Rule 133: (3, lift 125.2) [ss( A ,b),nss( A , B ,a)] = 0 [ss_beta( A ,lteq,1),nss_beta( A , B ,gt,5)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,6)] = 1 [ss_beta( A ,gt,1),nss_beta( A , B ,gt,5),nss_beta( B , C ,gt,10)] = 1 [ss_beta( A ,lteq,5),nss_beta( A , B ,gt,10),nss_beta( B , C ,gt,1)] = 1 [ss_alpha( A ,gt,10),nss_alpha( A , B ,gt,10),nss_alpha( B , C ,lteq,10)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,10),nss_coil( C , D ,lteq,6)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,10),nss_coil( B , C ,lteq,10),nss_coil( C , D ,gt,3),nss_coil( D , E ,lteq,830)] = 1 -> class 'Outer membrane constituents' [0.800] Evaluation on test data (712 items): ecoli1052 - 4,1,5 Structural elements Cell envelop Surface structures 'flgH' 'flagellar biosynthesis basal-body outer-membrane L (lipopolysaccharide layer) ring protein' ecoli116 - 3,5,7 Metabolism of small molecules Energy metabolism, carbon Pyruvate dehydrogenase 'lpdA' 'lipoamide dehydrogenase (NADH) ; component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex second part(2nd module)' ecoli2114 4,1,3 Structural elements Cell envelop Outer membrane constituents 'cirA' 'outer membrane receptor for iron-regulated colicin I receptor; porin; requires tonB gene product(1st module)' Test Accuracy: 1/3 (33.33%) Test Frequency class 'Outer membrane constituents': 4/712 (0.56%) Test Significance: dev(7.59) ; prob(1.675942E-02) Application to new data (2167 items): ecoli2823 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2887' 'putative oxidoreductase fe-s subunit (2nd module)' ecoli2191 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yfaL' 'orf' ecoli1142 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1169' 'orf' ecoli781 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0805' 'paral putative outer membrane receptor' ecoli1422 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1451' 'paral putative outer membrane receptor' ecoli4111 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ytfN' 'orf' ecoli2980 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3046' 'paral putative outer membrane protein (2nd module)' ecoli177 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0177' 'orf' ecoli1481 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeK' 'orf' Frequency rule on new data: 9/2167 (0.42%) Evaluation on training data (939 items): ecoli150 4,1,3 Structural elements Cell envelop Outer membrane constituents 'fhuA' 'outer membrane protein receptor for ferrichrome colicin M and phages T1 T5 and phi80(1st module)' ecoli904 4,1,3 Structural elements Cell envelop Outer membrane constituents 'ompF' 'outer membrane protein 1a (ia;b;f) (2nd module)' ecoli1959 4,1,3 Structural elements Cell envelop Outer membrane constituents 'b2000' 'phase-variable outer membrane associated fluffing protein(2nd module)' Training Accuracy: 3/3 (100.00%) Training Frequency class 'Outer membrane constituents': 6/939 (0.64%) Training Significance: dev(21.60) ; prob(2.608897E-07) Evaluation on validation data (471 items): ecoli3872 4,1,3 Structural elements Cell envelop Outer membrane constituents 'btuB' 'outer membrane receptor for transport of vitamin B12 E colicins and bacteriophage BF23(1st module)' Validation Accuracy: 1/1 (100.00%) Validation Frequency class 'Outer membrane constituents': 6/471 (1.27%) Validation Significance: dev(8.80) ; prob(1.273885E-02) ------------------ Rule 168: (3, lift 34.1) [ss_beta( A ,gt,1),nss_beta( A , B ,gt,1)] = 0 [ss_coil( A ,gt,10),nss_coil( A , B ,gt,6),nss_coil( B , C ,lteq,3)] = 1 [ss_coil( A ,lteq,1),nss_coil( A , B ,gt,5),nss_coil( B , C ,gt,5)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,5),nss_coil( B , C ,lteq,830),nss_coil( C , D ,gt,1),nss_coil( D , E ,lteq,830)] = 0 -> class 'Transposon-related functions' [0.800] 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' ecoli22 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_1' 'IS1 protein InsA' Test Accuracy: 1/2 (50.00%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(5.09) ; prob(3.618348E-02) Application to new data (2167 items): ecoli1432 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydcE' 'orf' ecoli3941 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbL' 'orf' ecoli3900 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjaI' 'zinc resistance-associated protein precursor' ecoli3305 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfY' 'orf' ecoli1005 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1031' 'putative ribosomal protein' ecoli3277 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yheU' 'orf' ecoli3216 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhdN' 'orf' ecoli4249 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjjA' 'putative glycoprotein/receptor' ecoli3960 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjcF' 'orf' ecoli3015 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygjM' 'orf' ecoli3458 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3535' 'orf' ecoli1966 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2007' 'putative alpha helix protein' ecoli1525 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1554' 'paral putative lysozyme' Frequency rule on new data: 13/2167 (0.60%) Evaluation on training data (939 items): 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' ecoli1862 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_5' 'IS1 protein InsA' 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): ecoli257 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_2' 'IS1 protein InsA 2' ecoli3367 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_6' 'IS1 protein InsA' 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 167: (3, lift 34.1) [ss_alpha( A ,gt,5),nss_alpha( A , B ,gt,3)] = 1 [ss_coil( A ,gt,5),nss_coil( A , B ,lteq,6),nss_coil( B , C ,lteq,10)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,lteq,5),nss_coil( D , E ,lteq,830)] = 1 -> class 'Transposon-related functions' [0.800] Evaluation on test data (712 items): ecoli1853 - 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'tap' 'methyl-accepting chemotaxis protein IV peptide sensor receptor (2nd module)' ecoli2435 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2484' 'hydrogenase 4 membrane subunit(1st module)' ecoli2979 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_5' 'IS2 protein' 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): ecoli3922 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbG' 'orf' ecoli191 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yaeJ' 'orf' ecoli2065 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2106' 'orf' ecoli3944 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbO' 'orf' ecoli4162 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4273' 'putative transposase' Frequency rule on new data: 5/2167 (0.23%) 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' ecoli353 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_1' 'IS22 protein 1' 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): ecoli2797 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi22_4' 'IS2 protein' Validation Accuracy: 1/1 (100.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(5.71) ; prob(2.972399E-02) ------------------ Rule 169: (7/1, lift 33.2) [ss_alpha( A ,lteq,830),nss_alpha( A , B ,lteq,1)] = 1 [ss_beta( A ,lteq,6),nss_beta( A , B ,lteq,3)] = 1 [ss_beta( A ,lteq,3),nss_beta( A , B ,lteq,1)] = 0 [ss_coil( A ,gt,5),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,5)] = 1 [ss_beta( A ,gt,3),nss_beta( A , B ,gt,10),nss_beta( B , C ,lteq,6)] = 1 [ss_beta( A ,gt,10),nss_beta( A , B ,lteq,6),nss_beta( B , C ,gt,1)] = 1 [ss_beta( A ,lteq,5),nss_beta( A , B ,gt,10),nss_beta( B , C ,gt,1)] = 0 -> class 'Transposon-related functions' [0.778] Evaluation on test data (712 items): ecoli471 - 3,3,18 Metabolism of small molecules Central intermediary metabolism Sugar-nucleotide biosynthesis, conversions 'ushA' 'UDP-sugar hydrolase 5-nucleotidase' ecoli3642 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'bglB' 'phospho-beta-glucosidase B; cryptic' ecoli4286 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'creD' 'tolerance to colicin E2' ecoli1989 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_7' 'IS5 protein' ecoli565 - 1,5,33 Cell processes Transport/binding proteins RNDfamily 'ybdE' 'RND family of transport protein paral putative transport system (2nd module)' ecoli3643 - 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'bglF' 'Sugar Specific PTS family beta-glucosides enzyme II cryptic (2nd module eiia (ei interaction)?)' ecoli2199 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'glpA' 'sn-glycerol-3-phosphate dehydrogenase (anaerobic) large subunit EC 1.1.99.5(1st module)' ecoli3392 - 1,5,30 Cell processes Transport/binding proteins P-type ATPase family 'b3469' 'P-type ATPase familyzinc-transporting ATPase(2nd module)' 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): ecoli3506 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yiaT' 'paral putative scaffolding protein' ecoli1239 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciQ' 'orf' ecoli3784 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihQ' 'orf' ecoli1935 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1971' 'putative reductase' ecoli3569 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yicF' 'putative enzyme' ecoli3611 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yidS' 'orf' ecoli2186 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2228' 'orf (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)' ecoli3578 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yicI' 'orf' Frequency rule on new data: 9/2167 (0.42%) Evaluation on training data (939 items): ecoli251 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_1' 'IS5 protein 1' ecoli907 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'pepN' 'aminopeptidase N' 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' ecoli683 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsC' 'rhsC protein in rhs element' ecoli2916 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_9' 'IS5 protein' Training Accuracy: 6/7 (85.71%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(14.58) ; prob(1.134567E-09) Evaluation on validation data (471 items): ecoli1302 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_4' 'IS5 protein' ecoli3515 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsA' 'rhsA protein in rhs element' ecoli475 - 1,5,4 Cell processes Transport/binding proteins Ars family 'b0484' 'Ars family of transport protein' ecoli3148 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi52_10' 'IS5 protein 10' ecoli1834 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'aspS' 'aspartate tRNA synthetase(2nd module)' ecoli2254 - 3,5,3 Metabolism of small molecules Energy metabolism, carbon Electron transport 'ackA' 'acetate kinase' Validation Accuracy: 3/6 (50.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(6.78) ; prob(4.797746E-04) ------------------ Rule 163: (5/1, lift 25.8) [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,6)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,10)] = 0 [ss_beta( A ,gt,1),nss_beta( A , B ,gt,5),nss_beta( B , C ,gt,10)] = 1 [ss_beta( A ,lteq,5),nss_beta( A , B ,gt,10),nss_beta( B , C ,gt,1)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,10),nss_coil( B , C ,lteq,10),nss_coil( C , D ,gt,3),nss_coil( D , E ,lteq,830)] = 0 -> class 'Surface structures' [0.714] Evaluation on test data (712 items): ecoli2711 - 1,5,21 Cell processes Transport/binding proteins MFS family 'b2771' 'MFS family of transport protein (3rd module (function unknown)' 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' ecoli45 - 1,5,21 Cell processes Transport/binding proteins MFS family 'yaaU' 'MFS family transport protein' ecoli790 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'ompX' 'outer membrane protease receptor for phage OX2' Test Accuracy: 0/4 (0.00%) Test Frequency class 'Surface structures': 22/712 (3.09%) Test Significance: dev(-0.36) ; prob(1.000000E+00) Application to new data (2167 items): ecoli1575 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1605' 'putative arginine/ornithine antiporter' ecoli435 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0443' 'orf' ecoli1634 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1664' 'possible enzyme(2nd module)' ecoli1625 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1655' 'orf' ecoli2013 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2054' 'paral putative acyl transferase in colanic acid biosynthesis' ecoli873 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ycaD' 'paral putative transport protein (1st module)' Frequency rule on new data: 6/2167 (0.28%) 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)' ecoli1010 4,1,5 Structural elements Cell envelop Surface structures 'csgG' 'curli production assembly/transport component 2nd curli operon; novel lipoprotein' ecoli1049 4,1,5 Structural elements Cell envelop Surface structures 'flgE' 'flagellar biosynthesis hook protein(1st module)' ecoli166 - 3,1,13 Metabolism of small molecules Amino acid biosynthesis Lysine 'dapD' '2345-tetrahydropyridine-2-carboxylate N-succinyltransferase(2nd module)' 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: 4/5 (80.00%) Training Frequency class 'Surface structures': 26/939 (2.77%) Training Significance: dev(10.52) ; prob(2.873907E-06) Evaluation on validation data (471 items): 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' ecoli3709 - 3,3,18 Metabolism of small molecules Central intermediary metabolism Sugar-nucleotide biosynthesis, conversions 'rffT' 'synthesis of enterobacterial common antigen (ECA): TDP-Fuc4NAc:lipidII transferase(1st module)' Validation Accuracy: 1/2 (50.00%) Validation Frequency class 'Surface structures': 12/471 (2.55%) Validation Significance: dev(4.26) ; prob(4.965719E-02) ------------------ Rule 62: (2/1, lift 78.2) [ss_beta( A ,lteq,5)] = 1 [ss( A ,b),nss( A , B ,a)] = 0 [ss_beta( A ,gt,1),nss_beta( A , B ,gt,1)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,3),nss_coil( C , D ,gt,6),nss_coil( D , E ,lteq,830)] = 1 -> class 'Chemotaxis and mobility' [0.500] Evaluation on test data (712 items): ecoli1400 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'tehA' 'tellurite resistance; K+-tellurite ethidium and proflavin transport; membrane protein' ecoli4213 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'uxuR' 'regulator for uxu operon' ecoli1160 - 3,4,4 Metabolism of small molecules Degradation of small molecules Fatty acids 'fadR' 'negative regulator for fad regulon and positive activator of fabA(1st module)' ecoli1808 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b1840' 'putative resistance protein' ecoli1361 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1390' 'phenylacetic acid degradation protein possibly part of multicomponent oxygenase' ecoli1633 - 1,5,20 Cell processes Transport/binding proteins MATE family 'ydhE' 'MATE family of transport protein(2nd module)' ecoli2523 - 6,1,1 Global functions Global regulatory functions Global regulatory functions 'rseA' 'sigma-E factor negative regulatory protein' ecoli1904 - 4,1,5 Structural elements Cell envelop Surface structures 'fliG' 'flagellar biosynthesis component of motor switching and energizing enabling rotation and determining its direction' Test Accuracy: 0/8 (0.00%) Test Frequency class 'Chemotaxis and mobility': 4/712 (0.56%) Test Significance: dev(-0.21) ; prob(1.000000E+00) Application to new data (2167 items): ecoli2111 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yeiB' 'orf' ecoli155 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yadQ' 'putative channel transporter' ecoli3976 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjcR' 'paral putative membrane protein' ecoli562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0572' 'orf' ecoli1553 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1583' 'orf' ecoli3731 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rarD' 'chloramphenicol resistance' ecoli1511 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1540' 'paral putative regulator protein' ecoli2079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2120' 'orf' ecoli3869 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yijC' 'orf' ecoli2349 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2392' 'putative transport system permease(1st module)' ecoli1421 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1450' 'hypothetical transcriptional regulator yncc lacks the first 19 aa of b1450' ecoli346 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0354' 'nucleoprotein/polynucleotide-associated enzyme' ecoli3281 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfK' 'orf' ecoli2906 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2972' 'paral putative peptidase' Frequency rule on new data: 14/2167 (0.65%) Evaluation on training data (939 items): ecoli113 - 3,5,7 Metabolism of small molecules Energy metabolism, carbon Pyruvate dehydrogenase 'pdhR' 'transcriptional regulator for pyruvate dehydrogenase complex(1st 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: 1/2 (50.00%) Training Frequency class 'Chemotaxis and mobility': 6/939 (0.64%) Training Significance: dev(8.76) ; prob(1.273872E-02) Evaluation on validation data (471 items): ecoli1858 1,1,1 Cell processes Chemotaxis, motility Chemotaxis and mobility 'motA' 'proton conductor component of motor; no effect on switching' ecoli2157 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ccmC' 'ABC superfamily (membrane)heme exporter protein C necessary for incorporation of heme into CcmE (cytochrome c-type biogenesis protein)' Validation Accuracy: 1/2 (50.00%) Validation Frequency class 'Chemotaxis and mobility': 2/471 (0.42%) Validation Significance: dev(10.78) ; prob(8.456507E-03) ------------------ Rule 108: (21/2, lift 35.5) [ss( A ,b),nss( A , B ,a)] = 1 [ss_coil( A ,gt,3),nss_coil( A , B ,gt,6),nss_coil( B , C ,gt,10)] = 1 [ss_coil( A ,gt,6),nss_coil( A , B ,gt,3),nss_coil( B , C ,lteq,3)] = 1 [ss_coil( A ,gt,10),nss_coil( A , B ,gt,1),nss_coil( B , C ,gt,5)] = 1 [ss_beta( A ,gt,1),nss_beta( A , B ,gt,5),nss_beta( B , C ,gt,10)] = 1 [ss_beta( A ,gt,10),nss_beta( A , B ,gt,3),nss_beta( B , C ,gt,3)] = 1 [ss_beta( A ,lteq,5),nss_beta( A , B ,gt,10),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,10),nss_coil( C , D ,gt,3),nss_coil( D , E ,lteq,830)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,gt,1),nss_coil( C , D ,lteq,830),nss_coil( D , E ,gt,10)] = 1 -> class 'MFS family' [0.870] Evaluation on test data (712 items): ecoli818 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b0842' 'transmembrane multidrug/chloramphenicol efflux transporter (2nd module)' ecoli1163 - 3,4,2 Metabolism of small molecules Degradation of small molecules Amino acids 'dadX' 'alanine racemase 2 catabolic' ecoli4016 - 3,5,8 Metabolism of small molecules Energy metabolism, carbon TCA cycle 'fumB' 'fumarase b= fumarate hydratase class i; anaerobic isozyme (2nd 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)' 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: 2/6 (33.33%) Test Frequency class 'MFS family': 14/712 (1.97%) Test Significance: dev(5.53) ; prob(5.502022E-03) Application to new data (2167 items): ecoli2593 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2647' 'orf' 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' ecoli1940 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1978' 'paral putative factor(2nd module)' 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' ecoli2814 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2878' 'paral putative oxidoreductase (2nd module)' ecoli3261 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yheB' 'putative enzyme' ecoli2982 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3048' 'orf' ecoli283 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagX' 'paral putative enzyme' ecoli2462 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2511' 'putative GTP-binding factor(1st module)' ecoli2802 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2866' 'orf' ecoli1287 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1316' 'orf' ecoli1143 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1170' 'orf' ecoli1943 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1981' 'shikimate and dehydroshikimate permease (2nd module)' ecoli1352 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1381' 'orf' Frequency rule on new data: 18/2167 (0.83%) 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)' 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)' ecoli1267 - 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'b1296' 'APC family paral putative amino-acid transport protein' ecoli2631 1,5,21 Cell processes Transport/binding proteins MFS family 'emrB' 'MFS family of transport protein multidrug resistance; probably membrane translocase(1st module)' 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)' 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)' ecoli3405 - 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'rhsB' 'rhsB protein in rhs element' 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: 19/21 (90.48%) Training Frequency class 'MFS family': 23/939 (2.45%) Training Significance: dev(26.10) ; prob(4.942562E-29) Evaluation on validation data (471 items): ecoli4014 - 1,5,16 Cell processes Transport/binding proteins GPH family 'melB' 'GPH family melibiose permease II' ecoli419 1,5,21 Cell processes Transport/binding proteins MFS family 'b0427' 'MFS family transport protein' ecoli3885 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'rpoB' 'RNA polymerase beta subunit' ecoli2637 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'alaS' 'alanyl-tRNA synthetase' 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)' 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)' ecoli1796 1,5,21 Cell processes Transport/binding proteins MFS family 'b1828' 'MFS family of transport protein (2nd module)' ecoli2782 - 1,5,36 Cell processes Transport/binding proteins STP family 'b2845' 'STP family of transport protein' 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)' ecoli3096 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'pnp' 'polynucleotide phosphorylase; member of mRNA degradosome (cytidylate kinase activity)' ecoli1737 1,5,21 Cell processes Transport/binding proteins MFS family 'ydjE' 'MFS family of transport protein (1st module)' Validation Accuracy: 6/12 (50.00%) Validation Frequency class 'MFS family': 14/471 (2.97%) Validation Significance: dev(9.59) ; prob(5.317243E-07) ------------------