Rule 1: (39/1, lift 3.4) [ss_coil( A ,gt,3),nss_coil( A , B ,lteq,830),nss_coil( B , C ,gt,1)] = 1 [ss_alpha( A ,gt,10),nss_alpha( A , B ,gt,3),nss_alpha( B , C ,gt,10)] = 1 [ss( A ,b),nss( A , B ,c),len_lteq( B ,10)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,5),nss_coil( B , C ,lteq,10),nss_coil( C , D ,lteq,6)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,gt,6),nss_coil( D , E ,lteq,5)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,10),nss_coil( B , C ,gt,5),nss_coil( C , D ,lteq,10),nss_coil( D , E ,gt,3)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,5),nss_coil( B , C ,gt,3),nss_coil( C , D ,gt,10),nss_coil( D , E ,gt,5)] = 0 -> class 'Cell processes' [0.951] Evaluation on test data (712 items): ecoli3338 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntT' 'high-affinity gluconate permease in GNT-I system' ecoli3967 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'nrfD' 'putative nitrate reductase formate dependent also paral putative STP family of transport protein' ecoli1485 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1514' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system' ecoli305 1,6,2 Cell processes Adaptation Osmotic adaptation 'betI' 'probable transcriptional repressor of bet genes' ecoli3374 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpE' 'ABC superfamily (membrane)sn-glycerol 3-phosphate transport system integral membrane protein(1st module)' ecoli4120 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ytfT' 'ABC superfamily (membrane)paral putative membrane component' ecoli808 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0832' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1588 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'gusR' 'repressor for uid operon' ecoli581 1,5,31 Cell processes Transport/binding proteins POT family 'ybdA' 'paral putative POT family of transport protein (1st module)' ecoli3980 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjcV' 'ABC superfamily (membrane) membrane component of allose ABC transport system(1st module)' ecoli3479 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi5A' 'IS5 protein' ecoli545 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0555' 'bacteriophage lambda lysozyme homolog' ecoli3290 1,5,14 Cell processes Transport/binding proteins FNT family 'nirC' 'FNT family transport protein' ecoli1887 - 4,1,5 Structural elements Cell envelop Surface structures 'fliA' 'regulation of late gene expression; sigma transcription factor F for class 3a and 3b operons' ecoli3645 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'phoU' 'regulatory gene for high affinity phosphate uptake under phosphate excess PhoU downregulates the PHO regulon' ecoli1457 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1486' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1853 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tap' 'methyl-accepting chemotaxis protein IV peptide sensor receptor (2nd module)' ecoli3380 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livH' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system(2nd module)' ecoli2246 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoA' 'NADH dehydrogenase I chain A' ecoli1249 - 2,2,7 Macromolecule metabolism Macromolecule synthesis, modification Phospholipids 'pgpB' 'non-essential phosphatidylglycerophosphate phosphatase membrane bound' ecoli1827 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'yebI' 'inner memrane component of a high affininty Zn transport system' ecoli408 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'nusB' 'transcription termination; L factor' 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)' ecoli2266 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisQ' 'ABC superfamily (membrane)histidine transport system' ecoli198 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yaeE' 'ABC superfamily (membrane) paral putative membrane component of transport system' 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)' ecoli4182 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'fecI' 'sigma factor in two component regulatory system wtih FecR FecR interacts wtih the periplasmic iron binding FecA' ecoli4155 1,5,19 Cell processes Transport/binding proteins GntP family 'yjgT' 'GntP family l-idonate transporter (2nd module)' ecoli2137 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejB' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli328 1,5,25 Cell processes Transport/binding proteins NCS1 family 'codB' 'NCS1 family transport protein cytosine permease/transport(2nd module)' ecoli3970 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'nrfG' 'part of formate-dependent nitrite reductase complex' ecoli1359 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1388' 'phenylacetic acid degradation protein possibly part of multicomponent oxygenase' ecoli807 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0831' 'paral putative membrane component of transport system' Test Accuracy: 21/33 (63.64%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(4.37) ; prob(3.971401E-05) Application to new data (2167 items): ecoli3445 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhjD' 'orf' ecoli1619 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1649' 'hypothetical transcriptional regulator' ecoli2634 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2689' 'orf' ecoli3028 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3095' 'orf' ecoli3893 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3995' 'regulator of sigma D has binding activity to the major sigma subunit of RNAP' ecoli2638 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'oraA' 'regulator' ecoli2329 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2372' 'putative receptor protein' ecoli3397 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhhT' 'paral putative transport protein (2nd module)' ecoli763 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0787' 'orf' ecoli2529 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfiK' 'paral putative transport protein' ecoli155 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yadQ' 'putative channel transporter' ecoli2095 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohD' 'orf' ecoli3972 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcO' 'orf(2nd module)' 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)' ecoli2397 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2446' 'orf' ecoli2943 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yghB' 'orf' ecoli2585 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2639' 'putative pump protein' ecoli987 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1013' 'putative tet operon regulator' ecoli1337 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1366' 'orf' ecoli1720 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1752' 'orf' ecoli3391 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3468' 'putative enzyme' ecoli2249 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2291' 'putative alpha helix protein' ecoli2097 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohG' 'orf' ecoli1656 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1688' 'orf' ecoli931 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycbG' 'putative dehydrogenase' ecoli3974 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcP' 'orf' ecoli3083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yraQ' 'orf' ecoli1530 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1559' 'orf' ecoli1936 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1972' 'orf' ecoli2506 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfhG' 'putative alpha helix protein' ecoli3194 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'envR' 'regulatory gene for envCD (acrEF)' ecoli4124 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjgA' 'putative alpha helix protein' ecoli3484 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiaA' 'orf' ecoli4028 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjdC' 'orf' ecoli2976 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3042' 'orf' ecoli822 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0846' 'paral putative regulator' ecoli1726 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1758' 'putative cytochrome oxidase' ecoli433 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0441' 'orf' ecoli2087 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehW' 'paral putative membrane component of transport system' ecoli2065 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2106' 'orf' ecoli1486 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1515' 'paral putative membrane component of ABC transport system' ecoli3563 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ttk' 'putative transcriptional regulator' ecoli2253 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2295' 'orf' ecoli1172 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1199' 'putative dihydroxyacetone kinase' ecoli3492 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3570' 'gene transcribed divergently from malS' ecoli762 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0786' 'orf' ecoli2275 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'dedA' 'orf' ecoli106 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofC' 'orf' ecoli1870 - 1 Cell processes 'yecI' 'ferritin-like protein' ecoli1251 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yciM' 'putative heat shock protein' Frequency rule on new data: 51/2167 (2.35%) Evaluation on training data (939 items): ecoli3359 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gntU_1' 'split gene low-affinity gluconate transport permease protein in GNT-I system first part of fragment 1(1st module)' 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)' ecoli128 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yadH' 'ABC superfamily (membrane) paral putative ABC superfamily (membrane)' ecoli1263 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapC' 'ABC superfamily (membrane) membrane component of peptide ABC transport system(2nd module)' ecoli3647 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstA' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' 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 )' ecoli1392 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'trg' 'methyl-accepting chemotaxis protein III ribose and galactose sensor receptor(2nd module)' ecoli2680 1,5,19 Cell processes Transport/binding proteins GntP family 'b2740' 'GntP family of transport protein function unknown (3rd module)' ecoli1264 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapB' 'ABC superfamily (membrane) membrane component of peptide ABC transport system' ecoli675 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'potE' 'APC family putrescine-lyase antiporter' ecoli643 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltK' 'ABC superfamily (membrane) glutamate/aspartate transport (1st module)' ecoli369 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sbmA' 'ABC superfamily (atp&memb) sensitivity to microcin B17; methylmalonyl-CoA mutase (mcm); ATP-binding and membrane component' 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)' ecoli2940 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'exbB' 'uptake of enterochelin; tonB-dependent uptake of B colicins' ecoli3379 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livM' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system (2nd module)' ecoli4121 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjfF' 'ABC superfamily (membrane) ABC superfamily of transport protein (1st module membrance component)' ecoli3648 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstC' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' 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)' ecoli1414 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1443' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1098 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potB' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli2343 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2386' 'Sugar Specific paral putative membrane component of transport system' ecoli2138 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysU' 'ABC superfamily (membrane) membrane component of sulfate thiosulfate ABC transport system (2nd module)' ecoli899 1,7,1 Cell processes Cell division Cell division 'mukB' 'kinesin-line cell division protein involved in sister chromosome partitioning (3rd module DNA binding ?)' ecoli533 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b0543' 'multidrug transporter methylviologen and ethidium resistance' ecoli389 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'sbcC' 'ATP-dependent dsDNA exonuclease (2nd module)' ecoli428 1,7,1 Cell processes Cell division Cell division 'tig' 'peptidyl-prolyl cis/trans isomerase trigger factor; a molecular chaperone involved in cell division' ecoli2279 1,7,1 Cell processes Cell division Cell division 'div' 'cell division protein' ecoli2478 1,3,1 Cell processes Folding and ushering proteins Chaperones 'yfhE' 'co-chaperone protein Hsc20 interactsi with HscA and stimulates its ATP ase activity' 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)' 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)' ecoli3284 1,7,1 Cell processes Cell division Cell division 'fic' 'induced in stationary phase recognized by rpoS filamentation affects cell division' ecoli2969 1,7,1 Cell processes Cell division Cell division 'tolC' 'outer membrane channel; specific tolerance to colicin E1; segregation of daughter chromosomes' ecoli3095 1,7,1 Cell processes Cell division Cell division 'yhbM' '(NlpI) lipoprotein believed to be involved in cell division' 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: 38/39 (97.44%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(9.73) ; prob(1.828971E-20) 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' ecoli1216 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppC' 'ABC superfamily (membrane)homolog of Salmonella oligopeptide transport permease protein(2nd module)' ecoli2987 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'glnE' 'adenylyl transferase for glutamine synthetase regulates P-II (GlnB) and GlnK' ecoli3375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpA' 'ABC superfamily (membrane) sn-glycerol 3-phosphate integral membrane protein ABC transport system' ecoli2089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yehY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2158 1,2,1 Cell processes Chromosome replication Chromosome replication 'ccmB' 'heme exporter protein B cytochrome c-type biogenesis protein' ecoli1282 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1311' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2436 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2485' 'hydrogenase 4 membrane subunit(1st module)' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' 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 )' 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' ecoli1199 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'narJ' 'nitrate reductase 1 delta subunit assembly function' ecoli1915 - 4,1,5 Structural elements Cell envelop Surface structures 'fliR' 'paral putative transport protein for flagellar biosynthesis' 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)' ecoli692 1,5,31 Cell processes Transport/binding proteins POT family 'b0709' 'POT family of transport protein (1st module)' ecoli909 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0934' 'ABC superfamily (membrane) probable membrane component of transport system' ecoli2887 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b2952' 'putative resistance protein' Validation Accuracy: 14/18 (77.78%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(4.61) ; prob(2.001589E-05) ------------------ Rule 4: (23/1, lift 3.3) [ss_beta( A ,gt,10),nss_beta( A , B ,gt,5)] = 1 [ss_alpha( A ,gt,5),nss_alpha( A , B ,lteq,830),nss_alpha( B , C ,gt,6)] = 0 [ss_alpha( A ,lteq,830),nss_alpha( A , B ,lteq,830),nss_alpha( B , C ,lteq,830)] = 1 [ss( A ,a),nss( A , B ,c),len_lteq( B ,5)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,3),nss_coil( C , D ,gt,1)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,lteq,5),nss_coil( C , D ,lteq,6),nss_coil( D , E ,gt,3)] = 1 -> class 'Cell processes' [0.920] 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)' ecoli886 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsA' '30S ribosomal subunit protein S1' ecoli470 1,5,21 Cell processes Transport/binding proteins MFS family 'fsr' 'MFS family of transport protein fosmidomycin resistance protein(2nd module)' ecoli112 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'aroP' 'APC family of transport protein aromatic amino acid transport protein' ecoli818 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b0842' 'transmembrane multidrug/chloramphenicol efflux transporter (2nd module)' 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' ecoli252 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'ykfD' 'APC family of transport protein S-methylmethionine permease' ecoli1209 - 3,3,17 Metabolism of small molecules Central intermediary metabolism Salvage of nucleosides and nucleotides 'tdk' 'thymidine kinase' ecoli3961 1,5,35 Cell processes Transport/binding proteins SSS family 'yjcG' 'SSS family transport protein' ecoli2427 - 3,7,1 Metabolism of small molecules Nucleotide biosynthesis Purine ribonucleotide biosynthesis 'purC' 'phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase' ecoli1290 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'b1319' 'outer membrane protein; novel porin' ecoli1514 1,5,21 Cell processes Transport/binding proteins MFS family 'b1543' 'MFS family of transport protein (1st module)' ecoli3594 1,5,21 Cell processes Transport/binding proteins MFS family 'emrD' 'MFS family of transport protein 2-module integral membrane pump; multidrug resistance (2nd module)' ecoli45 1,5,21 Cell processes Transport/binding proteins MFS family 'yaaU' 'MFS family transport protein' ecoli2302 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fadL' 'transport of long-chain fatty acids; sensitivity to phage T2' ecoli3165 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'hhoB' 'periplasmic serine endoprotease(2nd module)' Test Accuracy: 11/16 (68.75%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(3.50) ; prob(1.174514E-03) Application to new data (2167 items): ecoli3816 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiiM' 'orf' ecoli3506 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yiaT' 'paral putative scaffolding protein' ecoli2296 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2338' 'paral putative outer membrane protein (2nd module)' ecoli190 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaeQ' 'orf' ecoli2626 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2681' 'orf' ecoli4221 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiJ' 'paral putative transport protein (2nd module)' ecoli4231 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiT' 'orf' ecoli701 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0718' 'paral putative outer membrane protein (2nd module)' ecoli2715 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2775' 'orf' ecoli1466 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yddB' 'orf' ecoli4110 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfM' 'orf' ecoli1402 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1431' 'orf' ecoli3826 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiiQ' 'orf' ecoli283 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagX' 'paral putative enzyme' ecoli2204 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2246' 'putative transport protein' ecoli4073 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfK' 'orf' ecoli2067 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehA' 'putative type-1 fimbrial protein' ecoli873 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycaD' 'paral putative transport protein (1st module)' ecoli4245 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4356' 'paral putative transport protein cryptic orf joins former yjiZ and yjjL' 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)' ecoli3751 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigU' 'integral membrane protein part of sec-independent protein export' Frequency rule on new data: 21/2167 (0.97%) Evaluation on training data (939 items): ecoli1659 1,5,21 Cell processes Transport/binding proteins MFS family 'b1691' 'MFS family of transport protein' 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)' ecoli3783 1,5,16 Cell processes Transport/binding proteins GPH family 'yihP' 'GPH family paral putative transport protein' ecoli1267 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b1296' 'APC family paral putative amino-acid transport protein' ecoli2115 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'lysP' 'APC family lysine-specific permease (2nd module)' ecoli4226 1,5,21 Cell processes Transport/binding proteins MFS family 'yjiO' 'MFS family of transport protein (1st module)' ecoli2036 1,5,21 Cell processes Transport/binding proteins MFS family 'b2077' 'MFS family of transport protein (1st module)' ecoli2608 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gabP' 'transport permease protein of gamma-aminobutyrate' ecoli3675 1,5,21 Cell processes Transport/binding proteins MFS family 'yieO' 'MFS family of tranport protein (1st mdule)' ecoli3059 1,5,21 Cell processes Transport/binding proteins MFS family 'yhaU' 'MFS family of transport protein (D)-glucarate or galactarate transporter (1st module)' ecoli3930 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'lamB' 'phage lambda receptor protein; maltose high-affinity receptor' 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)' ecoli3011 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'ygjI' 'APC family paral putative amino-acid transport protein' ecoli3378 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'livG' 'ABC superfamily (atp_bind) ATP-binding component of high-affinity branched-chain amino acid ABC transport system' 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)' ecoli683 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsC' 'rhsC protein in rhs element' ecoli564 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b0574' 'putative resistance protein(2nd module)' ecoli1463 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'xasA' 'APC family acid sensitivity protein putative glutamate:gamma-aminobutyric acid antiporter (GadC)(2nd module)' ecoli3711 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'yifK' 'APC family paral putative amino-acid transport protein' ecoli3469 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'yhjX' 'putative resistance protein' 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)' ecoli4180 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fecA' 'outer membrane receptor; citrate-dependent iron transport outer membrane receptor(1st module)' Training Accuracy: 22/23 (95.65%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(7.28) ; prob(9.096482E-12) Evaluation on validation data (471 items): ecoli419 1,5,21 Cell processes Transport/binding proteins MFS family 'b0427' 'MFS family transport protein' 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)' ecoli3515 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsA' 'rhsA protein in rhs element' 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)' ecoli3226 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsE' '30S ribosomal subunit protein S5' ecoli1424 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1453' 'L-asparagine permease (2nd module)' ecoli4005 1,5,21 Cell processes Transport/binding proteins MFS family 'proP' 'MFS family of tranport protein low-affinity constitutive transport system; proline permease II transports proline and betaine under conditions of hyperosmolarity(2nd module)' ecoli1737 1,5,21 Cell processes Transport/binding proteins MFS family 'ydjE' 'MFS family of transport protein (1st module)' Validation Accuracy: 6/8 (75.00%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(2.90) ; prob(7.900816E-03) ------------------ Rule 2: (24/1, lift 3.3) [ss( A ,c),nss( A , B ,a)] = 1 [ss_alpha( A ,gt,6),nss_alpha( A , B ,gt,5)] = 0 [ss_beta( A ,gt,10),nss_beta( A , B ,lteq,6)] = 1 [ss_coil( A ,lteq,830),nss_coil( A , B ,lteq,6),nss_coil( B , C ,lteq,3)] = 1 [ss( A ,a),nss( A , B ,c),len_lteq( B ,5)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,5),nss_coil( B , C ,lteq,830),nss_coil( C , D ,lteq,5),nss_coil( D , E ,gt,1)] = 1 -> class 'Cell processes' [0.923] Evaluation on test data (712 items): ecoli1052 - 4,1,5 Structural elements Cell envelop Surface structures 'flgH' 'flagellar biosynthesis basal-body outer-membrane L (lipopolysaccharide layer) ring protein' ecoli1075 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fhuE' 'outer membrane receptor for Fe(III)-coprogen Fe(III)-ferrioxamine B and Fe(III)-rhodotrulic acid uptake' ecoli3228 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplF' '50S ribosomal subunit protein L6' ecoli35 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'caiE' 'stimulates carnitine racemase activity of CaiD and CaiB activity' ecoli112 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'aroP' 'APC family of transport protein aromatic amino acid transport protein' ecoli818 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b0842' 'transmembrane multidrug/chloramphenicol efflux transporter (2nd module)' 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' ecoli252 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'ykfD' 'APC family of transport protein S-methylmethionine permease' ecoli4134 - 3,7,2 Metabolism of small molecules Nucleotide biosynthesis Pyrimidine ribonucleotide biosynthesis 'pyrI' 'aspartate carbamoyltransferase regulatory subunit' ecoli2324 1,5,21 Cell processes Transport/binding proteins MFS family 'emrY' 'MFS family of transport protein multidrug resistance protein y (2nd module)' ecoli3587 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpT' 'MFS family of transport protein hexose phosphate transport protein (2nd module)' 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)' ecoli140 - 4,1,5 Structural elements Cell envelop Surface structures 'ecpD' 'probable pilin chaperone similar to PapD' ecoli1514 1,5,21 Cell processes Transport/binding proteins MFS family 'b1543' 'MFS family of transport protein (1st module)' ecoli866 1,2,1 Cell processes Chromosome replication Chromosome replication 'lolA' 'periplasmic protein effects translocation of lipoproteins from inner membrane to outer' ecoli44 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'fixX' 'related to carnitine metabolism' ecoli1750 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'b1782' 'scaffolding protein for murein-synthesising holoenzyme (in Ec strain B).' ecoli2141 1,5,21 Cell processes Transport/binding proteins MFS family 'bcr' 'MFS family of transport protein bicyclomycin resistance protein; transmembrane protein (2nd module)' ecoli2114 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'cirA' 'outer membrane receptor for iron-regulated colicin I receptor; porin; requires tonB gene product(1st module)' Test Accuracy: 11/19 (57.89%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(2.77) ; prob(8.171069E-03) Application to new data (2167 items): ecoli293 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ykgB' 'orf' ecoli525 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ybcG' 'paral putative fimbrial-like protein' ecoli2069 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehC' 'paral putative chaperone' ecoli4222 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiK' 'orf' ecoli2294 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2336' 'paral putative chaperone' ecoli4200 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjhA' 'orf' ecoli745 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0769' 'orf' ecoli3506 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yiaT' 'paral putative scaffolding protein' ecoli190 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaeQ' 'orf' ecoli3780 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihN' 'orf' ecoli1639 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1671' 'paral putative oxidoreductase (2nd module)' ecoli702 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ybgD' 'paral putative fimbrial-like protein' ecoli2033 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2074' 'paral putative membrane protein' ecoli1568 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1598' 'orf' ecoli919 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycbF' 'paral putative chaperone' ecoli3077 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yraK' 'paral putative fimbrial-like protein' ecoli2183 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2225' 'orf' ecoli3053 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhaB' 'orf' ecoli3074 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yraH' 'paral putative fimbrial-like protein' ecoli1940 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1978' 'paral putative factor(2nd module)' ecoli748 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ybhC' 'putative pectinesterase' ecoli664 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0681' 'orf' ecoli2002 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2043' 'orf' ecoli1475 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1504' 'paral putative fimbrial-like protein' ecoli701 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0718' 'paral putative outer membrane protein (2nd module)' ecoli1743 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1775' 'paral putative transport protein (1st module)' ecoli3145 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhcA' 'paral putative chaperone' ecoli506 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0515' 'orf' ecoli1611 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1641' 'orf' ecoli1466 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yddB' 'orf' ecoli1083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycfJ' 'orf' ecoli2013 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2054' 'paral putative acyl transferase in colanic acid biosynthesis' ecoli281 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yagV' 'orf' ecoli939 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0964' 'orf' ecoli347 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0355' 'putative esterase' ecoli2981 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3047' 'paral putative chaperone' ecoli2982 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3048' 'orf' ecoli1480 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1509' 'orf' ecoli283 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagX' 'paral putative enzyme' ecoli2204 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2246' 'putative transport protein' ecoli2696 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2756' 'orf' ecoli123 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yacK' 'orf' ecoli1893 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yedD' 'orf' ecoli1143 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1170' 'orf' ecoli1943 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1981' 'shikimate and dehydroshikimate permease (2nd module)' ecoli873 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycaD' 'paral putative transport protein (1st module)' ecoli1759 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1791' 'putative amino acid/amine transport protein (3rd module)' ecoli262 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagG' 'paral putative transport protein' ecoli3247 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yheE' 'orf' ecoli3751 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigU' 'integral membrane protein part of sec-independent protein export' Frequency rule on new data: 50/2167 (2.31%) Evaluation on training data (939 items): ecoli1659 1,5,21 Cell processes Transport/binding proteins MFS family 'b1691' 'MFS family of transport protein' 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)' ecoli3783 1,5,16 Cell processes Transport/binding proteins GPH family 'yihP' 'GPH family paral putative transport protein' ecoli2115 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'lysP' 'APC family lysine-specific permease (2nd module)' ecoli4226 1,5,21 Cell processes Transport/binding proteins MFS family 'yjiO' 'MFS family of transport protein (1st module)' ecoli574 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fepA' 'outer membrane receptor for ferric enterobactin (enterochelin) and colicins B and D(1st module)' ecoli2608 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'gabP' 'transport permease protein of gamma-aminobutyrate' ecoli1348 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'b1377' 'outer membrane protein n non-specific porin (2nd module)' ecoli3675 1,5,21 Cell processes Transport/binding proteins MFS family 'yieO' 'MFS family of tranport protein (1st mdule)' ecoli54 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'imp' 'organic solvent tolerance' ecoli1049 - 4,1,5 Structural elements Cell envelop Surface structures 'flgE' 'flagellar biosynthesis hook protein(1st 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' ecoli3930 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'lamB' 'phage lambda receptor protein; maltose high-affinity receptor' 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)' 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)' 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)' ecoli3793 1,4,2 Cell processes Protection responses Detoxification 'yihZ' 'D-Tyr-tRNA(Tyr) deacylase (recycles misaminoacylated tRNA in detoxification of cells)' ecoli2741 1,5,21 Cell processes Transport/binding proteins MFS family 'fucP' 'MFS family of transport protein fucose permease(1st module)' ecoli3469 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'yhjX' 'putative resistance protein' 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)' ecoli4180 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'fecA' 'outer membrane receptor; citrate-dependent iron transport outer membrane receptor(1st module)' ecoli477 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b0486' 'APC family of transport protein amino-acid transport protein' Training Accuracy: 23/24 (95.83%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(7.46) ; prob(2.626444E-12) Evaluation on validation data (471 items): 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)' ecoli4097 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'fklB' 'FKBP-type 22KD peptidyl-prolyl cis-trans isomerase (rotamase)' ecoli3515 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsA' 'rhsA protein in rhs element' 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)' ecoli488 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsD' 'rhsD protein in rhs element' ecoli2772 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'ygeD' 'putative resistance proteins' ecoli3872 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'btuB' 'outer membrane receptor for transport of vitamin B12 E colicins and bacteriophage BF23(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)' ecoli4168 1,5,21 Cell processes Transport/binding proteins MFS family 'yjhB' 'MFS family of tranport protein (1st module)' ecoli1424 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1453' 'L-asparagine permease (2nd module)' ecoli403 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'tsx' 'nucleoside channel; receptor of phage T6 and colicin K' ecoli1055 - 4,1,5 Structural elements Cell envelop Surface structures 'flgK' 'flagellar biosynthesis hook-filament junction protein 1 C-terminal involved in chaperone (probably FlgN) binding(2nd module)' ecoli3588 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpC' 'regulator of uhpT (1st module)' ecoli4005 1,5,21 Cell processes Transport/binding proteins MFS family 'proP' 'MFS family of tranport protein low-affinity constitutive transport system; proline permease II transports proline and betaine under conditions of hyperosmolarity(2nd module)' ecoli2280 1,5,21 Cell processes Transport/binding proteins MFS family 'b2322' 'MFS family of transport protein paral putative (2nd module)' ecoli334 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'lacA' 'thiogalactoside acetyltransferase' ecoli1737 1,5,21 Cell processes Transport/binding proteins MFS family 'ydjE' 'MFS family of transport protein (1st module)' Validation Accuracy: 11/17 (64.71%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(3.29) ; prob(1.749573E-03) ------------------ Rule 3: (24/1, lift 3.3) [ss_beta( A ,gt,1),nss_beta( A , B ,gt,1)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,6),nss_coil( B , C ,gt,3),nss_coil( C , D ,gt,5)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,5),nss_coil( B , C ,gt,1),nss_coil( C , D ,lteq,5),nss_coil( D , E ,lteq,5)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,5),nss_coil( B , C ,lteq,5),nss_coil( C , D ,lteq,10),nss_coil( D , E ,gt,1)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,lteq,5),nss_coil( C , D ,lteq,6),nss_coil( D , E ,gt,3)] = 1 -> class 'Cell processes' [0.923] Evaluation on test data (712 items): ecoli808 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0832' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2914 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'glcC' 'transcriptional activator for glc operon(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' ecoli3101 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'nusA' 'transcription pausing; L factor' ecoli1361 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1390' 'phenylacetic acid degradation protein possibly part of multicomponent oxygenase' ecoli566 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pheP' 'phenylalanine-specific transport system' ecoli580 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fepD' 'ABC superfamily (membrane) membrane component of ferric enterobactin (enterochelin) ABC transport' 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)' ecoli2523 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'rseA' 'sigma-E factor negative regulatory protein' ecoli3117 - 3,2,8 Metabolism of small molecules Biosynthesis of cofactors, carriers Menaquinone, ubiquinone 'ispB' 'octaprenyl diphosphate synthase' ecoli4155 1,5,19 Cell processes Transport/binding proteins GntP family 'yjgT' 'GntP family l-idonate transporter (2nd module)' ecoli807 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0831' 'paral putative membrane component of transport system' Test Accuracy: 8/13 (61.54%) Test Frequency class 'Cell processes': 207/712 (29.07%) Test Significance: dev(2.58) ; prob(1.496927E-02) Application to new data (2167 items): ecoli2445 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2494' 'orf(1st module)' ecoli3170 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcP' 'orf' ecoli2394 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2443' 'orf' ecoli117 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yacH' 'putative membrane protein' ecoli4225 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiN' 'orf' ecoli4099 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4209' 'orf' ecoli1562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1592' 'orf' ecoli279 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yagU' 'orf' ecoli155 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yadQ' 'putative channel transporter' ecoli53 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'surA' 'survival protein(1st module)' ecoli935 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0960' 'paral putative transport protein (1st module)' ecoli1293 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycjF' 'orf' ecoli3535 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yibP' '2nd module of a paral putative membrane protein (2nd module)' ecoli4100 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfF' 'orf (1st module)' ecoli562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0572' 'orf' ecoli2558 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2611' 'orf' ecoli2097 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohG' 'orf' ecoli2401 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2450' 'orf' ecoli3731 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rarD' 'chloramphenicol resistance' ecoli2098 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohH' 'orf' ecoli1926 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yedJ' 'orf' ecoli2506 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfhG' 'putative alpha helix protein' ecoli3476 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiaF' 'orf' ecoli2346 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2389' 'orf' ecoli2332 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2375' 'orf' ecoli2079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2120' 'orf' ecoli2285 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yfcA' 'putative structural 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' ecoli1571 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1601' 'paral putative transport protein (2nd module)' ecoli637 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0647' 'orf' ecoli603 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0613' 'orf (probable modifier of citrate lyase protein)' ecoli2322 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'dsdX' 'transport system permease (serine?)' ecoli1084 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1111' 'orf' ecoli2058 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2099' 'orf' ecoli3676 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yieP' 'orf' ecoli3281 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfK' 'orf' ecoli794 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0818' 'orf' ecoli2906 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2972' 'paral putative peptidase' ecoli3744 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yigN' 'putative alpha helix chain' Frequency rule on new data: 39/2167 (1.80%) 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)' 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' ecoli1456 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1485' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2680 1,5,19 Cell processes Transport/binding proteins GntP family 'b2740' 'GntP family of transport protein function unknown (3rd module)' ecoli675 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'potE' 'APC family putrescine-lyase antiporter' 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)' 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)' 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' ecoli1881 1,7,1 Cell processes Cell division Cell division 'sdiA' 'transcriptional regulator of ftsQAZ gene cluster(2nd module)' ecoli2940 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'exbB' 'uptake of enterochelin; tonB-dependent uptake of B colicins' 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)' 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)' 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)' ecoli2343 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2386' 'Sugar Specific paral putative membrane component of transport system' ecoli2138 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1283 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1312' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2279 1,7,1 Cell processes Cell division Cell division 'div' 'cell division protein' ecoli3001 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'rpoD' 'RNA polymerase sigma(70) factor; regulation of proteins induced at high temperatures(2nd module)' ecoli1679 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'btuC' 'ABC superfamily (membrane) membrane component of vitamin B12 ABC transport system' ecoli4185 1,5,19 Cell processes Transport/binding proteins GntP family 'yjhF' 'GntP family of transport protein (1st module)' 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: 23/24 (95.83%) Training Frequency class 'Cell processes': 260/939 (27.69%) Training Significance: dev(7.46) ; prob(2.626444E-12) Evaluation on validation data (471 items): ecoli1104 - 3,7,1 Metabolism of small molecules Nucleotide biosynthesis Purine ribonucleotide biosynthesis 'purB' 'adenylosuccinate lyase' ecoli1216 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppC' 'ABC superfamily (membrane)homolog of Salmonella oligopeptide transport permease protein(2nd module)' ecoli2987 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'glnE' 'adenylyl transferase for glutamine synthetase regulates P-II (GlnB) and GlnK' ecoli3375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpA' 'ABC superfamily (membrane) sn-glycerol 3-phosphate integral membrane protein ABC transport system' ecoli1858 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'motA' 'proton conductor component of motor; no effect on switching' ecoli2089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yehY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli4130 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'treB' 'PTS family enzyme II trehalose specific (maltose may be transported)' ecoli2929 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hybB' 'probable cytochrome Ni/Fe component of hydrogenase-2(1st module)' ecoli1282 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1311' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' 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 )' ecoli1199 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'narJ' 'nitrate reductase 1 delta subunit assembly function' ecoli2629 - 5,1,3 Extrachromosomal Laterally acquirred elements Plasmid-related functions 'emrR' 'controls level of microcin synthesis; negative regulation of EmrAB' ecoli3451 1,5,10 Cell processes Transport/binding proteins DAACS family 'dctA' 'DAACS family of transport protein uptake of C4-dicarboxylic acids' 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: 10/16 (62.50%) Validation Frequency class 'Cell processes': 135/471 (28.66%) Validation Significance: dev(2.99) ; prob(3.949689E-03) ------------------