABC transport system(2nd module)' ecoli3891 - 3,2,14 Metabolism of small molecules Biosynthesis of cofactors, carriers Thiamin 'thiE' 'thiamin biosynthesis thiazole moiety' ecoli573 - 3,2,4 Metabolism of small molecules Biosynthesis of cofactors, carriers Enterochelin 'entD' 'enterochelin synthetase component D' 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)' ecoli2995 - 3,5,4 Metabolism of small molecules Energy metabolism, carbon Fermentation 'ttdA' 'L-tartrate dehydratase' 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' ecoli883 - 3,1,5 Metabolism of small molecules Amino acid biosynthesis Chorismate 'aroA' '3-enolpyruvylshikimate-5-phosphate synthetase' ecoli2706 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'b2766' 'probable electron transfer flavoprotein-quinone oxidoreductase ygcn' 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)' ecoli2523 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'rseA' 'sigma-E factor negative regulatory protein' ecoli1875 1,5,43 Cell processes Transport/binding proteins ArAAP family 'tyrP' 'ArAAP family tyrosine-specific transport system' ecoli1206 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'hnr' 'response regulator involved in protein turnover N-terminal shows homology to two-component response regulators controls stability of RpoS(1st module)' Test Accuracy: 10/21 (47.62%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(1.87) ; prob(5.567471E-02) Application to new data (2167 items): ecoli4222 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiK' 'orf' ecoli476 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0485' 'orf' ecoli901 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0926' 'orf' ecoli3922 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbG' 'orf' ecoli2111 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yeiB' 'orf' ecoli2117 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yeiH' 'orf' ecoli1756 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1788' 'orf' ecoli3299 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfS' 'orf' ecoli1101 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycfD' 'orf' ecoli3139 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhbL' 'sigma cross-reacting protein 27A (SCRP-27A)' ecoli3032 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yqjE' 'orf' ecoli891 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0916' 'orf' ecoli1482 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1511' 'paral putative kinase' ecoli2697 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2757' 'orf' ecoli2306 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfdB' 'putative prophage (CPS-53) Sf6-like integrase' ecoli986 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1012' 'orf' ecoli764 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0788' 'orf (2nd module)' ecoli3068 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'agaS' 'orf (1st module)' ecoli1638 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1670' 'orf' ecoli2809 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2873' 'orf' ecoli4082 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfR' 'orf' ecoli3391 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3468' 'putative enzyme' ecoli721 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'tolR' 'putative inner membrane protein involved in the tonB-independent uptake of group A colicins' ecoli1429 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1458' 'orf' ecoli2649 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygaA' 'paral putative regulator protein' ecoli2558 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2611' 'orf' ecoli512 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybcF' 'orf' ecoli3640 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yieL' 'putative xylanase' ecoli2551 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yfiN' 'orf(2nd module)' ecoli991 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1017' 'putative cytochrome' ecoli1656 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1688' 'orf' ecoli157 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yadS' 'orf' ecoli2481 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2530' 'orf(1st module)' ecoli1505 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ydeF' 'paral putative transport protein (1st module)' ecoli845 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0869' 'putative dTDP-glucose enz' ecoli506 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0515' 'orf' ecoli3410 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiI' 'paral putative membrane protein' ecoli784 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0808' 'pral putative transport protein (2nd module)' ecoli3753 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yigW' 'orf; may be second part of tatD by frameshift with b3842' ecoli992 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1018' 'orf' ecoli3150 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcG' 'orf' ecoli1332 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1361' 'orf' ecoli2305 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfdC' 'putative transport' ecoli2698 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2758' 'orf' ecoli888 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycaI' 'orf' ecoli639 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0649' 'orf' ecoli4214 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiC' 'orf' ecoli3252 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'hofH' 'putative general protein secretion protein' ecoli1518 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1547' 'orf' ecoli2204 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2246' 'putative transport protein' ecoli2203 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2245' 'paral putative aldolase' ecoli3126 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbG' 'orf' ecoli3735 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigJ' 'threonine efflux protein' ecoli2993 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiH' 'orf' ecoli3153 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3223' 'ManNAc-6P epimerase' ecoli3031 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yqjD' 'orf' ecoli1726 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1758' 'putative cytochrome oxidase' ecoli1419 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1448' 'orf' ecoli1331 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1360' 'orf' ecoli979 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1005' 'orf' ecoli355 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0363' 'polysaccharide metabolism(1st module)' ecoli1640 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1672' 'orf' ecoli3869 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yijC' 'orf' ecoli1848 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1880' 'putative part of export apparatus for flagellar proteins' ecoli1781 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yeaB' 'orf' ecoli3130 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhbN' 'orf' ecoli1809 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1841' 'orf' ecoli3147 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcE' 'orf' ecoli274 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yagP' 'orf' ecoli4243 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiY' 'putative carbon starvation protein' ecoli1894 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yedE' 'paral putative membrane component of transport system' 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)' ecoli603 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0613' 'orf (probable modifier of citrate lyase protein)' ecoli693 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0710' 'orf' ecoli3635 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yieG' 'orf (2nd module)' ecoli1038 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1065' 'orf' ecoli4147 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4257' 'orf joins former yjgN and yjgO' ecoli246 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'perR' 'paral putative regulator' ecoli1992 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yefH' 'paral putative acyl transferase' 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' ecoli834 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0858' 'orf' ecoli4021 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjdJ' 'orf' Frequency rule on new data: 83/2167 (3.83%) Evaluation on training data (939 items): ecoli3425 1,5,4 Cell processes Transport/binding proteins Ars family 'arsB' 'Ars family arsenical pump membrane protein(2nd module)' ecoli1985 - 3,1,10 Metabolism of small molecules Amino acid biosynthesis Histidine 'hisI' 'bifunctional phosphoribosyl-amp cyclohydrolase and phosphoribosyl-ATP pyrophosphatase' ecoli161 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'htrA' 'periplasmic serine protease Do; heat shock protein HtrA(2nd module)' ecoli2267 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'hisJ' 'ABC superfamily (peri_perm) histidine-binding periplasmic protein of high-affinity histidine ABC transport system' 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)' 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' ecoli2843 - 3,2,8 Metabolism of small molecules Biosynthesis of cofactors, carriers Menaquinone, ubiquinone 'ubiH' '2-octaprenyl-6-methoxyphynol hydroxylase 2-octaprenyl-6-methoxyphenol--> 2-octaprenyl-6-methoxy-1 4-benzoquinone' ecoli2631 1,5,21 Cell processes Transport/binding proteins MFS family 'emrB' 'MFS family of transport protein multidrug resistance; probably membrane translocase(1st module)' ecoli3049 1,5,36 Cell processes Transport/binding proteins STP family 'tdcC' 'STP family of transport protein anaerobically inducible L-threonine/ L-serine permease' ecoli1091 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1118' 'ABC superfamily (membrane) paral putative membrane component of ABC transport system' 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)' ecoli345 1,5,21 Cell processes Transport/binding proteins MFS family 'b0353' 'MFS family transport protein (2nd module function unknown)' ecoli3240 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplB' '50S ribosomal subunit protein L2' 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' ecoli2991 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'bacA' 'bacitracin resistance; possibly phosphorylates undecaprenol' ecoli596 1,4,2 Cell processes Protection responses Detoxification 'ahpF' 'alkyl hydroperoxide reductase F52a subunit; detoxification of hydroperoxides(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)' ecoli3022 1,5,10 Cell processes Transport/binding proteins DAACS family 'ygjU' 'DAACS family Na+/serine (threonine) symporter' ecoli1851 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'cheB' 'response regulator for chemotaxis (cheA sensor); protein methylesterase(1st module)' ecoli3630 1,5,43 Cell processes Transport/binding proteins ArAAP family 'tnaB' 'ArAAP family low affinity tryptophan permease' ecoli3721 - 3,1,13 Metabolism of small molecules Amino acid biosynthesis Lysine 'dapF' 'diaminopimelate epimerase' ecoli833 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potI' 'ABC superfamily (membrane) membrane component of putrescine ABC transport system(2nd module)' ecoli547 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0557' 'bacteriophage lambda Bor protein homolog' 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' ecoli2437 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2486' 'hydrogenase 4 membrane subunit(2nd module)' 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)' ecoli3387 1,7,1 Cell processes Cell division Cell division 'ftsY' 'cell division membrane protein (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' 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' ecoli722 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'tolA' 'membrane spanning protein required for outer membrane integrity' ecoli611 1,5,13 Cell processes Transport/binding proteins DcuC 'b0621' 'DcuC family of tranport protein transport of dicarboxylates succinate efflux during glucose fermentation(2nd module)' ecoli1573 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'pntA' 'pyridine nucleotide transhydrogenase alpha subunit' ecoli3561 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'dfp' 'flavoprotein affecting synthesis of DNA and pantothenate metabolism' ecoli27 - 2,2,10 Macromolecule metabolism Macromolecule synthesis, modification Proteins - translation and modification 'lspA' 'prolipoprotein signal peptidase (SPase II)' ecoli1679 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'btuC' 'ABC superfamily (membrane) membrane component of vitamin B12 ABC transport system' ecoli3544 - 2,2,5 Macromolecule metabolism Macromolecule synthesis, modification Lipopolysaccharide 'rfaL' 'lipopolysaccharide core biosynthesis; O-antigen ligase(1st module)' Training Accuracy: 26/39 (66.67%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(5.44) ; prob(4.629946E-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' 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' ecoli2237 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoK' 'NADH dehydrogenase I chain K' ecoli630 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'holA' 'DNA polymerase III delta subunit' ecoli827 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'mdaA' 'oxygen sensitive NADPH nitroreductase' ecoli443 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'amtB' 'probable ammonium transporter' ecoli3429 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'slp' 'outer membrane protein induced after carbon starvation' ecoli1627 1,5,21 Cell processes Transport/binding proteins MFS family 'b1657' 'MFS family of transport protein (2nd module)' ecoli3686 - 3,1,21 Metabolism of small molecules Amino acid biosynthesis Valine 'ilvA' 'threonine deaminase (dehydratase)(1st module)' ecoli3644 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'bglG' 'positive regulation (transcriptional antiterminator ) of bgl operon' ecoli3908 - 3,3,5 Metabolism of small molecules Central intermediary metabolism Glyoxylate bypass 'aceB' 'malate synthase A' ecoli1944 - 3,3,17 Metabolism of small molecules Central intermediary metabolism Salvage of nucleosides and nucleotides 'amn' 'AMP nucleosidase' ecoli4250 1,2,1 Cell processes Chromosome replication Chromosome replication 'dnaC' 'chromosome replication; initiation and chain elongation' 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 )' 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)' ecoli2325 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'emrK' 'multidrug resistance protein K' ecoli3612 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'yidT' 'D-galactonate transport' 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' ecoli1867 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1899' 'split high-affinity L-arabinose transport system; membrane protein fragment 1' 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)' ecoli2280 1,5,21 Cell processes Transport/binding proteins MFS family 'b2322' 'MFS family of transport protein paral putative (2nd module)' ecoli1864 1,6,2 Cell processes Adaptation Osmotic adaptation 'otsA' 'trehalose-6-phosphate synthase' ecoli4031 1,5,12 Cell processes Transport/binding proteins Dcu family 'dcuA' 'Dcu family anaerobic dicarboxylate transport' ecoli1275 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'pspA' 'phage shock protein; negative regulatory gene for stress sigma (54) dependent phage-shock-protein operon' ecoli3821 1,5,6 Cell processes Transport/binding proteins CDF family 'yiiP' 'CDF family of transport protein (1st module)' ecoli3006 - 3,1,2 Metabolism of small molecules Amino acid biosynthesis Arginine 'ygjG' 'probable ornithine aminotransferase(2nd module)' ecoli2433 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2482' 'hydrogenase 4 membrane subunit(1st module)' Validation Accuracy: 17/29 (58.62%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(3.57) ; prob(5.361329E-04) ------------------ Rule 31: (6, lift 5.7) ecoli_hydro <= 0.214 amino_acid_ratio_c > 0.5 amino_acid_pair_ratio_cr <= 1.6 amino_acid_pairs_tl > 7 amino_acid_pairs_tp > 1 -> class 'Macromolecule metabolism' [0.875] Evaluation on test data (712 items): ecoli2726 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'barA' 'sensor module of sensor-regulator activates ompr by phophorylation (2nd module potential phosphoacceptor 665-784)' ecoli4132 - 1,5,30 Cell processes Transport/binding proteins P-type ATPase family 'mgtA' 'P-type ATPase familyMg2+ transport ATPase P-type 1(2nd module)' ecoli988 - 3,4,2 Metabolism of small molecules Degradation of small molecules Amino acids 'putA' 'bifunctional in plasma membrane proline dehydrogenase and pyrroline-5-carboxylate dehydrogenase OR in cytoplasm a transcriptional repressor(2nd module)' ecoli3142 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'gltB' 'glutamate synthase large subunit' ecoli678 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'kdpD' 'sensor for high-affinity potassium transport system bifunctional enzyme catalyzing the autophosphorylation by ATP and the dephosphorylation of the corresponding response regulator KdpE(3rd module)' ecoli3952 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'uvrA' 'excision nuclease subunit (3rd module prob. DNA binding)' Test Accuracy: 1/6 (16.67%) Test Frequency class 'Macromolecule metabolism': 97/712 (13.62%) Test Significance: dev(0.22) ; prob(5.846916E-01) Application to new data (2167 items): ecoli2425 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2474' 'orf' ecoli3784 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihQ' 'orf' ecoli935 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0960' 'paral putative transport protein (1st module)' ecoli2282 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2324' 'putative a peptidase' ecoli2500 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2549' 'orf' ecoli2077 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehI' 'paral putative regulator (3rd module)' ecoli2327 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'evgS' 'with evga two component regulatory system environmentally responsive (3rd module)' ecoli2079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2120' 'orf' ecoli1484 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1513' 'paral putative ATP-binding component of transport system (2nd module)' ecoli4003 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjdA' 'putative vimentin' ecoli3281 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfK' 'orf' Frequency rule on new data: 11/2167 (0.51%) Evaluation on training data (939 items): 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)' ecoli1925 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'dcm' 'DNA cytosine methylase' ecoli1681 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'pheT' 'phenylalanine tRNA synthetase beta-subunit' ecoli3692 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'rep' 'rep helicase a single-stranded DNA dependent ATPase(1st module)' ecoli3339 2,1,3 Macromolecule metabolism Macromolecule degradation Degradation of polysaccharides 'malQ' '4-alpha-glucanotransferase (amylomaltase)' ecoli389 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'sbcC' 'ATP-dependent dsDNA exonuclease (2nd module)' Training Accuracy: 6/6 (100.00%) Training Frequency class 'Macromolecule metabolism': 145/939 (15.44%) Training Significance: dev(5.73) ; prob(1.355859E-05) Evaluation on validation data (471 items): ecoli2987 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'glnE' 'adenylyl transferase for glutamine synthetase regulates P-II (GlnB) and GlnK' ecoli475 - 1,5,4 Cell processes Transport/binding proteins Ars family 'b0484' 'Ars family of transport protein' ecoli339 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b0347' '3-(3-hydroxy-phenyl)propionate hydroxylase' ecoli3935 2,2,7 Macromolecule metabolism Macromolecule synthesis, modification Phospholipids 'plsB' 'glycerolphosphate acyltransferase activity MAY ALSO FUNCTION IN THE REGULATION OF MEMBRANE BIOGENESIS' ecoli4239 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'hsdR' 'host restriction; endonuclease R (2nd 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)' ecoli576 - 3,2,4 Metabolism of small molecules Biosynthesis of cofactors, carriers Enterochelin 'entF' 'nonribosomal peptide synthetase / enterobactin synthetase component F (it contains four domains (condensation-adenylation-peptidyl carrier protein-thioesterase(elongation and cyclolactonization))' Validation Accuracy: 4/7 (57.14%) Validation Frequency class 'Macromolecule metabolism': 71/471 (15.07%) Validation Significance: dev(3.11) ; prob(1.106968E-02) ------------------ Rule 54: (27, lift 11.3) ecoli_hydro <= 0.214 ecoli_theo_pI > 9.25 amino_acid_ratio_m <= 5.3 amino_acid_ratio_n > 1.7 amino_acid_pair_ratio_de <= 13.4 amino_acid_pair_ratio_dh <= 4 amino_acid_pair_ratio_ff <= 8 amino_acid_pair_ratio_mn <= 12.5 amino_acid_pair_ratio_my <= 2.8 amino_acid_pair_ratio_qw <= 5.7 amino_acid_pair_ratio_sf <= 8.1 amino_acid_pair_ratio_ty <= 9.5 amino_acid_pairs_cl <= 1 amino_acid_pairs_hq <= 0 amino_acid_pairs_kq <= 1 amino_acid_pairs_kw <= 0 amino_acid_pairs_qp <= 3 amino_acid_pairs_rx <= 0 -> class 'Structural elements' [0.966] Evaluation on test data (712 items): ecoli540 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'b0550' 'endodeoxyribonuclease RUS (Holliday junction resolvase)' ecoli3118 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'nlp' 'regulatory factor of maltose metabolism; similar to Ner repressor protein of phage Mu' ecoli25 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'yaaC' 'flavokinase and FAD synthetase' ecoli3555 4,1,4 Structural elements Cell envelop Surface polysaccharides & antigens 'kdtA' '3-deoxy-D-manno-octulosonic-acid transferase (KDO transferase)' ecoli3243 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplC' '50S ribosomal subunit protein L3' ecoli3238 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplV' '50S ribosomal subunit protein L22' ecoli4172 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi91' 'IS911 protein' ecoli3882 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplA' '50S ribosomal subunit protein L1 regulates synthesis of L1 and L11' ecoli3241 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplW' '50S ribosomal subunit protein L23' ecoli1831 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'ruvC' 'Holliday junction nuclease; resolution of structures; repair' ecoli2460 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'xseA' 'exonuclease VII large subunit' ecoli3231 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplE' '50S ribosomal subunit protein L5' ecoli3229 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsH' '30S ribosomal subunit protein S8 and regulator' ecoli23 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsT' '30S ribosomal subunit protein S20' ecoli1846 4,1,5 Structural elements Cell envelop Surface structures 'b1878' 'flagellar protein' ecoli1 - 3,1,18 Metabolism of small molecules Amino acid biosynthesis Threonine 'thrL' 'thr operon leader peptide' ecoli1916 4,1,4 Structural elements Cell envelop Surface polysaccharides & antigens 'rcsA' 'positive regulator of capsular polysaccharide synthesis activates its own expression' ecoli2682 - 2,2,6 Macromolecule metabolism Macromolecule synthesis, modification Lipoprotein 'nlpD' 'lipoprotein(2nd module)' 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)' ecoli3749 - 1,2,1 Cell processes Chromosome replication Chromosome replication 'b3837' 'twin arginine translocation part of sec-independent protein export' ecoli1045 4,1,5 Structural elements Cell envelop Surface structures 'flgA' 'flagellar biosynthesis; assembly of basal-body periplasmic P ring' Test Accuracy: 11/21 (52.38%) Test Frequency class 'Structural elements': 64/712 (8.99%) Test Significance: dev(6.95) ; prob(4.632439E-07) Application to new data (2167 items): ecoli3250 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofF' 'orf' ecoli1025 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1052' 'orf' ecoli272 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0280' 'orf' ecoli2600 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2655' 'orf' ecoli2603 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2658' 'orf' ecoli2294 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2336' 'paral putative chaperone' ecoli1115 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1142' 'orf' ecoli2801 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2865' 'orf (2nd module)' ecoli774 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybiA' 'orf' ecoli2511 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yfhB' 'orf' ecoli3916 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbC' 'orf' ecoli3941 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbL' 'orf' ecoli522 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0531' 'paral putative chaperone' ecoli3533 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yibN' 'orf' ecoli1774 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1806' 'paral putative membrance protein' ecoli3795 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiiE' 'orf' ecoli1574 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1604' 'orf' ecoli1240 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciL' 'orf' ecoli227 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yafP' 'orf' ecoli1138 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1165' 'orf' ecoli1005 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1031' 'putative ribosomal protein' ecoli3084 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yraR' 'orf' ecoli284 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yagY' 'orf' ecoli2888 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2953' 'orf' ecoli3285 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfG' 'orf' ecoli237 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0245' 'orf' ecoli3905 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjaA' 'orf' ecoli653 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0663' 'putative RNA' ecoli501 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0510' 'orf' ecoli1311 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1340' 'orf' ecoli2565 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2618' 'orf' ecoli2134 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2175' 'suppresses thermosensitivity of prc mutants at low osmolality; in turn suppressed by multicopy expression of PBP 7' ecoli1230 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciG' 'orf' ecoli3317 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrfC' 'orf' ecoli744 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ybhD' 'paral putative regulator' ecoli224 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'dinP' 'damage-inducible protein P; putative tRNA synthetase(1st module)' ecoli3033 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3100' 'orf' ecoli2981 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3047' 'paral putative chaperone' ecoli56 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yabP' 'orf' ecoli1317 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1346' 'orf' ecoli5 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0005' 'orf' ecoli963 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0989' 'cold shock-like protein' ecoli1178 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ychH' 'orf' ecoli2970 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiA' 'orf' ecoli368 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yaiH' 'paral putative enzyme' ecoli979 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1005' '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)' ecoli852 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0876' 'orf' ecoli1516 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1545' 'orf' ecoli511 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0520' 'orf' ecoli1848 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1880' 'putative part of export apparatus for flagellar proteins' ecoli2253 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2295' 'orf' ecoli1529 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'cspF' 'cold shock protein' ecoli2567 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'smpB' 'orf; small protein B' ecoli2874 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yqgB' 'orf' ecoli250 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ykfC' 'orf' ecoli1210 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ychG' 'orf' ecoli2470 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2519' 'paral putative peptidoglycan enzyme (1st module)' ecoli995 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1021' 'orf homologue of Yersinia pestis hmsS involved in haemin uptake/storage ?cryptic' ecoli3843 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiiX' 'orf' ecoli1345 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1374' 'putative transposon resolvase' ecoli548 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0558' 'putative envelop protein (nohA?)' ecoli4174 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4285' 'putative transposase' ecoli11 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0011' 'putative oxidoreductase' ecoli247 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0255' 'orf' ecoli1260 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycjD' 'orf' ecoli1646 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1678' 'orf' ecoli1824 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yebA' 'orf(1st module)' ecoli2061 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2102' 'orf' Frequency rule on new data: 69/2167 (3.18%) Evaluation on training data (939 items): ecoli3559 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmB' '50S ribosomal subunit protein L28' ecoli3217 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplQ' '50S ribosomal subunit protein L17' ecoli2386 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'amiA' 'N-acetylmuramoyl-l-alanine amidase I' ecoli3881 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplK' '50S ribosomal subunit protein L11' ecoli2898 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'yggZ' 'membrane-bound lytic murein transglycosylase C(2nd module)' ecoli3220 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsK' '30S ribosomal subunit protein S11' ecoli4201 4,1,5 Structural elements Cell envelop Surface structures 'fimB' 'regulator for fimA' ecoli2760 4,1,5 Structural elements Cell envelop Surface structures 'ppdC' 'prepilin peptidase dependent protein C' ecoli3240 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplB' '50S ribosomal subunit protein L2' ecoli2093 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'pbpG' 'paral putative carboxypeptidase penicillin-binding protein 7' ecoli1053 4,1,5 Structural elements Cell envelop Surface structures 'flgI' 'homolog of Salmonella P-ring of flagella basal body' ecoli1645 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'lpp' 'murein lipoprotein links outer and inner membranes' ecoli1684 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplT' '50S ribosomal subunit protein L20 and regulator' ecoli4202 4,1,5 Structural elements Cell envelop Surface structures 'fimE' 'regulator for fimA' ecoli147 4,2,3 Structural elements Ribosome constituents Ribosomes - maturation and modification 'yadP' '2-5 RNA ligase' ecoli3234 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsQ' '30S ribosomal subunit protein S17' ecoli3230 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsN' '30S ribosomal subunit protein S14' ecoli3558 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmG' '50S ribosomal subunit protein L33' ecoli3235 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmC' '50S ribosomal subunit protein L29' ecoli3224 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplO' '50S ribosomal subunit protein L15' ecoli3624 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmH' '50S ribosomal subunit protein L34' ecoli1062 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmF' '50S ribosomal subunit protein L32' ecoli4205 4,1,5 Structural elements Cell envelop Surface structures 'fimC' 'periplasmic chaperone required for type 1 fimbriae' ecoli3265 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsL' '30S ribosomal subunit protein S12' ecoli3161 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplM' '50S ribosomal subunit protein L13' ecoli3222 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmJ' '50S ribosomal subunit protein X' ecoli3233 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplN' '50S ribosomal subunit protein L14' Training Accuracy: 27/27 (100.00%) Training Frequency class 'Structural elements': 80/939 (8.52%) Training Significance: dev(17.03) ; prob(1.322692E-29) Evaluation on validation data (471 items): ecoli546 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0556' 'bacteriophage lambda endopeptidase homolog' ecoli1014 4,1,5 Structural elements Cell envelop Surface structures 'csgB' 'minor curlin subunit precursor similar ro CsgA' ecoli2999 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsU' '30S ribosomal subunit protein S21' ecoli3237 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsC' '30S ribosomal subunit protein S3' ecoli1540 - 1,7,1 Cell processes Cell division Cell division 'dicC' 'regulator of dicB' ecoli3226 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsE' '30S ribosomal subunit protein S5' ecoli1676 - 2,2,6 Macromolecule metabolism Macromolecule synthesis, modification Lipoprotein 'nlpC' 'lipoprotein' ecoli196 4,1,4 Structural elements Cell envelop Surface polysaccharides & antigens 'rcsF' 'regulator in colanic acid synthesis; overexpression confers mucoid phenotype increases capsule synthesis' ecoli1810 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'holE' 'DNA polymerase III theta subunit' ecoli3160 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsI' '30S ribosomal subunit protein S9' ecoli3898 - 2,2,2 Macromolecule metabolism Macromolecule synthesis, modification Basic proteins - synthesis, modification 'hupA' 'DNA-binding protein HU-alpha (HU-2)' ecoli3689 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'ppiC' 'peptidyl-prolyl cis-trans isomerase C (rotamase C)' ecoli1166 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'b1193' 'murein transglycosylase E' Validation Accuracy: 7/13 (53.85%) Validation Frequency class 'Structural elements': 45/471 (9.55%) Validation Significance: dev(5.43) ; prob(6.826383E-05) ------------------ Rule 15: (13/1, lift 20.3) ecoli_theo_pI > 9.25 amino_acid_pair_ratio_qw > 5.7 -> class 'Extrachromosomal' [0.867] Evaluation on test data (712 items): ecoli3957 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'soxR' 'redox-sensing activator of soxS' ecoli1989 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_7' 'IS5 protein' ecoli266 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_3' 'IS1 protein InsB' ecoli1541 - 1,7,1 Cell processes Cell division Cell division 'dicA' 'regulator of dicB' ecoli545 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0555' 'bacteriophage lambda lysozyme homolog' ecoli3116 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplU' '50S ribosomal subunit protein L21' ecoli1953 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_6' 'IS5 protein' Test Accuracy: 4/7 (57.14%) Test Frequency class 'Extrachromosomal': 25/712 (3.51%) Test Significance: dev(7.71) ; prob(4.884632E-05) Application to new data (2167 items): ecoli690 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybgA' 'orf' ecoli685 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybfB' 'orf' ecoli2832 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2896' 'orf' ecoli1527 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1556' 'orf' ecoli3616 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidW' 'putative regulator protein' ecoli3037 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhaI' 'orf' ecoli4252 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjjB' 'orf' ecoli1520 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1549' 'orf' ecoli3854 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yijI' 'orf' ecoli3736 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigK' 'homoserine/homoserine lactone efflux protein' ecoli1553 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1583' 'orf' ecoli3731 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rarD' 'chloramphenicol resistance' ecoli2348 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2391' 'orf' ecoli1186 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1213' 'orf' ecoli895 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycbC' 'orf' ecoli4079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfO' 'orf' ecoli3029 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yqjB' 'orf' ecoli4163 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgW' 'orf' ecoli3827 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiiR' 'orf' ecoli3315 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrfA' 'orf' ecoli3769 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yihG' 'putative endonuclease' ecoli4236 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiW' 'orf' ecoli956 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0982' 'putative phosphatase' Frequency rule on new data: 23/2167 (1.06%) 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' ecoli646 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_3' 'IS5 protein' ecoli3368 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_6' 'IS1 protein InsB' ecoli1341 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_5' 'IS5 protein' ecoli17 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi82_1' 'homolog IS186 and IS421 protein' ecoli1861 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_5' 'IS1 protein InsB' ecoli3002 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'b3068' 'G/U mismatch specific DNA glycosylase' ecoli544 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0554' 'homolog of Rz of phage PA-2' ecoli21 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_1' 'IS1 protein InsB' ecoli2916 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_9' 'IS5 protein' Training Accuracy: 12/13 (92.31%) Training Frequency class 'Extrachromosomal': 40/939 (4.26%) Training Significance: dev(15.72) ; prob(4.459171E-16) Evaluation on validation data (471 items): ecoli928 - 4,2,3 Structural elements Ribosome constituents Ribosomes - maturation and modification 'rmf' 'ribosome modulation factor (involved in dimerization of 70S ribosomes)' ecoli1302 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_4' 'IS5 protein' ecoli3762 - 3,2,6 Metabolism of small molecules Biosynthesis of cofactors, carriers Heme, porphyrin 'b3850' 'protoporphyrin oxidase' ecoli962 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_4' 'IS1 protein InsB' ecoli229 - 2,2,10 Macromolecule metabolism Macromolecule synthesis, modification Proteins - translation and modification 'prfH' 'paral putative peptide chain release factor' ecoli838 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' ecoli256 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_2' 'IS1 protein InsB 2' ecoli3148 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_10' 'IS5 protein 10' Validation Accuracy: 4/8 (50.00%) Validation Frequency class 'Extrachromosomal': 26/471 (5.52%) Validation Significance: dev(5.51) ; prob(5.179218E-04) ------------------