Rule 103: (4, lift 30.1) amino_acid_pair_ratio_lc <= 0 [hom( A ),classification( A ,amphibia)] = 1 [hom( A ),species( A ,mycoplasma_hyorhinis)] = 1 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,asteridae)] = 0 [hom( A ),species( A ,mycoplasma_genitalium),mol_wt_lteq( A ,55220)] = 0 -> class 'Surface structures' [0.833] Evaluation on test data (712 items): ecoli139 4,1,5 Structural elements Cell envelop Surface structures 'htrE' 'probable outer membrane porin protein involved in fimbrial assembly (2nd module)' Test Accuracy: 1/1 (100.00%) Test Frequency class 'Surface structures': 22/712 (3.09%) Test Significance: dev(5.60) ; prob(3.089888E-02) Application to new data (2167 items): ecoli3077 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yraK' 'paral putative fimbrial-like protein' ecoli2297 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2339' 'paral putative fimbrial-like protein' ecoli366 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0374' 'flagellar protein; similar to 3rd module of ATP-binding components of transporters (2nd module)' ecoli2070 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehD' 'paral putative fimbrial-like protein' ecoli2977 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygiL' 'paral putative fimbrial-like protein' ecoli2295 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2337' 'paral putative outer membrane protein' ecoli3146 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhcD' 'paral putative outer membrane protein (2nd module)' ecoli220 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yafL' 'orf' ecoli1474 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1503' 'paral putative fimbrial-like protein' ecoli2456 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2505' 'orf' ecoli141 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yadN' 'paral putative fimbrial-like protein' Frequency rule on new data: 11/2167 (0.51%) Evaluation on training data (939 items): ecoli1888 4,1,5 Structural elements Cell envelop Surface structures 'fliC' 'flagellar biosynthesis; flagellin filament structural protein(2nd module)' ecoli1049 4,1,5 Structural elements Cell envelop Surface structures 'flgE' 'flagellar biosynthesis hook protein(1st module)' ecoli4208 4,1,5 Structural elements Cell envelop Surface structures 'fimG' 'fimbrial morphology' ecoli4209 4,1,5 Structural elements Cell envelop Surface structures 'fimH' 'minor fimbrial subunit D-mannose specific adhesin N-terminal binds carbohydrate c-terminal binds periplasmic chaperone' Training Accuracy: 4/4 (100.00%) Training Frequency class 'Surface structures': 26/939 (2.77%) Training Significance: dev(11.85) ; prob(5.878020E-07) Evaluation on validation data (471 items): ecoli1889 4,1,5 Structural elements Cell envelop Surface structures 'fliD' 'flagellar biosynthesis; filament capping protein; enables filament assembly' ecoli1056 4,1,5 Structural elements Cell envelop Surface structures 'flgL' 'flagellar biosynthesis; hook-filament junction protein C-terminal involved in chaperone (probably FlgN) binding' Validation Accuracy: 2/2 (100.00%) Validation Frequency class 'Surface structures': 12/471 (2.55%) Validation Significance: dev(8.75) ; prob(6.491136E-04) ------------------ Rule 25: (5/1, lift 27.9) amino_acid_pair_ratio_dk <= 0.9 amino_acid_pair_ratio_ms <= 3.7 [hom( A ),e_val_gt( A ,2e-37),classification( A ,bangiaceae)] = 0 [hom( A ),psi_iter_gt( A ,5),classification( A ,alveolata)] = 0 [hom( A ),species( A ,rhodobacter_sphaeroides__rhodopseudomonas_sphaeroides_),mol_wt_gt( A ,43194)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 [hom( A ),mol_wt_gt( A ,77359),classification( A ,cricetinae)] = 1 -> class 'Cell division' [0.714] Evaluation on test data (712 items): ecoli3913 - 3,1,14 Metabolism of small molecules Amino acid biosynthesis Methionine 'metH' 'B12-dependent homocysteine-N5-methyltetrahydrofolate transmethylase repressor of metE and metF(1st module)' ecoli3329 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'greB' 'transcription elongation factor and transcript cleavage' ecoli3111 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'greA' 'transcription elongation factor: cleaves 3 nucleotide of paused mRNA' ecoli1035 - 3,7,2 Metabolism of small molecules Nucleotide biosynthesis Pyrimidine ribonucleotide biosynthesis 'pyrC' 'dihydro-orotase' ecoli2720 - 3,3,11 Metabolism of small molecules Central intermediary metabolism Nucleotide interconversions 'pyrG' 'CTP synthetase' ecoli4144 - 3,1,2 Metabolism of small molecules Amino acid biosynthesis Arginine 'argI' 'ornithine carbamoyltransferase 1(1st module)' Test Accuracy: 0/6 (0.00%) Test Frequency class 'Cell division': 9/712 (1.26%) Test Significance: dev(-0.28) ; prob(1.000000E+00) Application to new data (2167 items): ecoli2635 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2690' 'orf' ecoli2806 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2870' 'paral putative carbamoyl transferase(1st module)' ecoli1073 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycfH' 'orf(1st module)' ecoli2045 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2086' 'orf' ecoli2097 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohG' 'orf' ecoli418 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0426' 'orf' ecoli270 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagL' 'DNA-binding protein' ecoli1448 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1477' 'orf' ecoli1870 - 1 Cell processes 'yecI' 'ferritin-like protein' ecoli247 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0255' 'orf' Frequency rule on new data: 10/2167 (0.46%) Evaluation on training data (939 items): ecoli3839 1,7,1 Cell processes Cell division Cell division 'ftsN' 'essential cell division protein' ecoli1147 1,7,1 Cell processes Cell division Cell division 'minE' 'cell division topological specificity factor reverses MinC inhibition of ftsZ ring formation' 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' ecoli3728 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'corA' 'Mg2+ transport system I' Training Accuracy: 4/5 (80.00%) Training Frequency class 'Cell division': 24/939 (2.56%) Training Significance: dev(10.97) ; prob(2.090164E-06) Evaluation on validation data (471 items): ecoli3311 1,7,1 Cell processes Cell division Cell division 'damX' 'membrane protein(2nd module)' Validation Accuracy: 1/1 (100.00%) Validation Frequency class 'Cell division': 9/471 (1.91%) Validation Significance: dev(7.16) ; prob(1.910828E-02) ------------------ Rule 96: (14, lift 40.0) [hom( A ),e_val_gt( A ,2e-37),keyword( A ,plasmid)] = 0 [hom( A ),psi_iter_lteq( A ,7),classification( A ,bangiophyceae)] = 1 [hom( A ),species( A ,cyanophora_paradoxa),mol_wt_lteq( A ,32892)] = 1 -> class 'Ribosomal proteins - synthesis modificationRiboso' [0.938] Evaluation on test data (712 items): ecoli3228 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplF' '50S ribosomal subunit protein L6' ecoli3798 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'fdoI' 'formate dehydrogenase cytochrome B556 (FDO) subunit' ecoli3264 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsG' '30S ribosomal subunit protein S7 initiates assembly' 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' ecoli4092 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsR' '30S ribosomal subunit protein S18' ecoli3882 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplA' '50S ribosomal subunit protein L1 regulates synthesis of L1 and L11' ecoli3231 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplE' '50S ribosomal subunit protein L5' ecoli169 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsB' '30S ribosomal subunit protein S2' 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' ecoli1447 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'fdnI' 'formate dehydrogenase-N nitrate-inducible cytochrome B556(Fdn) gamma subunit' ecoli2556 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsP' '30S ribosomal subunit protein S16' ecoli3323 - 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'yrfH' 'heat shock protein 15 DNA/RNA binding' ecoli2553 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplS' '50S ribosomal subunit protein L19' ecoli3244 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsJ' '30S ribosomal subunit protein S10' Test Accuracy: 13/16 (81.25%) Test Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 23/712 (3.23%) Test Significance: dev(17.65) ; prob(2.131753E-17) Application to new data (2167 items): Frequency rule on new data: 0/2167 (0.00%) Evaluation on training data (939 items): ecoli3559 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmB' '50S ribosomal subunit protein L28' ecoli4090 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsF' '30S ribosomal subunit protein S6' ecoli3881 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplK' '50S ribosomal subunit protein L11' ecoli3220 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsK' '30S ribosomal subunit protein S11' ecoli3240 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplB' '50S ribosomal subunit protein L2' ecoli1684 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplT' '50S ribosomal subunit protein L20 and regulator' 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' ecoli3624 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmH' '50S ribosomal subunit protein L34' 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: 14/14 (100.00%) Training Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 22/939 (2.34%) Training Significance: dev(24.16) ; prob(1.501756E-23) Evaluation on validation data (471 items): ecoli3237 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsC' '30S ribosomal subunit protein S3' ecoli3226 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsE' '30S ribosomal subunit protein S5' ecoli3239 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsS' '30S ribosomal subunit protein S19' ecoli3236 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplP' '50S ribosomal subunit protein L16' ecoli1685 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmI' '50S ribosomal subunit protein A' ecoli3227 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplR' '50S ribosomal subunit protein L18' ecoli3160 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsI' '30S ribosomal subunit protein S9' ecoli3221 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsM' '30S ribosomal subunit protein S13' Validation Accuracy: 8/8 (100.00%) Validation Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 12/471 (2.55%) Validation Significance: dev(17.49) ; prob(1.775345E-13) ------------------ Rule 30: (4/1, lift 104.3) [hom( A ),species( A ,mycoplasma_hyorhinis)] = 1 [hom( A ),species( A ,streptomyces_lividans),mol_wt_lteq( A ,55220)] = 1 [hom( A ),species( A ,mycoplasma_genitalium),mol_wt_lteq( A ,55220)] = 1 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 [hom( A ),species( A ,cyanophora_paradoxa),mol_wt_lteq( A ,32892)] = 0 -> class 'Chemotaxis and mobility' [0.667] Evaluation on test data (712 items): ecoli1905 - 4,1,5 Structural elements Cell envelop Surface structures 'fliH' 'flagellar biosynthesis; export of flagellar proteins?' ecoli1853 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tap' 'methyl-accepting chemotaxis protein IV peptide sensor receptor (2nd module)' ecoli2173 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'ompC' 'outer membrane protein 1b (ib;c) (2nd module)' ecoli3005 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'air' 'aerotaxis sensor receptor flavoprotein(2nd module)' Test Accuracy: 1/4 (25.00%) Test Frequency class 'Chemotaxis and mobility': 4/712 (0.56%) Test Significance: dev(6.54) ; prob(2.228325E-02) Application to new data (2167 items): ecoli3976 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjcR' 'paral putative membrane protein' ecoli523 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0532' 'paral putative outer membrane protein (2nd module)' ecoli3410 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiI' 'paral putative membrane protein' ecoli255 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0263' 'paral putative membrane component of transport system' ecoli1076 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycfF' 'orf' Frequency rule on new data: 5/2167 (0.23%) Evaluation on training data (939 items): ecoli3526 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'lctR' 'transcriptional regulator(1st module)' ecoli1392 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'trg' 'methyl-accepting chemotaxis protein III ribose and galactose sensor receptor(2nd module)' ecoli4244 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tsr' 'methyl-accepting chemotaxis protein I serine sensor receptor(2nd module)' ecoli1854 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tar' 'methyl-accepting chemotaxis protein II aspartate sensor receptor (2nd module)' Training Accuracy: 3/4 (75.00%) Training Frequency class 'Chemotaxis and mobility': 6/939 (0.64%) Training Significance: dev(18.66) ; prob(1.038558E-06) Evaluation on validation data (471 items): ecoli1856 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'cheA' 'sensory transducer kinase between chemo- signal receptors and CheB and CheY(2nd module)' Validation Accuracy: 1/1 (100.00%) Validation Frequency class 'Chemotaxis and mobility': 2/471 (0.42%) Validation Significance: dev(15.31) ; prob(4.246285E-03) ------------------ Rule 109: (3, lift 34.1) [hom( A ),classification( A ,ciliophora)] = 1 [hom( A ),species( A ,mycoplasma_hyorhinis)] = 0 [hom( A ),e_val_gt( A ,6e-14),classification( A ,delta_subdivision)] = 0 [hom( A ),e_val_gt( A ,2e-37),classification( A ,bangiaceae)] = 0 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,solanaceae)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,fabaceae)] = 0 [hom( A ),psi_iter_gt( A ,7),classification( A ,burkholderia_group)] = 0 [hom( A ),species( A ,bacillus_stearothermophilus),mol_wt_lteq( A ,32892)] = 0 [hom( A ),mol_wt_lteq( A ,43194),classification( A ,leishmania)] = 0 -> class 'Transposon-related functions' [0.800] Evaluation on test data (712 items): ecoli266 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_3' 'IS1 protein InsB' 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)' ecoli2007 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'cpsG' 'phosphomannomutase in colanic acid gene cluster' ecoli4238 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'hsdM' 'host modification; DNA methylase M' ecoli3307 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'trpS' 'tryptophan tRNA synthetase' ecoli632 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'leuS' 'leucine tRNA synthetase(1st module)' ecoli1045 - 4,1,5 Structural elements Cell envelop Surface structures 'flgA' 'flagellar biosynthesis; assembly of basal-body periplasmic P ring' ecoli1560 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1590' 'putative DMSO reductase anchor subunit' Test Accuracy: 1/8 (12.50%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(2.26) ; prob(1.370662E-01) Application to new data (2167 items): ecoli2550 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2603' 'orf' ecoli3784 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihQ' 'orf' ecoli325 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0333' 'PrpC propionate catabolism operon' ecoli3750 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3838' 'transmembrane protein part of sec-independent protein export' ecoli1003 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1029' 'orf' ecoli270 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagL' 'DNA-binding protein' ecoli3924 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbA' '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' ecoli2187 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2229' 'orf' ecoli3772 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihI' 'orf' ecoli3578 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yicI' 'orf' Frequency rule on new data: 11/2167 (0.51%) Evaluation on training data (939 items): ecoli3368 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_6' 'IS1 protein InsB' ecoli1861 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_5' 'IS1 protein InsB' ecoli21 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_1' 'IS1 protein InsB' Training Accuracy: 3/3 (100.00%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(11.18) ; prob(1.286090E-05) Evaluation on validation data (471 items): ecoli962 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_4' 'IS1 protein InsB' ecoli256 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insB_2' 'IS1 protein InsB 2' Validation Accuracy: 2/2 (100.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(8.08) ; prob(8.835157E-04) ------------------ Rule 102: (3, lift 75.1) [hom( A ),classification( A ,acanthopterygii)] = 1 [hom( A ),classification( A ,mesocricetus)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 1 [hom( A ),species( A ,bacillus_stearothermophilus),mol_wt_lteq( A ,43194)] = 1 -> class 'Sugar-specific PTS system' [0.800] Evaluation on test data (712 items): ecoli3409 - 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b3486' 'ABC superfamily (membrance) paral putative membrane component of transport system (3rd module)' ecoli1467 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yddA' 'ABC superfamily (atp_bind) paral putative ATP-binding module (2nd module)' ecoli3961 - 1,5,35 Cell processes Transport/binding proteins SSS family 'yjcG' 'SSS family transport protein' 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)?)' Test Accuracy: 1/4 (25.00%) Test Frequency class 'Sugar-specific PTS system': 14/712 (1.97%) Test Significance: dev(3.32) ; prob(7.636216E-02) Application to new data (2167 items): Frequency rule on new data: 0/2167 (0.00%) Evaluation on training data (939 items): 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' ecoli2343 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2386' 'Sugar Specific paral putative membrane component of transport system' 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)' Training Accuracy: 3/3 (100.00%) Training Frequency class 'Sugar-specific PTS system': 10/939 (1.06%) Training Significance: dev(16.69) ; prob(1.207823E-06) Evaluation on validation data (471 items): 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' ecoli4130 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'treB' 'PTS family enzyme II trehalose specific (maltose may be transported)' ecoli3223 - 1,2,1 Cell processes Chromosome replication Chromosome replication 'prlA' 'protein secretion inner membrane preprotein translocase SecY subunit interacts with SecE (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)' ecoli2380 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'b2429' 'Sugar Specific paral putative PTS system enzyme II' Validation Accuracy: 4/5 (80.00%) Validation Frequency class 'Sugar-specific PTS system': 15/471 (3.18%) Validation Significance: dev(9.78) ; prob(4.979610E-06) ------------------ Rule 108: (10/1, lift 35.6) amino_acid_ratio_h > 3.6 amino_acid_pair_ratio_aq <= 1.5 amino_acid_pairs_hq > 1 [hom( A ),e_val_gt( A ,2e-37),species( A ,streptococcus_mutans)] = 0 -> class 'Transposon-related functions' [0.833] Evaluation on test data (712 items): ecoli3863 - 3,1,2 Metabolism of small molecules Amino acid biosynthesis Arginine 'argE' 'acetylornithine deacetylase(1st module)' ecoli76 - 3,1,12 Metabolism of small molecules Amino acid biosynthesis Leucine 'leuO' 'affects expression of small regulatory Dsr-RNA translational regulation of rpoS relieves bgl silencing(1st module)' ecoli1989 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_7' 'IS5 protein' ecoli22 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_1' 'IS1 protein InsA' ecoli2738 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'exo' '5-3 exonuclease' ecoli1953 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_6' 'IS5 protein' ecoli3764 - 3,2,9 Metabolism of small molecules Biosynthesis of cofactors, carriers Molybdopterin 'mobA' 'molybdopterin ---> molybdopterin-guanine dinucleotide protein Ar' Test Accuracy: 3/7 (42.86%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(8.11) ; prob(2.016224E-04) Application to new data (2167 items): ecoli3362 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhhW' 'orf' ecoli3430 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhiF' 'orf' ecoli356 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0364' 'orf' ecoli1506 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeH' 'orf(2nd module)' ecoli4082 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfR' 'orf' ecoli2732 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2792' 'orf' ecoli3596 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yidG' 'orf' ecoli3413 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhiL' 'orf(2nd module)' ecoli1304 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydaA' 'orf(2nd module)' ecoli2496 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2545' 'paral putative oxidoreductase' ecoli876 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycaK' 'orf' ecoli1806 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1838' 'protein phosphatase 1 modulates phosphoproteins signals protein misfolding' Frequency rule on new data: 12/2167 (0.55%) 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' ecoli3887 - 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'htrC' 'heat shock protein htrC' 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' ecoli1341 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_5' 'IS5 protein' ecoli267 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_3' 'IS1 protein InsA' ecoli1862 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_5' 'IS1 protein InsA' ecoli2916 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_9' 'IS5 protein' Training Accuracy: 9/10 (90.00%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(18.33) ; prob(2.082372E-14) Evaluation on validation data (471 items): ecoli1969 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'yeeC' 'paral putative carboxypeptidase penicillin binding protein 6b (1st module)' ecoli257 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_2' 'IS1 protein InsA 2' ecoli1302 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_4' 'IS5 protein' ecoli3148 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_10' 'IS5 protein 10' ecoli3367 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_6' 'IS1 protein InsA' Validation Accuracy: 4/5 (80.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(10.14) ; prob(3.786987E-06) ------------------ Rule 65: (21, lift 39.1) amino_acid_pair_ratio_id <= 2.4 [hom( A ),e_val_lteq( A ,3e-06),species( A ,streptococcus_mutans)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 1 [hom( A ),species( A ,bacillus_stearothermophilus),mol_wt_lteq( A ,43194)] = 1 -> class 'MFS family' [0.957] 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)' ecoli2711 1,5,21 Cell processes Transport/binding proteins MFS family 'b2771' 'MFS family of transport protein (3rd module (function unknown)' ecoli470 1,5,21 Cell processes Transport/binding proteins MFS family 'fsr' 'MFS family of transport protein fosmidomycin resistance protein(2nd module)' ecoli818 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b0842' 'transmembrane multidrug/chloramphenicol efflux transporter (2nd module)' ecoli333 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'cynX' 'cyanate transport' ecoli1499 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ydeA' 'ABC superfamily (membrane)putative membrane component of ABC transport system appears to facilitate arabinose export contributes to control of arabinose regulon' ecoli3961 - 1,5,35 Cell processes Transport/binding proteins SSS family 'yjcG' 'SSS family transport protein' ecoli3587 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpT' 'MFS family of transport protein hexose phosphate transport protein (2nd module)' ecoli2538 1,5,21 Cell processes Transport/binding proteins MFS family 'kgtP' 'MFS family of transport protein alpha-ketoglutarate permease(1st module)' ecoli2198 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glpT' 'sn-glycerol-3-phosphate permease' ecoli1514 1,5,21 Cell processes Transport/binding proteins MFS family 'b1543' 'MFS family of transport protein (1st module)' ecoli2357 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'xapB' 'xanthosine permease' 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' ecoli3026 1,5,21 Cell processes Transport/binding proteins MFS family 'exuT' 'MFS family of transport protein transport of hexuronates (2nd module)' ecoli2487 1,5,21 Cell processes Transport/binding proteins MFS family 'b2536' 'MFS family of transport protein (1st module)' Test Accuracy: 10/16 (62.50%) Test Frequency class 'MFS family': 14/712 (1.97%) Test Significance: dev(17.44) ; prob(6.209006E-14) Application to new data (2167 items): ecoli1604 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1634' 'orf' ecoli3780 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihN' 'orf' ecoli1221 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'kch' 'putative potassium channel protein' ecoli3419 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhiP' '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)' ecoli1743 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1775' 'paral putative transport protein (1st module)' 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' ecoli2204 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2246' 'putative transport protein' 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)' ecoli4245 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4356' 'paral putative transport protein cryptic orf joins former yjiZ and yjjL' ecoli1038 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1065' 'orf' ecoli1759 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1791' 'putative amino acid/amine transport protein (3rd module)' 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)' Frequency rule on new data: 16/2167 (0.74%) Evaluation on training data (939 items): ecoli2057 1,5,21 Cell processes Transport/binding proteins MFS family 'b2098' 'MFS family of transport protein (2nd module)' ecoli1659 1,5,21 Cell processes Transport/binding proteins MFS family 'b1691' 'MFS family of transport protein' ecoli3396 1,5,21 Cell processes Transport/binding proteins MFS family 'yhhS' 'MFS family of transport protein (2nd module)' ecoli1566 1,5,21 Cell processes Transport/binding proteins MFS family 'b1596' 'MFS familty transport protein (2nd module)' ecoli3154 1,5,21 Cell processes Transport/binding proteins MFS family 'nanT' 'MFS family of transport protein sialic acid transporter cryptic in K12?(1st module)' ecoli2631 1,5,21 Cell processes Transport/binding proteins MFS family 'emrB' 'MFS family of transport protein multidrug resistance; probably membrane translocase(1st module)' ecoli1026 1,5,21 Cell processes Transport/binding proteins MFS family 'yceE' 'MFS family of transport protein (2nd module)' ecoli425 1,5,21 Cell processes Transport/binding proteins MFS family 'ampG' 'MFS family of transport protein ampicillin resistance (1st 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)' 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)' 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)' ecoli2899 1,5,21 Cell processes Transport/binding proteins MFS family 'nupG' 'MFS family of transport protein transport of nucleosides (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)' ecoli3287 1,5,21 Cell processes Transport/binding proteins MFS family 'yhfC' 'MFS family of transport protein paral putative 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)' ecoli2741 1,5,21 Cell processes Transport/binding proteins MFS family 'fucP' 'MFS family of transport protein fucose permease(1st module)' ecoli3583 1,5,21 Cell processes Transport/binding proteins MFS family 'yicM' 'MFS family of tranport protein (1st mdule)' 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)' Training Accuracy: 21/21 (100.00%) Training Frequency class 'MFS family': 23/939 (2.45%) Training Significance: dev(28.92) ; prob(1.480155E-34) 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)' ecoli1196 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'narK' 'nitrite extrusion protein(2nd module)' ecoli1627 1,5,21 Cell processes Transport/binding proteins MFS family 'b1657' 'MFS family of transport protein (2nd module)' ecoli2772 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'ygeD' 'putative resistance proteins' ecoli1630 1,5,21 Cell processes Transport/binding proteins MFS family 'ydhC' 'MFS family transport protein (2nd module)' ecoli4168 1,5,21 Cell processes Transport/binding proteins MFS family 'yjhB' 'MFS family of tranport protein (1st module)' ecoli1796 1,5,21 Cell processes Transport/binding proteins MFS family 'b1828' 'MFS family of transport protein (2nd module)' ecoli3925 1,5,21 Cell processes Transport/binding proteins MFS family 'xylE' 'MFS family of tranport protein xylose-proton symport (2nd module)' ecoli3612 - 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'yidT' 'D-galactonate transport' ecoli3588 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpC' 'regulator of uhpT (1st module)' ecoli2280 1,5,21 Cell processes Transport/binding proteins MFS family 'b2322' 'MFS family of transport protein paral putative (2nd module)' Validation Accuracy: 9/12 (75.00%) Validation Frequency class 'MFS family': 14/471 (2.97%) Validation Significance: dev(14.69) ; prob(3.639760E-12) ------------------ Rule 2: (6/1, lift 20.1) [hom( A ),classification( A ,amphibia)] = 0 [hom( A ),species( A ,mycoplasma_hyorhinis)] = 1 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 -> class 'ABC superfamily (membrane)' [0.750] Evaluation on test data (712 items): ecoli3927 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'malF' 'ABC superfamily (membrane) membrane component of maltose ABC transport system (2nd module)' 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' ecoli808 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0832' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3200 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1020 - 1,6,2 Cell processes Adaptation Osmotic adaptation 'b1047' 'membrane protein required for succinyl substitution of glucan backbone of OPG (osmoregulated periplasmic glucan) possible succinyl transferase' ecoli2266 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisQ' 'ABC superfamily (membrane)histidine transport system' ecoli3825 - 3,5,5 Metabolism of small molecules Energy metabolism, carbon Glycolysis 'tpiA' 'triosephosphate isomerase' Test Accuracy: 5/7 (71.43%) Test Frequency class 'ABC superfamily (membrane)': 26/712 (3.65%) Test Significance: dev(9.56) ; prob(1.281905E-06) Application to new data (2167 items): ecoli3932 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbI' 'orf' ecoli3997 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4103' 'orf' ecoli562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0572' 'orf' ecoli701 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0718' 'paral putative outer membrane protein (2nd module)' 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' ecoli2087 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehW' 'paral putative membrane component of transport system' ecoli3147 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcE' 'orf' ecoli255 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0263' 'paral putative membrane component of transport system' ecoli1076 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ycfF' 'orf' ecoli1442 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1471' 'putative glycoportein' Frequency rule on new data: 10/2167 (0.46%) Evaluation on training data (939 items): ecoli1456 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1485' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli1091 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1118' 'ABC superfamily (membrane) paral putative membrane component of ABC transport system' ecoli643 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'gltK' 'ABC superfamily (membrane) glutamate/aspartate transport (1st 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)' ecoli722 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'tolA' 'membrane spanning protein required for outer membrane integrity' ecoli1413 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1442' 'ABC superfamily (membrane) paral putative membrane component of transport system' Training Accuracy: 5/6 (83.33%) Training Frequency class 'ABC superfamily (membrane)': 35/939 (3.73%) Training Significance: dev(10.29) ; prob(4.182729E-07) Evaluation on validation data (471 items): ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' 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)' 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)' Validation Accuracy: 2/3 (66.67%) Validation Frequency class 'ABC superfamily (membrane)': 19/471 (4.03%) Validation Significance: dev(5.51) ; prob(4.684941E-03) ------------------ Rule 1: (23, lift 37.6) amino_acid_pair_ratio_nm <= 3 [hom( A ),classification( A ,ascaridida)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 1 -> class 'ABC superfamily (atp_bind)' [0.960] Evaluation on test data (712 items): ecoli924 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0949' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli3275 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yheS' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli805 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0829' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli785 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'glnQ' 'ABC superfamily (atp_bind) ATP-binding component of glutamine high-affinity ABC transport system(2nd module)' ecoli2622 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'proV' 'ABC superfamily (atp_bind) ATP-binding component of transport system for glycine betaine and proline(1st module)' ecoli3125 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b3195' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli4248 - 1,6,2 Cell processes Adaptation Osmotic adaptation 'mdoB' 'phosphoglycerol transferase I add phosphoglycerols to OPG backbone' ecoli1089 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1116' 'ABC superfamily (membrane) paral putative membrane component of ABC transport system' ecoli3201 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yhdZ' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2264 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'hisP' 'ABC superfamily (atp_bind) ATP-binding component of histidine ABC transport system' ecoli578 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fepC' 'ABC superfamily (atp_bind) ATP-binding component of ferric enterobactin transport(2nd module)' ecoli1261 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'sapF' 'ABC superfamily (atp_bind) ATP-binding protein of peptide ABC transport system(2nd module)' ecoli358 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0366' 'ABC superfamily (atp_bind) ATP-binding component of a taurine transport system' ecoli3981 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yjcW' 'ABC superfamily (atp_bind) ATP-binding component of allose transport system (2nd module)' ecoli3805 - 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'frvB' 'PTS family fructose-like enzyme IIBC component(2nd module)' ecoli4277 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yjjK' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system (2nd module)' ecoli1826 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1858' 'ABC superfamily (atp_bind) ATP-binding component of a high affinity Zn transport system(1st module)' ecoli840 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'artP' 'ABC superfamily (atp&memb) ATP-binding component of 3rd arginine transport system(2nd module)' ecoli2373 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'cysA' 'ABC superfamily (atp_bind) ATP-binding component of sulfate permease A protein of ABC transport; chromate resistance (1st module)' ecoli3131 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yhbG' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli127 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yadG' 'ABC superfamily (atp_bind) ATP-binding component of transport protein (1st module)' ecoli1455 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1484' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli3952 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'uvrA' 'excision nuclease subunit (3rd module prob. DNA binding)' ecoli770 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0794' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli254 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yagC' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' Test Accuracy: 21/25 (84.00%) Test Frequency class 'ABC superfamily (atp_bind)': 27/712 (3.79%) Test Significance: dev(21.00) ; prob(1.565342E-26) Application to new data (2167 items): ecoli4153 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgR' 'orf' ecoli2858 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yggA' '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)' ecoli2863 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yggC' 'paral putative kinase' ecoli2498 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2547' 'paral putative ATP-binding component of transport system' ecoli2769 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2832' 'putative transport protein' ecoli1454 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1483' 'paral putative ATP-binding component of transport system' Frequency rule on new data: 7/2167 (0.32%) Evaluation on training data (939 items): ecoli1099 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'potA' 'ABC superfamily (atp_bind) ATP-binding component of spermidine/putrescine ABC transport system (1st module)' ecoli3489 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'xylG' 'ABC superfamily (atp_bind) ATP-binding component of D-xylose ABC transport system(2nd module)' ecoli3991 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'phnK' 'ABC superfamily (atp_bind) ATP-binding component of phosphonate ABC transportbelieved to be part of carbon-phosphorus (C-P) lyase in phosphonate metabolism' ecoli3386 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ftsE' 'ABC superfamily (atp_bind) ATP-binding component of a membrane-associated complex involved in cell division' ecoli66 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'yabJ' 'ABC superfamily (atp_bind) ATP-binding component of thiamine ABC transport system' ecoli3403 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'nikE' 'ABC superfamily (stp_bind) ATP-binding component of nickel ABC transport system probably couples energy to transport system' ecoli1650 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1682' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli3373 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ugpC' 'ABC superfamily (atp_bind) ATP-binding component of sn-glycerol 3-phosphate ABC transport system (1st module)' ecoli3670 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'rbsA' 'ABC superfamily (atp_bind) ATP-binding component of d-ribose high-affinity transport system (2nd module)' ecoli1090 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1117' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli908 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ycbE' 'paral putative ATP-binding component of transport system' ecoli1262 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'sapD' 'ABC superfamily (atp_bind) ATP-binding protein of peptide transport system(2nd module) affects potassium transport;' ecoli3463 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'dppF' 'ABC superfamily (atp_bind) ATP-binding component of a dipeptide transport system(1st module)' 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' 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' ecoli1218 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'oppF' 'ABC superfamily (atp_bind) ATP-binding protein of oligopeptide ABC transport system' ecoli2159 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ccmA' 'ABC superfamily (atp_bind) ATP-binding component of heme exporter A heme exporter protein A cytochrome c-type biogenesis protein' ecoli2108 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'mglA' 'ABC superfamily (atp_bind) ATP-binding component of methyl-galactoside transport and galactose taxis (2nd module)' 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)' ecoli1882 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1917' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli481 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0490' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli736 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'modF' 'ABC superfamily (atp_bind) ATP-binding component of molybdenum transport system (2nd module)' ecoli440 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'mdlA' 'ATP-binding component of a transport system (2nd module)' Training Accuracy: 23/23 (100.00%) Training Frequency class 'ABC superfamily (atp_bind)': 24/939 (2.56%) Training Significance: dev(29.61) ; prob(2.363469E-37) Evaluation on validation data (471 items): 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' ecoli4119 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ytfS' 'ABC superfamily (atp_bind) putative ATP-binding component of a transport system' ecoli3990 - 3,3,13 Metabolism of small molecules Central intermediary metabolism Phosphorus compounds 'phnL' 'ABC superfamily (atp_bind) ATP-binding component of phosphonate ABC transport believed to be part of carbon-phosphorus (C-P) lyase in phosphonate metabolism' 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' ecoli2271 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'cvpA' 'membrane protein required for colicin V production' ecoli642 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'gltL' 'ABC superfamily (atp_bind) ATP-binding protein of glutamate/aspartate transport system' ecoli3377 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'livF' 'ABC superfamily (atp_bind) ATP-binding component of leucine ABC transport system' ecoli1677 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'btuD' 'ABC superfamily (atp_bind) ATP-binding component of vitamin B12 ABC transport system(2nd module)' ecoli199 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'abc' 'ABC superfamily (atp_bind) ATP-binding component of ABC transport system(1st module)' ecoli1868 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'araG' 'ABC superfamily (atp_bind) ATP-binding component of high-affinity l-arabinose transport system (2nd module)' 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)' ecoli1724 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1756' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli831 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'potG' 'ABC superfamily (atp_bind) ATP-binding component of putrescine ABC transport system(1st module)' ecoli4000 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'phnC' 'ABC superfamily (atp_bind) ATP-binding component of phosphonate ABC transport system' ecoli1412 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1441' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2169 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yojI' 'ABC superfamily (atp&memb) paral putative ATP-binding component of transport system' ecoli727 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pnuC' 'required for NMN transport' ecoli1217 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'oppD' 'ABC superfamily (atp_bind) ATP-binding protein of oligopeptide ABC transport system' Validation Accuracy: 12/18 (66.67%) Validation Frequency class 'ABC superfamily (atp_bind)': 17/471 (3.61%) Validation Significance: dev(14.34) ; prob(7.278090E-14) ------------------ Rule 11: (7/1, lift 45.6) [hom( A ),classification( A ,acanthopterygii)] = 1 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,gentiananae)] = 0 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,solanaceae)] = 1 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,zea)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,eurotiales)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 [hom( A ),mol_wt_lteq( A ,43194),classification( A ,leishmania)] = 0 -> class 'Amino acyl tRNA syn; tRNA modificn' [0.778] Evaluation on test data (712 items): ecoli4148 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'valS' 'valine tRNA synthetase' ecoli2465 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'hisS' 'histidine tRNA synthetase' ecoli144 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'yadB' 'paral putative tRNA synthetase (1st module)' Test Accuracy: 3/3 (100.00%) Test Frequency class 'Amino acyl tRNA syn; tRNA modificn': 17/712 (2.39%) Test Significance: dev(11.07) ; prob(1.361152E-05) Application to new data (2167 items): ecoli162 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaeG' 'orf' ecoli3248 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yheF' 'orf (2nd module)' ecoli1343 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1372' 'putative membrane protein' ecoli915 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0940' 'paral putative outer membrane protein (2nd module)' ecoli2079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2120' 'orf' ecoli1272 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ordL' 'probable oxidoreductase' ecoli1376 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydbA_2' 'split orf fragment 2 (2nd module)' ecoli2980 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3046' 'paral putative outer membrane protein (2nd module)' ecoli2908 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2974' 'putative endoglucanase' Frequency rule on new data: 9/2167 (0.42%) Evaluation on training data (939 items): ecoli3180 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'mreC' 'rod shape-determining protein' ecoli1682 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'pheS' 'phenylalanine tRNA synthetase alpha-subunit' ecoli1607 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'tyrS' 'tyrosine tRNA synthetase' ecoli2073 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'metG' 'methionine tRNA synthetase (3rd module substrate recognition/ dimerisation/proof reading )' ecoli1681 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'pheT' 'phenylalanine tRNA synthetase beta-subunit' ecoli517 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'cysS' 'cysteine tRNA synthetase(2nd module)' ecoli905 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'asnS' 'asparagine tRNA synthetase (3rd module)' Training Accuracy: 6/7 (85.71%) Training Frequency class 'Amino acyl tRNA syn; tRNA modificn': 16/939 (1.70%) Training Significance: dev(17.17) ; prob(1.688242E-10) Evaluation on validation data (471 items): ecoli1687 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'thrS' 'threonine tRNA synthetase(2nd module)' ecoli2126 - 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'fruA' 'Sugar Specific PTS system fructose-specific transport protein(2nd module)' ecoli194 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'proS' 'proline tRNA synthetase(1st module)' ecoli339 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b0347' '3-(3-hydroxy-phenyl)propionate hydroxylase' ecoli2355 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'gltX' 'glutamate tRNA synthetase catalytic subunit(1st module)' ecoli1834 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'aspS' 'aspartate tRNA synthetase(2nd module)' ecoli4048 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'yjeA' 'paral putative tRNA synthetase' ecoli1223 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'tonB' 'energy transducer; uptake of iron cyanocobalimin; sensitivity to phages colicins(1st module)' Validation Accuracy: 5/8 (62.50%) Validation Frequency class 'Amino acyl tRNA syn; tRNA modificn': 11/471 (2.34%) Validation Significance: dev(11.27) ; prob(3.624580E-07) ------------------ Rule 4: (20, lift 44.8) amino_acid_pair_ratio_er <= 13.8 amino_acid_pairs_ak > 0 [hom( A ),classification( A ,shigella)] = 0 [hom( A ),species( A ,bacillus_licheniformis)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,eukaryota)] = 0 [hom( A ),psi_iter_lteq( A ,13),classification( A ,rosidae)] = 0 [hom( A ),psi_iter_lteq( A ,7),classification( A ,archosauria)] = 0 [hom( A ),species( A ,mus_musculus__mouse_),mol_wt_lteq( A ,43194)] = 0 [hom( A ),mol_wt_gt( A ,77359),classification( A ,viridiplantae)] = 0 [hom( A ),keyword( A ,membrane),classification( A ,firmicutes)] = 1 -> class 'ABC superfamily (peri_perm)' [0.955] Evaluation on test data (712 items): ecoli806 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b0830' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' ecoli2110 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'galS' 'mgl repressor ga lactose operon inducer' ecoli80 - 3,5,5 Metabolism of small molecules Energy metabolism, carbon Glycolysis 'fruR' 'transcriptional repressor of fru operon and others' ecoli4154 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'yjgS' 'L-idonate regulator (hypothetical positive transcriptional regulator for gntS (yjgT) in GNT-II system)(2nd module)' ecoli337 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'lacI' 'transcriptional repressor of the lac operon' ecoli4117 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'ytfQ' 'ABC superfamily (peri_perm) putative LACI-type transcriptional regulator/paral putative periplasmic binding protein of ABC transport system (1st module)' ecoli3008 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'ebgR' 'regulator of ebg operon' ecoli2954 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b3020' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' ecoli890 - 2,2,5 Macromolecule metabolism Macromolecule synthesis, modification Lipopolysaccharide 'ycaH' 'tetraacyldisaccharide 4 kinase (lipid A 4kinase)' ecoli2624 - 1,6,2 Cell processes Adaptation Osmotic adaptation 'proX' 'high-affinity transport system for glycine betaine and proline ATP-driven/binding protein dependent ransports proline and betaine under conditions of hyperosmolarity' Test Accuracy: 3/10 (30.00%) Test Frequency class 'ABC superfamily (peri_perm)': 9/712 (1.26%) Test Significance: dev(8.13) ; prob(2.267600E-04) Application to new data (2167 items): ecoli525 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ybcG' 'paral putative fimbrial-like protein' ecoli1291 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1320' 'paral putative regulator/periplasmic binding protein' ecoli2090 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehZ' 'putative transport system permease protein' ecoli158 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yadT' 'orf' ecoli197 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yaeC' 'paral putative lipoprotein' ecoli3138 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yrbM' 'monofunctional biosynthetic peptidoglycan transglycosylase' ecoli2226 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2268' 'orf' ecoli3820 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3914' 'orf' ecoli3194 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'envR' 'regulatory gene for envCD (acrEF)' ecoli1711 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1743' 'periplasmic protein related to spheroblast formation' ecoli2070 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehD' 'paral putative fimbrial-like protein' ecoli3255 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yheJ' 'putative export protein J for general secretion pathway (GSP)' ecoli2082 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yehR' 'orf' ecoli1406 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1435' 'orf' ecoli1300 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1329' 'murein peptide binding periplasmic protein also a negative regulator of mulitple antibiotic resistance' Frequency rule on new data: 15/2167 (0.69%) Evaluation on training data (939 items): ecoli2136 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'yejA' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' 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' ecoli1214 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'oppA' 'ABC superfamily (peri_perm) oligopeptide binding periplasmic protein of transport system with chaperone properties' ecoli3672 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'rbsB' 'ABC superfamily (peri_perm) D-ribose periplasmic binding protein of ABC transport system' ecoli3928 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'malE' 'ABC superfamily (bind_prot) periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis with chaperone properties(2nd module)' ecoli1265 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'sapA' 'ABC superfamily (peri_perm) peptide binding periplasmic protein of ABC transport system' ecoli1281 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1310' 'ABC superfamily (peri_perm) ABC super family transport protein peri_perm subunit' ecoli2109 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'mglB' 'ABC superfamily (peri_perm) galactose-binding transport protein; receptor for galactose taxis results suggest that bacterial periplasmic substrate-binding proteins also chaperone activity (2nd module)' ecoli3999 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'phnD' 'ABC superfamily (bind_prot) periplasmic binding protein component of Pn transporter' ecoli3982 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'yjcX' 'ABC superfamily (peri_perm) periplasminc D-allose binding protein of allose ABC transport system(2nd module)' ecoli2376 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'cysP' 'thiosulfate binding protein' ecoli1487 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1516' 'ABC superfamily (peri_perm) paral putative regulator/periplasmic binding protein' ecoli1096 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'potD' 'ABC superfamily (peri_perm) spermidine/putrescine binding periplasmic ABC transport protein' ecoli2499 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b2548' 'ABC superfamily (peri_perm) paral putative regulator/periplasmic binding protein' ecoli3399 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'nikA' 'ABC superfamily (peri_perm) nickel-binding perimplasmic protein precursor in nickel ABC transport system(1st module)' ecoli830 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'potF' 'ABC superfamily (peri_perm) periplasmic putrescine-binding protein ABC transport system(1st module)' ecoli645 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'ybeJ' 'ABC superfamily (peri_perm) periplasmic binding ABC transport protein' ecoli1458 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1487' 'ABC superfamily (peri_perm) paral putative periplasmic binding protein of transport system' ecoli4179 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'fecB' 'ABC superfamily (peri_perm) citrate-dependent periplasmic iron binding protein of ABC transport system' ecoli1869 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'araF' 'ABC superfamily (peri_perm) L-arabinose-binding periplasmic protein of ABC transport system(1st module)' Training Accuracy: 20/20 (100.00%) Training Frequency class 'ABC superfamily (peri_perm)': 20/939 (2.13%) Training Significance: dev(30.32) ; prob(3.692224E-34) Evaluation on validation data (471 items): ecoli582 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'fepB' 'ABC superfamily (peri_perm) ferric enterobactin (enterochelin) binding protein; periplasmic component of ABC tranport (1st module)' ecoli4207 - 4,1,5 Structural elements Cell envelop Surface structures 'fimF' 'fimbrial morphology' ecoli3376 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'ugpB' 'ABC superfamily (peri_perm) ABC super family transport protein peri_perm subunit sn-glycerol 3-phosphate periplasmic binding protein of ABC transport system(2nd module)' ecoli2774 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'galR' 'repressor of galETK operon' ecoli3649 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'pstS' 'high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein' ecoli3823 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'sbp' 'periplasmic sulfate-binding protein' ecoli3112 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'dacB' 'D-alanyl-D-alanine carboxypeptidase fraction B; penicillin-binding protein 4' ecoli3689 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'ppiC' 'peptidyl-prolyl cis-trans isomerase C (rotamase C)' Validation Accuracy: 4/8 (50.00%) Validation Frequency class 'ABC superfamily (peri_perm)': 7/471 (1.49%) Validation Significance: dev(11.34) ; prob(3.216584E-06) ------------------ Rule 107: (12/1, lift 36.6) amino_acid_pairs_ah > 0 [hom( A ),species( A ,mycoplasma_hyorhinis)] = 0 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,gentiananae)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,eurotiales)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,fabaceae)] = 0 [hom( A ),psi_iter_gt( A ,7),classification( A ,burkholderia_group)] = 1 [hom( A ),species( A ,rhodobacter_sphaeroides__rhodopseudomonas_sphaeroides_),mol_wt_gt( A ,43194)] = 0 [hom( A ),species( A ,cyanophora_paradoxa),mol_wt_lteq( A ,32892)] = 0 [hom( A ),mol_wt_lteq( A ,43194),classification( A ,leishmania)] = 0 [hom( A ),mol_wt_lteq( A ,32892),classification( A ,euascomycetes)] = 0 -> class 'Transposon-related functions' [0.857] Evaluation on test data (712 items): ecoli1375 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'tra8_2' 'transposase 2 for IS30' ecoli1989 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_7' 'IS5 protein' ecoli3479 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi5A' 'IS5 protein' ecoli4173 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'tra8_3' 'transposase for IS30' ecoli1374 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi21_2' 'IS21 protein 2' ecoli2979 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_5' 'IS2 protein' ecoli1953 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_6' 'IS5 protein' ecoli2527 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'srmB' 'ATP-dependent RNA helicase (2nd module)' Test Accuracy: 7/8 (87.50%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(18.10) ; prob(5.325239E-12) Application to new data (2167 items): ecoli2143 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yejH' 'paral putative helicase' ecoli2635 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2690' 'orf' ecoli1721 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1753' 'orf' ecoli1000 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'tra5_3' 'putative transposase for IS3' ecoli2951 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'sufI' 'suppressor of ftsI' ecoli438 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'cof' 'complements deletion mutant for growth on succinate(1st module)' ecoli4260 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjjG' 'orf' ecoli2442 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2491' 'paral putative regulator protein' ecoli2885 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2950' 'putative protein transport(2nd module)' ecoli3128 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbI' 'orf formerly yrbI and yrbJ' ecoli291 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0299' 'putative IS tranposase' ecoli531 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'tra5_2' 'putative transposase for insertion sequence IS3' ecoli1304 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydaA' 'orf(2nd module)' ecoli3322 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrfG' 'orf' ecoli669 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0686' 'orf' ecoli4161 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4272' 'orf' ecoli1758 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1790' 'paral putative regulator' ecoli364 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'tra5_1' 'putative transposase 5 of IS3' ecoli259 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yagA' 'orf' ecoli1664 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1696' 'paral putative regulator' ecoli2048 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'tra5_4' 'putative transposase for IS3' ecoli1288 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1317' 'orf' ecoli1548 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1578' 'orf' ecoli187 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0187' 'orf' ecoli1776 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1808' 'paral putative (SOS) repair enzyme' ecoli4162 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4273' 'putative transposase' Frequency rule on new data: 26/2167 (1.20%) Evaluation on training data (939 items): ecoli251 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_1' 'IS5 protein 1' ecoli1373 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_2' 'IS22 protein 2' ecoli248 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'tra8_1' 'transposase1 for IS30' ecoli1955 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_3' 'IS2 protein' ecoli1956 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi21_3' 'IS2 protein' ecoli3428 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_11' 'IS5 protein 11' ecoli2150 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_8' 'IS5 protein' ecoli542 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_2' 'IS 5 protein' ecoli1341 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_5' 'IS5 protein' ecoli353 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_1' 'IS22 protein 1' ecoli84 - 1,7,1 Cell processes Cell division Cell division 'ftsI' 'septum formation; penicillin-binding protein 3; septal peptidoglycan synthesis; membrane protein with catalytic domain in periplasm(2nd module)' ecoli2916 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_9' 'IS5 protein' Training Accuracy: 11/12 (91.67%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(20.46) ; prob(1.371135E-17) Evaluation on validation data (471 items): ecoli775 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'dinG' 'LexA regulated (SOS) repair enzyme' ecoli1302 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_4' 'IS5 protein' ecoli352 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi21_1' 'IS21 protein 1' ecoli625 - 1,7,1 Cell processes Cell division Cell division 'mrdA' 'cell elongation e phase; peptidoglycan synthetase; penicillin-binding protein 2(2nd module)' ecoli2798 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi21_4' 'IS2 protein' ecoli4250 - 1,2,1 Cell processes Chromosome replication Chromosome replication 'dnaC' 'chromosome replication; initiation and chain elongation' ecoli3148 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_10' 'IS5 protein 10' ecoli148 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'hrpB' 'helicase ATP-dependent(1st module)' ecoli2652 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hypF' 'transcriptional regulatory protein(2nd module)' ecoli1314 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'dbpA' 'binds DNA RNA only hydrolyses ATP in presence of 23S rRNA(2nd module)' ecoli2797 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_4' 'IS2 protein' ecoli2978 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi21_5' 'IS2 protein' Validation Accuracy: 6/12 (50.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(9.59) ; prob(5.317243E-07) ------------------