Rule 146: (7, lift 37.9) ecoli_hydro <= -0.525 amino_acid_pair_ratio_da > 10.4 [ss_beta( A ,lteq,10),nss_beta( A , B ,gt,1),nss_beta( B , C ,lteq,5)] = 1 -> class 'Transposon-related functions' [0.889] Evaluation on test data (712 items): ecoli540 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'b0550' 'endodeoxyribonuclease RUS (Holliday junction resolvase)' ecoli1989 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_7' 'IS5 protein' ecoli2173 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'ompC' 'outer membrane protein 1b (ib;c) (2nd module)' Test Accuracy: 1/3 (33.33%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(4.08) ; prob(5.378126E-02) Application to new data (2167 items): ecoli379 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaiI' 'orf' ecoli4002 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'phnA' 'orf' ecoli1746 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1778' 'orf' ecoli490 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0499' 'orf' ecoli2891 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yggM' 'putative alpha helix chain' Frequency rule on new data: 5/2167 (0.23%) Evaluation on training data (939 items): ecoli251 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_1' 'IS5 protein 1' ecoli3428 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_11' 'IS5 protein 11' ecoli2150 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_8' 'IS5 protein' ecoli542 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_2' 'IS 5 protein' 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' ecoli2916 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_9' 'IS5 protein' Training Accuracy: 7/7 (100.00%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(17.08) ; prob(3.875249E-12) Evaluation on validation data (471 items): ecoli1302 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_4' 'IS5 protein' ecoli3148 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_10' 'IS5 protein 10' Validation Accuracy: 2/2 (100.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(8.08) ; prob(8.835157E-04) ------------------ Rule 132: (6, lift 37.3) ecoli_hydro <= 0.322 ecoli_theo_pI > 10.06 [ss_alpha( A ,lteq,830),nss_alpha( A , B ,gt,3)] = 0 [ss_coil( A ,gt,6),nss_coil( A , B ,lteq,6),nss_coil( B , C ,lteq,10)] = 1 -> class 'Ribosomal proteins - synthesis modificationRiboso' [0.875] Evaluation on test data (712 items): ecoli3232 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplX' '50S ribosomal subunit protein L24' ecoli4204 - 4,1,5 Structural elements Cell envelop Surface structures 'fimI' 'fimbrial protein internal segment' ecoli1846 - 4,1,5 Structural elements Cell envelop Surface structures 'b1878' 'flagellar protein' ecoli2556 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsP' '30S ribosomal subunit protein S16' ecoli2553 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplS' '50S ribosomal subunit protein L19' Test Accuracy: 3/5 (60.00%) Test Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 23/712 (3.23%) Test Significance: dev(7.18) ; prob(3.209656E-04) Application to new data (2167 items): ecoli1625 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1655' 'orf' ecoli4163 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgW' 'orf' ecoli3390 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhhM' 'putative receptor' Frequency rule on new data: 3/2167 (0.14%) Evaluation on training data (939 items): ecoli3559 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmB' '50S ribosomal subunit protein L28' 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' ecoli3224 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplO' '50S ribosomal subunit protein L15' ecoli3265 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsL' '30S ribosomal subunit protein S12' ecoli3233 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplN' '50S ribosomal subunit protein L14' Training Accuracy: 6/6 (100.00%) Training Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 22/939 (2.34%) Training Significance: dev(15.81) ; prob(1.654027E-10) Evaluation on validation data (471 items): ecoli3239 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsS' '30S ribosomal subunit protein S19' ecoli1685 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmI' '50S ribosomal subunit protein A' Validation Accuracy: 2/2 (100.00%) Validation Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 12/471 (2.55%) Validation Significance: dev(8.75) ; prob(6.491136E-04) ------------------ Rule 147: (6, lift 37.3) ecoli_hydro <= 0.322 [ss_coil( A ,gt,6),nss_coil( A , B ,lteq,6),nss_coil( B , C ,lteq,10)] = 0 [ss_coil( A ,gt,10),nss_coil( A , B ,lteq,10),nss_coil( B , C ,lteq,10)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,lteq,830),nss_coil( D , E ,lteq,830)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,10),nss_coil( B , C ,gt,1),nss_coil( C , D ,lteq,830),nss_coil( D , E ,gt,10)] = 0 -> class 'Transposon-related functions' [0.875] Evaluation on test data (712 items): ecoli1067 - 3,2,1 Metabolism of small molecules Biosynthesis of cofactors, carriers Acyl carrier protein (ACP) 'acpP' 'acyl carrier protein' ecoli3503 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'yiaQ' 'probable 3-hexulose 6-phosphate synthase' ecoli22 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_1' 'IS1 protein InsA' ecoli4086 - 3,3,15 Metabolism of small molecules Central intermediary metabolism Pool, multipurpose conversions of intermed. met'm 'yjfV' 'probable hexulose-6-phosphate synthase' ecoli2979 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_5' 'IS2 protein' ecoli3245 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'pinO' 'calcium-binding protein required for initiation of chromosome replication' Test Accuracy: 2/6 (33.33%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(5.76) ; prob(4.762032E-03) Application to new data (2167 items): ecoli892 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0917' 'orf' ecoli4141 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4251' 'orf' ecoli3941 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbL' 'orf' ecoli319 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0327' 'orf' ecoli1527 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1556' 'orf' ecoli1005 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1031' 'putative ribosomal protein' ecoli2412 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2461' 'orf' ecoli478 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0487' 'paral putative regulator' ecoli1711 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1743' 'periplasmic protein related to spheroblast formation' ecoli3206 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yrdD' 'putative DNA topoisomerase' ecoli4078 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfN' 'orf' ecoli1018 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1045' 'orf' ecoli1901 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1936' 'orf' ecoli324 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0332' 'orf' ecoli4162 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4273' 'putative transposase' Frequency rule on new data: 15/2167 (0.69%) Evaluation on training data (939 items): ecoli1373 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_2' 'IS22 protein 2' ecoli1955 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_3' 'IS2 protein' ecoli17 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi82_1' 'homolog IS186 and IS421 protein' ecoli267 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_3' 'IS1 protein InsA' ecoli353 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_1' 'IS22 protein 1' ecoli1862 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_5' 'IS1 protein InsA' Training Accuracy: 6/6 (100.00%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(15.81) ; prob(1.654027E-10) Evaluation on validation data (471 items): ecoli257 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_2' 'IS1 protein InsA 2' ecoli4183 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_7' 'IS1 protein InsA' ecoli3689 - 2,2,9 Macromolecule metabolism Macromolecule synthesis, modification Protein modufication 'ppiC' 'peptidyl-prolyl cis-trans isomerase C (rotamase C)' ecoli2797 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_4' 'IS2 protein' 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 99: (21, lift 39.1) ecoli_hydro > 0.322 [ss_beta( A ,gt,10),nss_beta( A , B ,lteq,6),nss_beta( B , C ,gt,1)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,lteq,6),nss_coil( D , E ,gt,10)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,10),nss_coil( B , C ,lteq,830),nss_coil( C , D ,gt,5),nss_coil( D , E ,gt,1)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,5),nss_coil( B , C ,gt,1),nss_coil( C , D ,gt,3),nss_coil( D , E ,gt,3)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,gt,10),nss_coil( D , E ,lteq,10)] = 1 -> class 'MFS family' [0.957] Evaluation on test data (712 items): ecoli2324 1,5,21 Cell processes Transport/binding proteins MFS family 'emrY' 'MFS family of transport protein multidrug resistance protein y (2nd module)' ecoli2538 1,5,21 Cell processes Transport/binding proteins MFS family 'kgtP' 'MFS family of transport protein alpha-ketoglutarate permease(1st module)' ecoli3580 1,5,21 Cell processes Transport/binding proteins MFS family 'yicK' 'MFS family of transport protein two-module paral putative transport protein (2nd module)' ecoli2198 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glpT' 'sn-glycerol-3-phosphate permease' ecoli3188 - 1,5,35 Cell processes Transport/binding proteins SSS family 'panF' 'SSS family transport protein sodium/pantothenate symporter(1st module)' ecoli2141 1,5,21 Cell processes Transport/binding proteins MFS family 'bcr' 'MFS family of transport protein bicyclomycin resistance protein; transmembrane protein (2nd module)' Test Accuracy: 4/6 (66.67%) Test Frequency class 'MFS family': 14/712 (1.97%) Test Significance: dev(11.41) ; prob(2.172282E-06) Application to new data (2167 items): ecoli4009 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4115' 'putative amino acid/amine transport protein cryptic' ecoli4034 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjeH' 'putative transport' ecoli3780 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihN' 'orf' ecoli1658 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1690' 'paral putative MFS family of transport protein' ecoli3600 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidK' 'putative cotransporter' ecoli1505 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ydeF' 'paral putative transport protein (1st 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' 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)' ecoli1759 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1791' 'putative amino acid/amine transport protein (3rd module)' ecoli3023 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygjV' 'orf' 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: 14/2167 (0.65%) 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): ecoli2778 1,5,21 Cell processes Transport/binding proteins MFS family 'araE' 'MFS family of transport protein low-affinity L-arabinose transport system proton symport protein(1st module)' ecoli4098 - 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'cycA' 'APC family transport of D-alanine D-serine and glycine (2nd module)' 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)' ecoli70 1,5,21 Cell processes Transport/binding proteins MFS family 'yabM' 'MFS family of transport protein proton-coupled beta-galactosidase/sugar efflux pump ? role in lactose metabolism (2nd module)' ecoli3446 1,5,21 Cell processes Transport/binding proteins MFS family 'yhjE' 'MFS family of transport protein (2nd module)' 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)' ecoli3588 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpC' 'regulator of uhpT (1st module)' ecoli3093 - 1,5,43 Cell processes Transport/binding proteins ArAAP family 'mtr' 'ArAAP family tryptophan-specific transport protein' ecoli2280 1,5,21 Cell processes Transport/binding proteins MFS family 'b2322' 'MFS family of transport protein paral putative (2nd module)' ecoli1737 1,5,21 Cell processes Transport/binding proteins MFS family 'ydjE' 'MFS family of transport protein (1st module)' Validation Accuracy: 10/14 (71.43%) Validation Frequency class 'MFS family': 14/471 (2.97%) Validation Significance: dev(15.08) ; prob(4.776244E-13) ------------------