Rule 50: (7, lift 9.4) [ss_alpha( A ,lteq,1),nss_alpha( A , B ,gt,1)] = 0 [ss_coil( A ,gt,5),nss_coil( A , B ,gt,3),nss_coil( B , C ,gt,10)] = 1 [ss_coil( A ,lteq,10),nss_coil( A , B ,lteq,6),nss_coil( B , C ,lteq,6)] = 0 [ss_beta( A ,lteq,6),nss_beta( A , B ,lteq,830),nss_beta( B , C ,lteq,6)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,830),nss_coil( B , C ,lteq,10),nss_coil( C , D ,lteq,5)] = 1 -> class 'Energy metabolism carbon' [0.889] Evaluation on test data (712 items): ecoli3642 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'bglB' 'phospho-beta-glucosidase B; cryptic' ecoli2538 - 1,5,21 Cell processes Transport/binding proteins MFS family 'kgtP' 'MFS family of transport protein alpha-ketoglutarate permease(1st module)' ecoli3965 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'nrfB' 'formate-dependent nitrite reductase; a penta-haeme cytochrome c' ecoli1383 - 3,6,1 Metabolism of small molecules Fatty acid biosynthesis Fatty acid and phosphatidic acid biosynth 'acpD' 'acyl carrier protein phosphodiesterase' ecoli2660 3,5,4 Metabolism of small molecules Energy metabolism, carbon Fermentation 'hycF' 'probable iron-sulfur protein of hydrogenase 3 (part of FHL complex)' ecoli2664 3,5,4 Metabolism of small molecules Energy metabolism, carbon Fermentation 'hycB' 'probable small subunit of hydrogenase-3 iron-sulfur protein (part of formate hydrogenlyase (FHL) complex)' Test Accuracy: 3/6 (50.00%) Test Frequency class 'Energy metabolism carbon': 70/712 (9.83%) Test Significance: dev(3.30) ; prob(1.512314E-02) Application to new data (2167 items): ecoli4080 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfP' 'orf' ecoli535 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0545' 'orf' ecoli3932 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbI' 'orf' ecoli1124 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1151' 'orf' ecoli2572 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2626' 'orf' ecoli2957 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3023' 'orf' ecoli4096 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b4206' 'orf' ecoli749 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybhB' 'orf' ecoli1154 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1181' 'orf' ecoli1272 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ordL' 'probable oxidoreductase' ecoli220 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yafL' 'orf' ecoli1809 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1841' 'orf' ecoli2312 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2355' 'putative RNA polymerase beta' ecoli2825 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2889' 'orf' ecoli2185 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2227' 'orf' ecoli1507 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeI' 'orf' ecoli324 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0332' 'orf' ecoli490 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0499' 'orf' Frequency rule on new data: 18/2167 (0.83%) Evaluation on training data (939 items): ecoli2653 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hydN' 'involved in electron transport from formate to hydrogen Fe-S centers' ecoli2163 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'napG' 'ferredoxin-type protein: electron transfer' ecoli2930 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'hybA' 'thought to be hydrogenase-2 small subunit now identified as hybO(2nd module)' ecoli2245 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoB' 'NADH dehydrogenase I chain B' ecoli2166 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'napF' 'ferredoxin-type protein: electron transfer' ecoli2234 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoN' 'NADH dehydrogenase I chain N(2nd module)' ecoli2432 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'yffE' 'hydrogenase 4 Fe-S subunit' Training Accuracy: 7/7 (100.00%) Training Frequency class 'Energy metabolism carbon': 89/939 (9.48%) Training Significance: dev(8.18) ; prob(6.871806E-08) Evaluation on validation data (471 items): ecoli2641 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'mltB' 'membrane-bound lytic murein transglycosylase B' ecoli2160 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'napC' 'cytochrome c-type protein' ecoli2239 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoI' 'NADH dehydrogenase I chain I' ecoli2439 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2488' 'hydrogenase 4 Fe-S subunit' ecoli3973 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'fdhF' 'selenopolypeptide subunit of formate dehydrogenase H (part of formate hydrogen-lyase complex: FHL complex) EC 1.2.1.2 CONSISTS OF TWO SEPARABLE ENZYMATIC ACTIVITIES: A FORMATE DEHYDROGENASE COMPONENT(1st module)' Validation Accuracy: 4/5 (80.00%) Validation Frequency class 'Energy metabolism carbon': 44/471 (9.34%) Validation Significance: dev(5.43) ; prob(3.452264E-04) ------------------ Rule 68: (4/1, lift 15.7) [ss_coil( A ,lteq,5),nss_coil( A , B ,lteq,10)] = 0 [ss_coil( A ,gt,10),nss_coil( A , B ,lteq,6)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,6),nss_coil( B , C ,gt,1)] = 0 [ss( A ,c),nss( A , B ,a),len_lteq( B ,5)] = 1 -> class 'Laterally acquirred elements' [0.667] Evaluation on test data (712 items): ecoli4092 - 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsR' '30S ribosomal subunit protein S18' ecoli22 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_1' 'IS1 protein InsA' ecoli2363 - 1,7,1 Cell processes Cell division Cell division 'b2412' 'cell division protein involved in FtsZ ring(1st module)' Test Accuracy: 1/3 (33.33%) Test Frequency class 'Laterally acquirred elements': 25/712 (3.51%) Test Significance: dev(2.81) ; prob(1.016817E-01) Application to new data (2167 items): ecoli4107 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfK' 'orf' ecoli1391 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1420' 'orf' ecoli826 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ybjC' 'orf' ecoli1899 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1934' 'orf' ecoli319 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0327' 'orf' ecoli638 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0648' 'orf' ecoli2543 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2596' 'orf' ecoli387 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0395' 'orf' ecoli4242 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjiX' 'orf' ecoli571 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0581' 'orf' ecoli1230 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciG' 'orf' ecoli381 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaiA' 'orf' ecoli738 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0762' 'orf' ecoli2347 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2390' 'orf' ecoli4113 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjfA' 'orf' ecoli604 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0614' 'orf' ecoli656 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0671' 'putative RNA' ecoli165 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0165' 'orf' ecoli592 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0602' 'orf' ecoli1538 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1567' 'orf' Frequency rule on new data: 20/2167 (0.92%) Evaluation on training data (939 items): ecoli3400 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'nikB' 'ABC superfamily (membrane) membrane component in nickel transport system probably forms heterodimeric pore with NikC(2nd module)' ecoli267 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_3' 'IS1 protein InsA' ecoli684 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'b0701' 'small orf part of the RhsC element' ecoli1862 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_5' 'IS1 protein InsA' Training Accuracy: 3/4 (75.00%) Training Frequency class 'Laterally acquirred elements': 40/939 (4.26%) Training Significance: dev(7.01) ; prob(2.993240E-04) Evaluation on validation data (471 items): ecoli257 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_2' 'IS1 protein InsA 2' ecoli4118 - 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ytfR' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli1254 - 1,6,2 Cell processes Adaptation Osmotic adaptation 'osmB' 'osmotically inducible lipoprotein' ecoli3367 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_6' 'IS1 protein InsA' Validation Accuracy: 2/4 (50.00%) Validation Frequency class 'Laterally acquirred elements': 26/471 (5.52%) Validation Significance: dev(3.90) ; prob(1.632053E-02) ------------------