Rule 55: (5, lift 26.8) [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,5),nss_coil( C , D ,lteq,830),nss_coil( D , E ,lteq,1)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,streptomyces)] = 1 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 [hom( A ),keyword( A ,transmembrane),classification( A ,rhodobacter)] = 1 -> class 'Global regulatory functions' [0.857] Evaluation on test data (712 items): ecoli2726 6,1,1 Global functions Global regulatory functions Global regulatory functions 'barA' 'sensor module of sensor-regulator activates ompr by phophorylation (2nd module potential phosphoacceptor 665-784)' ecoli3901 - 3,5,4 Metabolism of small molecules Energy metabolism, carbon Fermentation 'hydH' 'sensor kinase for HydG hydrogenase 3 activity(2nd module)' ecoli2037 6,1,1 Global functions Global regulatory functions Global regulatory functions 'baeS' 'suppresses envZ and phoR/creC mutations(2nd module)' ecoli678 6,1,1 Global functions Global regulatory functions Global regulatory functions 'kdpD' 'sensor for high-affinity potassium transport system bifunctional enzyme catalyzing the autophosphorylation by ATP and the dephosphorylation of the corresponding response regulator KdpE(3rd module)' ecoli4006 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'basS' 'sensor protein for basR(2nd module)' Test Accuracy: 3/5 (60.00%) Test Frequency class 'Global regulatory functions': 16/712 (2.25%) Test Significance: dev(8.71) ; prob(1.096894E-04) Application to new data (2167 items): ecoli560 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0570' 'paral putative sensor/kinase in regulatory system' ecoli2419 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yffG' 'paral putative oxidoreductase (2nd module)' ecoli2507 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2556' 'paral putative sensor/kinase in regulatory system' ecoli2960 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3026' 'paral putative sensor/kinase in regulatory system' ecoli1932 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1968' 'paral putative sensor/kinase in regulatory system' Frequency rule on new data: 5/2167 (0.23%) Evaluation on training data (939 items): ecoli3327 6,1,1 Global functions Global regulatory functions Global regulatory functions 'envZ' 'protein histidine kinase/phosphatase sensor for ompR modulates expression of ompF and ompC (sensor)(2nd module)' ecoli1579 6,1,1 Global functions Global regulatory functions Global regulatory functions 'rstB' 'sensor histidine protein kinase (RstA regulator)(2nd module)' ecoli4285 6,1,1 Global functions Global regulatory functions Global regulatory functions 'creC' 'catabolite repression sensor kinase for PhoB; alternative sensor for pho regulon(2nd module)' ecoli3817 6,1,1 Global functions Global regulatory functions Global regulatory functions 'cpxA' 'membrane sensor in 2-component cpxAR signal transduction system(2nd module)' ecoli1102 6,1,1 Global functions Global regulatory functions Global regulatory functions 'phoQ' 'periplasmic sensor protein in two component system with PhoP ligand is Mg+(2nd module)' Training Accuracy: 5/5 (100.00%) Training Frequency class 'Global regulatory functions': 30/939 (3.19%) Training Significance: dev(12.31) ; prob(3.328728E-08) Evaluation on validation data (471 items): ecoli392 6,1,1 Global functions Global regulatory functions Global regulatory functions 'phoR' 'positive and negative sensor protein for pho regulon (and asr gene)(2nd module)' Validation Accuracy: 1/1 (100.00%) Validation Frequency class 'Global regulatory functions': 8/471 (1.70%) Validation Significance: dev(7.61) ; prob(1.698514E-02) ------------------ Rule 53: (3, lift 187.8) [ss_beta( A ,lteq,830),nss_beta( A , B ,lteq,6),nss_beta( B , C ,gt,10)] = 1 [hom( A ),species( A ,pseudomonas_putida)] = 1 [hom( A ),e_val_gt( A ,6e-14),classification( A ,aculeata)] = 1 [hom( A ),e_val_lteq( A ,3e-06),species( A ,streptococcus_mutans)] = 1 -> class 'GPH family' [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)' ecoli3579 1,5,16 Cell processes Transport/binding proteins GPH family 'yicJ' 'GPH family paral putative transport protein' 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 'GPH family': 1/712 (0.14%) Test Significance: dev(15.35) ; prob(4.207568E-03) Application to new data (2167 items): ecoli262 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yagG' 'paral putative transport protein' ecoli2908 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2974' 'putative endoglucanase' Frequency rule on new data: 2/2167 (0.09%) Evaluation on training data (939 items): ecoli3783 1,5,16 Cell processes Transport/binding proteins GPH family 'yihP' 'GPH family paral putative transport protein' ecoli3782 1,5,16 Cell processes Transport/binding proteins GPH family 'b3876' 'GPH family paral putative transport protein (2nd module)' ecoli1586 1,5,16 Cell processes Transport/binding proteins GPH family 'uidB' 'GPH family glucuronide permease' Training Accuracy: 3/3 (100.00%) Training Frequency class 'GPH family': 4/939 (0.43%) Training Significance: dev(26.48) ; prob(7.730066E-08) Evaluation on validation data (471 items): ecoli4014 1,5,16 Cell processes Transport/binding proteins GPH family 'melB' 'GPH family melibiose permease II' Validation Accuracy: 1/1 (100.00%) Validation Frequency class 'GPH family': 1/471 (0.21%) Validation Significance: dev(21.68) ; prob(2.123142E-03) ------------------ Rule 93: (14, lift 40.0) [ss_coil( A ,gt,6),nss_coil( A , B ,lteq,1)] = 0 [ss_coil( A ,lteq,1),nss_coil( A , B ,lteq,830),nss_coil( B , C ,gt,5)] = 0 [hom( A ),psi_iter_gt( A ,5),classification( A ,corynebacteriaceae)] = 0 [hom( A ),species( A ,mycoplasma_pneumoniae),mol_wt_lteq( A ,43194)] = 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)] = 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' ecoli3658 - 1,5,24 Cell processes Transport/binding proteins Membrane-bound ATP synthase 'atpE' 'membrane-bound ATP synthase F0 sector subunit c' 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' ecoli1059 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'yceC' '23S rRNA pseudouridylate 955 2504 2580 synthase' ecoli1067 - 3,2,1 Metabolism of small molecules Biosynthesis of cofactors, carriers Acyl carrier protein (ACP) 'acpP' 'acyl carrier protein' 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' ecoli3116 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplU' '50S ribosomal subunit protein L21' ecoli3656 - 3,4,0 Metabolism of small molecules Degradation of small molecules ATP-proton motive force interconversion 'atpH' 'membrane-bound ATP synthase F1 sector delta-subunit' ecoli3231 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplE' '50S ribosomal subunit protein L5' ecoli23 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsT' '30S ribosomal subunit protein S20' ecoli3219 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsD' '30S ribosomal subunit protein S4' ecoli3652 - 1,5,24 Cell processes Transport/binding proteins Membrane-bound ATP synthase 'atpC' 'membrane-bound ATP synthase F1 sector epsilon-subunit' ecoli3259 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'bfr' 'bacterioferrin an iron storage homoprotein' 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: 11/18 (61.11%) Test Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 23/712 (3.23%) Test Significance: dev(13.89) ; prob(1.030767E-12) Application to new data (2167 items): ecoli3916 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbC' 'orf' ecoli3085 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhbO' 'orf' ecoli499 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'gip' 'glyoxylate-induced protein(2nd module)' ecoli2649 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygaA' 'paral putative regulator protein' ecoli2853 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'ygfD' 'membrane-bound ATP-binding transport protein phosphorylates AO and LAO periplasmic proteins' ecoli3769 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yihG' 'putative endonuclease' ecoli1870 - 1 Cell processes 'yecI' 'ferritin-like protein' Frequency rule on new data: 7/2167 (0.32%) 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): ecoli4035 - 1,7,1 Cell processes Cell division Cell division 'mopB' 'GroES 10 Kd chaperone binds to Hsp60 suppressing its ATPase activity; affects cell division' 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' 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: 7/8 (87.50%) Validation Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 12/471 (2.55%) Validation Significance: dev(15.25) ; prob(5.432555E-11) ------------------ Rule 65: (22/1, lift 37.4) [ss_beta( A ,lteq,830),nss_beta( A , B ,lteq,6),nss_beta( B , C ,gt,10)] = 1 [hom( A ),species( A ,pseudomonas_putida)] = 1 [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 -> class 'MFS family' [0.917] 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)' 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' ecoli2324 1,5,21 Cell processes Transport/binding proteins MFS family 'emrY' 'MFS family of transport protein multidrug resistance protein y (2nd module)' ecoli3587 1,5,21 Cell processes Transport/binding proteins MFS family 'uhpT' 'MFS family of transport protein hexose phosphate transport protein (2nd module)' 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' 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)' 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: 12/16 (75.00%) Test Frequency class 'MFS family': 14/712 (1.97%) Test Significance: dev(21.04) ; prob(5.649800E-18) Application to new data (2167 items): ecoli3780 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihN' 'orf' 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' ecoli1658 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1690' 'paral putative MFS family of transport protein' ecoli4221 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiJ' 'paral putative transport protein (2nd module)' 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)' 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' 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)' ecoli3469 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'yhjX' 'putative resistance protein' 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: 21/22 (95.45%) Training Frequency class 'MFS family': 23/939 (2.45%) Training Significance: dev(28.22) ; prob(3.180205E-33) 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)' ecoli70 1,5,21 Cell processes Transport/binding proteins MFS family 'yabM' 'MFS family of transport protein proton-coupled beta-galactosidase/sugar efflux pump ? role in lactose metabolism (2nd module)' ecoli4168 1,5,21 Cell processes Transport/binding proteins MFS family 'yjhB' 'MFS family of tranport protein (1st module)' 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)' ecoli4005 1,5,21 Cell processes Transport/binding proteins MFS family 'proP' 'MFS family of tranport protein low-affinity constitutive transport system; proline permease II transports proline and betaine under conditions of hyperosmolarity(2nd module)' ecoli3631 1,5,21 Cell processes Transport/binding proteins MFS family 'yidY' 'MFS family of tranport protein (1st mdule)' ecoli1737 1,5,21 Cell processes Transport/binding proteins MFS family 'ydjE' 'MFS family of transport protein (1st module)' Validation Accuracy: 12/15 (80.00%) Validation Frequency class 'MFS family': 14/471 (2.97%) Validation Significance: dev(17.57) ; prob(1.976891E-16) ------------------ Rule 6: (14/1, lift 41.1) [ss_coil( A ,gt,3),nss_coil( A , B ,gt,5),nss_coil( B , C ,gt,5)] = 1 [ss_coil( A ,lteq,5),nss_coil( A , B ,lteq,3),nss_coil( B , C ,lteq,3)] = 1 [ss_beta( A ,gt,1),nss_beta( A , B ,gt,5),nss_beta( B , C ,lteq,5)] = 1 [ss_beta( A ,lteq,3),nss_beta( A , B ,lteq,5),nss_beta( B , C ,gt,5)] = 0 [ss_beta( A ,lteq,3),nss_beta( A , B ,gt,5),nss_beta( B , C ,gt,1)] = 0 [hom( A ),classification( A ,zymomonas)] = 0 [hom( A ),species( A ,cyanophora_paradoxa),mol_wt_lteq( A ,32892)] = 0 [hom( A ),mol_wt_gt( A ,55220),keyword( A ,inner_membrane)] = 0 [hom( A ),keyword( A ,membrane),classification( A ,bacillus1)] = 1 -> class 'ABC superfamily (peri_perm)' [0.875] Evaluation on test data (712 items): 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' ecoli90 - 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'murG' 'UDP-N-acetylglucosamine:N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase' ecoli4144 - 3,1,2 Metabolism of small molecules Amino acid biosynthesis Arginine 'argI' 'ornithine carbamoyltransferase 1(1st module)' ecoli3361 - 3,3,3 Metabolism of small molecules Central intermediary metabolism Entner-Douderoff 'gntR' 'transcriptional repressor in GNT-I (gluconate utilization system )' ecoli2557 - 1,2,1 Cell processes Chromosome replication Chromosome replication 'ffh' '4.5S-RNP protein (1st module GTPase activity)' Test Accuracy: 0/6 (0.00%) Test Frequency class 'ABC superfamily (peri_perm)': 9/712 (1.26%) Test Significance: dev(-0.28) ; prob(1.000000E+00) Application to new data (2167 items): ecoli1291 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1320' 'paral putative regulator/periplasmic binding 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' ecoli1403 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1432' 'putative virulence protein' ecoli2009 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yefD' 'PUTATIVE GLYCOSYL TRANSFERASE in colanic acid biosynthesis (2nd module)' Frequency rule on new data: 5/2167 (0.23%) Evaluation on training data (939 items): ecoli1590 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'malI' 'repressor of malX and Y genes' 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)' 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' 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)' 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: 13/14 (92.86%) Training Frequency class 'ABC superfamily (peri_perm)': 20/939 (2.13%) Training Significance: dev(23.51) ; prob(2.547943E-21) 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)' ecoli3383 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'livJ' 'high-affinity amino acid transport system; periplasmic binding protein' ecoli1411 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b1440' 'ABC superfamily (peri_perm) ABC superfamily of transport protein peri_perm subunit' ecoli3823 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'sbp' 'periplasmic sulfate-binding protein' Validation Accuracy: 3/4 (75.00%) Validation Frequency class 'ABC superfamily (peri_perm)': 7/471 (1.49%) Validation Significance: dev(12.15) ; prob(1.293566E-05) ------------------ Rule 105: (5/1, lift 30.5) [ss_coil( A ,lteq,3),nss_coil( A , B ,lteq,5)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,10),nss_coil( B , C ,lteq,10)] = 1 [hom( A ),e_val_gt( A ,2e-37),species( A ,streptococcus_agalactiae)] = 0 [hom( A ),species( A ,mycoplasma_pneumoniae),mol_wt_lteq( A ,32892)] = 0 [hom( A ),species( A ,drosophila_melanogaster__fruit_fly_),keyword( A ,repeat)] = 1 [hom( A ),keyword( A ,transmembrane),classification( A ,rhodobacter)] = 0 -> class 'Transposon-related functions' [0.714] Evaluation on test data (712 items): ecoli1375 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'tra8_2' 'transposase 2 for IS30' ecoli2182 - 3,4,4 Metabolism of small molecules Degradation of small molecules Fatty acids 'b2224' 'acetyl-CoA acetyltransferase' ecoli4172 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi91' 'IS911 protein' ecoli4173 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'tra8_3' 'transposase for IS30' ecoli22 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_1' 'IS1 protein InsA' ecoli790 - 4,1,3 Structural elements Cell envelop Outer membrane constituents 'ompX' 'outer membrane protease receptor for phage OX2' Test Accuracy: 4/6 (66.67%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(11.86) ; prob(1.618706E-06) 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' ecoli2879 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'sprT' 'orf' ecoli2208 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2250' 'orf' ecoli2718 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2778' 'orf' 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' 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' ecoli220 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yafL' 'orf' ecoli3147 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcE' 'orf' ecoli2581 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2635' 'orf' ecoli2058 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2099' 'orf' Frequency rule on new data: 11/2167 (0.51%) Evaluation on training data (939 items): ecoli248 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'tra8_1' 'transposase1 for IS30' ecoli1956 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'yi21_3' 'IS2 protein' ecoli267 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_3' 'IS1 protein InsA' ecoli1678 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'btuE' 'not required for vitamin B12 transport perhaps periplasmic protein' ecoli1862 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_5' 'IS1 protein InsA' Training Accuracy: 4/5 (80.00%) Training Frequency class 'Transposon-related functions': 22/939 (2.34%) Training Significance: dev(11.48) ; prob(1.478363E-06) 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' ecoli514 - 3,7,1 Metabolism of small molecules Nucleotide biosynthesis Purine ribonucleotide biosynthesis 'purE' 'phosphoribosylaminoimidazole carboxylase = AIR carboxylase catalytic subunit' ecoli3367 5,1,4 Extrachromosomal Laterally acquirred elements Transposon-related functions 'insA_6' 'IS1 protein InsA' Validation Accuracy: 3/4 (75.00%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(8.48) ; prob(1.019240E-04) ------------------ Rule 4: (5/1, lift 19.2) [ss_alpha( A ,lteq,10),nss_alpha( A , B ,lteq,10)] = 1 [ss_beta( A ,gt,3),nss_beta( A , B ,gt,1)] = 0 [ss_coil( A ,lteq,830),nss_coil( A , B ,lteq,1)] = 1 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 [hom( A ),keyword( A ,transmembrane),classification( A ,rhodobacter)] = 1 -> class 'ABC superfamily (membrane)' [0.714] Evaluation on test data (712 items): ecoli3833 - 1,5,22 Cell processes Transport/binding proteins MIP family 'glpF' 'MIP family facilitated diffusion of glycerol' 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' ecoli1436 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'narV' 'nitrate reductase 2 gamma subunit' ecoli2364 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'cysZ' 'required for sulfate transport' ecoli1808 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'b1840' 'putative resistance protein' ecoli1457 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1486' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2266 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisQ' 'ABC superfamily (membrane)histidine transport system' ecoli3258 - 2,1,4 Macromolecule metabolism Macromolecule degradation Degradation of proteins, peptides, glyco 'hofD' 'leader peptidase integral membrane protein cryptic gene integral membrane protein' ecoli3005 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'air' 'aerotaxis sensor receptor flavoprotein(2nd module)' Test Accuracy: 4/10 (40.00%) Test Frequency class 'ABC superfamily (membrane)': 26/712 (3.65%) Test Significance: dev(6.13) ; prob(3.127397E-04) Application to new data (2167 items): ecoli3250 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofF' 'orf' ecoli2095 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yohD' 'orf' ecoli1600 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1630' 'orf' ecoli1638 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1670' 'orf' ecoli2993 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiH' 'orf' ecoli2079 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2120' 'orf' ecoli65 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yabI' 'orf(1st module)' ecoli2087 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehW' 'paral putative membrane component of transport system' ecoli3568 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yicG' 'orf' ecoli2216 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2258' 'paral putative ABC superfamily transport protein' ecoli106 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofC' 'orf' Frequency rule on new data: 11/2167 (0.51%) 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' ecoli1951 - 3,2,3 Metabolism of small molecules Biosynthesis of cofactors, carriers Cobalamin 'cobS' 'cobalamin 5-phosphate synthase(1st module)' 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)' 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: 4/5 (80.00%) Training Frequency class 'ABC superfamily (membrane)': 35/939 (3.73%) Training Significance: dev(9.00) ; prob(9.363379E-06) Evaluation on validation data (471 items): ecoli1200 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'narI' 'nitrate reductase 1 cytochrome b(NR) gamma subunit' ecoli1282 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1311' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli838 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'artQ' 'ABC superfamily (membrane) membrane component of 3rd arginine ABC transport system' ecoli579 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fepG' 'ABC superfamily (membrane) ferric enterobactin transport protein' ecoli4177 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fecD' 'ABC superfamily (membrane) membrane component of citrate-dependent ABC transport system of iron' 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)' ecoli2433 - 3,5,2 Metabolism of small molecules Energy metabolism, carbon Anaerobic respiration 'b2482' 'hydrogenase 4 membrane subunit(1st module)' Validation Accuracy: 5/7 (71.43%) Validation Frequency class 'ABC superfamily (membrane)': 19/471 (4.03%) Validation Significance: dev(9.06) ; prob(2.065941E-06) ------------------ Rule 2: (25/2, lift 34.8) [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)' [0.889] Evaluation on test data (712 items): ecoli3646 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'pstB' 'ABC superfamily (atp_bind) ATP-binding component of high-affinity phosphate-specific ABC transport system' 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' ecoli151 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fhuC' 'ABC superfamily (atp_bind) ATP-binding component of hydroxymate-dependent iron transport' 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)' ecoli4176 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'fecE' 'ABC superfamily (atp_bind) ATP-binding component of citrate-dependent iron(III) transport protein' 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' ecoli796 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b0820' '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' ecoli486 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'ybbA' 'ABC superfamily (atp_bind) putative' 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: 26/30 (86.67%) Test Frequency class 'ABC superfamily (atp_bind)': 27/712 (3.79%) Test Significance: dev(23.76) ; prob(2.655764E-33) Application to new data (2167 items): ecoli2585 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2639' 'putative pump protein' 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' ecoli2088 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehX' 'paral putative ATP-binding component of transport system' ecoli103 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yacE' 'putative DNA repair protein' 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: 10/2167 (0.46%) Evaluation on training data (939 items): ecoli855 - 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0879' 'ABC superfamily (atp&memb) paral putative ATP-binding component of transport system' 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' ecoli380 - 3,1,5 Metabolism of small molecules Amino acid biosynthesis Chorismate 'aroL' 'shikimate kinase II' 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: 23/25 (92.00%) Training Frequency class 'ABC superfamily (atp_bind)': 24/939 (2.56%) Training Significance: dev(28.34) ; prob(6.747322E-35) Evaluation on validation data (471 items): ecoli3929 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'malK' 'ABC superfamily (atp_bind) ATP-binding component of transport system for maltose phenotypic repressor of mal operon(1st module)' 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' ecoli1289 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'b1318' 'ABC superfamily (atp_bind) paral putative ATP-binding component of transport system' ecoli2271 - 5,1,1 Extrachromosomal Laterally acquirred elements Colicin-related functions 'cvpA' 'membrane protein required for colicin V production' ecoli3464 1,5,1 Cell processes Transport/binding proteins ABC superfamily (atp_bind) 'dppD' 'ABC superfamily (atp_bind) ATP-binding component of dipeptide tABCransport system(2nd module)' 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: 15/21 (71.43%) Validation Frequency class 'ABC superfamily (atp_bind)': 17/471 (3.61%) Validation Significance: dev(16.66) ; prob(1.000326E-17) ------------------ Rule 94: (11/1, lift 36.1) [ss_beta( A ,lteq,1),nss_beta( A , B ,lteq,6)] = 0 [ss_beta( A ,gt,6),nss_beta( A , B ,gt,1)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,5),nss_coil( B , C ,gt,10)] = 0 [hom( A ),e_val_gt( A ,2e-37),species( A ,streptococcus_agalactiae)] = 0 [hom( A ),species( A ,mycoplasma_pneumoniae),mol_wt_lteq( A ,32892)] = 1 [hom( A ),species( A ,azotobacter_vinelandii),mol_wt_lteq( A ,55220)] = 0 [hom( A ),mol_wt_gt( A ,55220),keyword( A ,inner_membrane)] = 0 -> class 'Ribosomal proteins - synthesis modificationRiboso' [0.846] Evaluation on test data (712 items): ecoli3658 - 1,5,24 Cell processes Transport/binding proteins Membrane-bound ATP synthase 'atpE' 'membrane-bound ATP synthase F0 sector subunit c' ecoli2518 - 2,1,2 Macromolecule metabolism Macromolecule degradation Degradation of RNA 'rnc' 'RNase III ds RNA C-terminal domain binds dsRNA N-terminal phosphorylation and conserved asp and glutamic acid residues' ecoli4213 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'uxuR' 'regulator for uxu operon' ecoli2914 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'glcC' 'transcriptional activator for glc operon(1st module)' 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)' ecoli4092 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsR' '30S ribosomal subunit protein S18' ecoli1887 - 4,1,5 Structural elements Cell envelop Surface structures 'fliA' 'regulation of late gene expression; sigma transcription factor F for class 3a and 3b operons' ecoli3842 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmE' '50S ribosomal subunit protein L31' ecoli23 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsT' '30S ribosomal subunit protein S20' ecoli3219 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsD' '30S ribosomal subunit protein S4' ecoli3323 - 1,6,1 Cell processes Adaptation Adaptations, atypical conditions 'yrfH' 'heat shock protein 15 DNA/RNA binding' ecoli2118 - 2,1,1 Macromolecule metabolism Macromolecule degradation Degradation of DNA 'nfo' 'endonuclease IV' Test Accuracy: 4/12 (33.33%) Test Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 23/712 (3.23%) Test Significance: dev(5.90) ; prob(4.375119E-04) Application to new data (2167 items): ecoli2422 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yffB' 'orf' ecoli81 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yabB' 'orf' ecoli1008 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1035' 'paral putative oxidoreductase component' ecoli4264 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjjV' 'orf(1st module)' ecoli3616 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidW' 'putative regulator protein' ecoli4051 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjeO' 'orf' ecoli2249 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2291' 'putative alpha helix protein' ecoli1511 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1540' 'paral putative regulator protein' ecoli2993 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygiH' 'orf' ecoli3296 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfP' 'orf' 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' ecoli2567 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'smpB' 'orf; small protein B' ecoli2584 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2638' 'orf' Frequency rule on new data: 13/2167 (0.60%) Evaluation on training data (939 items): ecoli3559 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmB' '50S ribosomal subunit protein L28' ecoli3217 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplQ' '50S ribosomal subunit protein L17' ecoli3883 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplJ' '50S ribosomal subunit protein L10' ecoli1684 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplT' '50S ribosomal subunit protein L20 and regulator' ecoli3230 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsN' '30S ribosomal subunit protein S14' ecoli3235 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmC' '50S ribosomal subunit protein L29' ecoli3224 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rplO' '50S ribosomal subunit protein L15' ecoli3624 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmH' '50S ribosomal subunit protein L34' ecoli1062 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmF' '50S ribosomal subunit protein L32' ecoli544 - 5,1,2 Extrachromosomal Laterally acquirred elements Phage-related functions and prophages 'b0554' 'homolog of Rz of phage PA-2' ecoli3222 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmJ' '50S ribosomal subunit protein X' Training Accuracy: 10/11 (90.91%) Training Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 22/939 (2.34%) Training Significance: dev(19.42) ; prob(5.365541E-16) Evaluation on validation data (471 items): ecoli1685 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpmI' '50S ribosomal subunit protein A' ecoli2618 - 3,2,15 Metabolism of small molecules Biosynthesis of cofactors, carriers Thioredoxin, glutaredoxin, glutathione 'b2673' 'glutaredoxin-like protein; hydrogen donor' ecoli3097 4,2,2 Structural elements Ribosome constituents Ribosomal proteins - synthesis, modificationRiboso 'rpsO' '30S ribosomal subunit protein S15' Validation Accuracy: 2/3 (66.67%) Validation Frequency class 'Ribosomal proteins - synthesis modificationRiboso': 12/471 (2.55%) Validation Significance: dev(7.05) ; prob(1.897727E-03) ------------------ Rule 104: (3, lift 34.1) [hom( A ),classification( A ,chordopoxvirinae)] = 0 [hom( A ),classification( A ,zymomonas)] = 0 [hom( A ),e_val_gt( A ,2e-37),species( A ,streptococcus_agalactiae)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,eurotiales)] = 0 [hom( A ),psi_iter_lteq( A ,7),classification( A ,ciliophora)] = 1 [hom( A ),psi_iter_lteq( A ,7),species( A ,methanobacterium_thermoautotrophicum)] = 0 [hom( A ),species( A ,mycoplasma_pneumoniae),mol_wt_lteq( A ,32892)] = 0 [hom( A ),keyword( A ,transmembrane),classification( A ,rhodobacter)] = 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' 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' ecoli2246 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'nuoA' 'NADH dehydrogenase I chain A' ecoli3106 - 3,3,7 Metabolism of small molecules Central intermediary metabolism Misc. glucose metabolism 'mrsA' 'putative phosphoglucomutases and phosphomannomutases(1st module)' 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' Test Accuracy: 1/6 (16.67%) Test Frequency class 'Transposon-related functions': 13/712 (1.83%) Test Significance: dev(2.72) ; prob(1.046701E-01) Application to new data (2167 items): ecoli2550 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2603' 'orf' 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' ecoli1376 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydbA_2' 'split orf fragment 2 (2nd module)' ecoli1481 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeK' 'orf' ecoli2187 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2229' 'orf' ecoli2307 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2350' 'orf' ecoli3772 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yihI' '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' ecoli896 - 3,3,16 Metabolism of small molecules Central intermediary metabolism S-adenosyl methionine 'smtA' 'S-adenosylmethionine-dependent methyltransferase(1st module)' Validation Accuracy: 2/3 (66.67%) Validation Frequency class 'Transposon-related functions': 14/471 (2.97%) Validation Significance: dev(6.50) ; prob(2.571762E-03) ------------------ Rule 3: (27, lift 25.9) [ss_coil( A ,gt,6),nss_coil( A , B ,lteq,5)] = 1 [ss_beta( A ,lteq,830),nss_beta( A , B ,lteq,6),nss_beta( B , C ,gt,10)] = 0 [ss_coil( A ,gt,1),nss_coil( A , B ,lteq,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,lteq,1)] = 0 [hom( A ),classification( A ,ascaridida)] = 1 [hom( A ),species( A ,clostridium_acetobutylicum)] = 0 [hom( A ),e_val_lteq( A ,3e-06),classification( A ,enterococcaceae)] = 0 [hom( A ),e_val_lteq( A ,3e-06),classification( A ,zymomonas_group)] = 0 [hom( A ),e_val_lteq( A ,6e-14),classification( A ,ralstonia)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 1 [hom( A ),species( A ,lactococcus_lactis__subsp__lactis___streptococcus_lactis_),keyword( A ,transmembrane)] = 1 [hom( A ),mol_wt_lteq( A ,55220),classification( A ,rhizobiaceae)] = 1 -> class 'ABC superfamily (membrane)' [0.966] Evaluation on test data (712 items): ecoli456 - 1,5,29 Cell processes Transport/binding proteins Outer membrane channel 'b0465' 'component of the MscS mechanosensitive channel(3rd module)' ecoli1485 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1514' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system' ecoli1400 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'tehA' 'tellurite resistance; K+-tellurite ethidium and proflavin transport; membrane protein' ecoli3374 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpE' 'ABC superfamily (membrane)sn-glycerol 3-phosphate transport system integral membrane protein(1st module)' ecoli4120 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ytfT' 'ABC superfamily (membrane)paral putative membrane component' ecoli1467 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yddA' 'ABC superfamily (atp_bind) paral putative ATP-binding module (2nd module)' ecoli786 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'glnP' 'glutamine high-affinity transport system; membrane component(1st module)' ecoli1097 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potC' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli3604 - 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'glvC' 'PTS family arbutin-like IIC component' ecoli67 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yabK' 'ABC superfamily (membrane) membrane component of thiamine ABC transport system(1st module)' ecoli198 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yaeE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2497 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b2546' 'ABC superfamily (membrane)paral putative membrane component of ABC transport system (2nd module)' ecoli768 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0792' 'ABC superfamily (membrane)putative membrane component of ABC transport system(2nd module)' ecoli1022 - 1,6,2 Cell processes Adaptation Osmotic adaptation 'mdoH' 'membrane glycosyltransferase; synthesis of membrane-derived oligosaccharide (MDO)/synthesis of OPGs (osmoregulated periplasmic glucans)(2nd module)' ecoli420 - 3,5,1 Metabolism of small molecules Energy metabolism, carbon Aerobic respiration 'cyoE' 'protohaeme IX farnesyltransferase (haeme O biosynthesis)' ecoli807 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0831' 'paral putative membrane component of transport system' Test Accuracy: 10/16 (62.50%) Test Frequency class 'ABC superfamily (membrane)': 26/712 (3.65%) Test Significance: dev(12.55) ; prob(2.757716E-11) Application to new data (2167 items): ecoli3170 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhcP' 'orf' ecoli3028 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b3095' 'orf' ecoli1766 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b1798' 'paral putative transport protein' ecoli1504 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeD' 'orf' ecoli3731 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rarD' 'chloramphenicol resistance' ecoli502 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0511' 'orf' ecoli3083 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yraQ' 'orf' ecoli3126 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yrbG' 'orf' ecoli320 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0328' 'paral putative transport protein' ecoli1486 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1515' 'paral putative membrane component of ABC transport system' ecoli7 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yaaJ' 'putative inner membrane transport protein' ecoli2275 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'dedA' '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)' Frequency rule on new data: 13/2167 (0.60%) Evaluation on training data (939 items): ecoli740 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'modB' 'ABC superfamily (membrane) membrane component of molybdate ABC transport system (2nd module)' ecoli128 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yadH' 'ABC superfamily (membrane) paral putative ABC superfamily (membrane)' ecoli1263 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapC' 'ABC superfamily (membrane) membrane component of peptide ABC transport system(2nd module)' ecoli1723 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1755' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3647 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstA' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli2265 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'hisM' 'ABC superfamily (membrane)histidine transport membrane protein m (2nd module transport function )' ecoli153 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'fhuB' 'ABC superfamily (membrane) split gene C-term module hydroxamate-dependent iron uptake (2nd module iron uptake )' ecoli1264 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sapB' 'ABC superfamily (membrane) membrane component of peptide ABC transport system' ecoli3199 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhdX' 'ABC superfamily (membrane)paral putative membrane component of transport system' ecoli369 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'sbmA' 'ABC superfamily (atp&memb) sensitivity to microcin B17; methylmalonyl-CoA mutase (mcm); ATP-binding and membrane component' ecoli3466 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'dppB' 'ABC superfamily (membrane) membrane component of dipeptide ABC transport system; permease protein 1(2nd module)' ecoli3671 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'rbsC' 'ABC superfamily (membrane) ABC superfamily of transport protein D-ribose high-affinity ABC transport system(1st module ATP-binding subunit)' ecoli3379 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'livM' 'ABC superfamily (membrane) membrane component of high-affinity branched-chain amino acid ABC transport system (2nd module)' ecoli4121 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yjfF' 'ABC superfamily (membrane) ABC superfamily of transport protein (1st module membrance component)' ecoli3648 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'pstC' 'ABC superfamily (membrane) membrane component of high-affinity phosphate-specific ABC transport system (2nd module)' ecoli833 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potI' 'ABC superfamily (membrane) membrane component of putrescine ABC transport system(2nd module)' ecoli1414 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1443' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli862 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cydD' 'ABC superfamily (atp&memb) ATP-binding and membrane components of cytochrome-related ABC transport Zn sensitive(2nd module)' ecoli1098 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'potB' 'ABC superfamily (membrane) membrane component of spermidine/putrescine ABC transport system(2nd module)' ecoli2138 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yejE' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli2375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'cysU' 'ABC superfamily (membrane) membrane component of sulfate thiosulfate ABC transport system (2nd module)' ecoli1283 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b1312' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3408 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yhhJ' 'ABC superfamily (membrane)paral putative transport system membrane (2nd module)' ecoli1215 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'oppB' 'ABC superfamily (membrane) membrane component of oligopeptide ABC transport system(2nd module)' ecoli2107 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'mglC' 'ABC superfamily (membrane) membrane component of methyl-galactoside ABC transport system and galactose taxis(1st module)' ecoli1679 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'btuC' 'ABC superfamily (membrane) membrane component of vitamin B12 ABC transport system' ecoli359 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0367' 'ABC superfamily (membrane) membrane component of taurine ABC transport system' Training Accuracy: 27/27 (100.00%) Training Frequency class 'ABC superfamily (membrane)': 35/939 (3.73%) Training Significance: dev(26.41) ; prob(2.678343E-39) Evaluation on validation data (471 items): ecoli837 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'artM' 'arginine 3rd transport system permease protein' ecoli1883 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yecC' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3521 - 1,5,37 Cell processes Transport/binding proteins Sugar-specific PTS system 'mtlA' 'Sugar Specific PTS family mannitol-specific enzyme IIABC components (3rd module eii a domain phosphoryl by p-hpr 491-637)' ecoli3416 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'pitA' 'low-affinity phosphate transport' ecoli3926 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'malG' 'ABC superfamily (membrane) membrane component of maltose ABC transport system (2nd module)' ecoli3375 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'ugpA' 'ABC superfamily (membrane) sn-glycerol 3-phosphate integral membrane protein ABC transport system' ecoli2623 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'proW' 'ABC superfamily (membrane) membrane component of high-affinity ABC transport system for glycine betaine and proline (2nd module)' ecoli2089 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'yehY' 'ABC superfamily (membrane) paral putative membrane component of transport system' ecoli3490 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'xylH' 'ABC superfamily (membrane)d-xylose transport permease (2nd module might interact with atp hydrolysing subunit )' ecoli1867 - 1,5,23 Cell processes Transport/binding proteins Mechanism not stated 'b1899' 'split high-affinity L-arabinose transport system; membrane protein fragment 1' 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)' ecoli2280 - 1,5,21 Cell processes Transport/binding proteins MFS family 'b2322' 'MFS family of transport protein paral putative (2nd module)' ecoli909 1,5,2 Cell processes Transport/binding proteins ABC superfamily (membrane) 'b0934' 'ABC superfamily (membrane) probable membrane component of transport system' Validation Accuracy: 7/13 (53.85%) Validation Frequency class 'ABC superfamily (membrane)': 19/471 (4.03%) Validation Significance: dev(9.13) ; prob(2.329975E-07) ------------------ Rule 73: (4/1, lift 39.1) [ss_beta( A ,gt,10)] = 0 [ss_alpha( A ,lteq,6),nss_alpha( A , B ,lteq,1)] = 0 [ss_beta( A ,lteq,3),nss_beta( A , B ,lteq,5),nss_beta( B , C ,gt,5)] = 1 [hom( A ),e_val_gt( A ,2e-37),species( A ,streptococcus_agalactiae)] = 0 [hom( A ),e_val_lteq( A ,2e-37),classification( A ,eurotiales)] = 0 [hom( A ),mol_wt_gt( A ,55220),keyword( A ,inner_membrane)] = 0 [hom( A ),keyword( A ,membrane),classification( A ,bacillus1)] = 1 -> class 'Murein sacculus peptidoglycan' [0.667] Evaluation on test data (712 items): ecoli4059 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'amiB' 'N-acetylmuramoyl-l-alanine amidase II; a murein hydrolase(2nd module)' ecoli1059 - 2,2,1 Macromolecule metabolism Macromolecule synthesis, modification Amino acyl tRNA syn; tRNA modification 'yceC' '23S rRNA pseudouridylate 955 2504 2580 synthase' ecoli815 - 1,7,1 Cell processes Cell division Cell division 'dacC' 'D-alanyl-D-alanine carboxypeptidase; penicillin-binding protein 6; level of enzyme affects cell division(1st module)' ecoli149 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'mrcB' 'peptidoglycan synthetase; penicillin-binding protein 1b (3rd module transpeptidase)' ecoli2527 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'srmB' 'ATP-dependent RNA helicase (2nd module)' ecoli4131 - 1,6,2 Cell processes Adaptation Osmotic adaptation 'treR' 'repressor of treABC' Test Accuracy: 2/6 (33.33%) Test Frequency class 'Murein sacculus peptidoglycan': 8/712 (1.12%) Test Significance: dev(7.49) ; prob(1.837673E-03) Application to new data (2167 items): ecoli3694 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rhlB' 'paral putative helicase' ecoli590 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0600' 'paral putative regulator protein' ecoli1410 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1439' 'multimodular; putative ATP-binding component of a transport system; also regulator(1st module)' ecoli3063 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'agaR' 'paral putative transcriptional regulator(2nd module)' ecoli2590 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2644' 'orf' ecoli4229 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiR' 'paral putative regulator protein' ecoli368 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yaiH' 'paral putative enzyme' ecoli1776 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1808' 'paral putative (SOS) repair enzyme' Frequency rule on new data: 8/2167 (0.37%) Evaluation on training data (939 items): ecoli2386 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'amiA' 'N-acetylmuramoyl-l-alanine amidase I' ecoli3319 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'mrcA' 'peptidoglycan synthetase (penicillin-binding protein 1a (transpeptidase) (2nd module)' ecoli2093 4,1,2 Structural elements Cell envelop Murein sacculus, peptidoglycan 'pbpG' 'paral putative carboxypeptidase penicillin-binding protein 7' ecoli4043 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'ampC' 'beta-lactamase; penicillin resistance' Training Accuracy: 3/4 (75.00%) Training Frequency class 'Murein sacculus peptidoglycan': 16/939 (1.70%) Training Significance: dev(11.33) ; prob(1.953607E-05) 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)' ecoli625 - 1,7,1 Cell processes Cell division Cell division 'mrdA' 'cell elongation e phase; peptidoglycan synthetase; penicillin-binding protein 2(2nd module)' Validation Accuracy: 1/2 (50.00%) Validation Frequency class 'Murein sacculus peptidoglycan': 6/471 (1.27%) Validation Significance: dev(6.14) ; prob(2.515315E-02) ------------------ Rule 101: (4, lift 30.1) [ss_beta( A ,lteq,1),nss_beta( A , B ,gt,1)] = 1 [hom( A ),classification( A ,zymomonas)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 0 [hom( A ),mol_wt_gt( A ,55220),keyword( A ,inner_membrane)] = 1 [hom( A ),mol_wt_gt( A ,43194),classification( A ,shigella)] = 1 [hom( A ),keyword( A ,transmembrane),classification( A ,rhodobacter)] = 0 -> class 'Surface structures' [0.833] Evaluation on test data (712 items): ecoli222 4,1,5 Structural elements Cell envelop Surface structures 'fhiA' 'flagellar biosynthesis paral putative transport protein' ecoli454 - 1,4,3 Cell processes Protection responses Drug/analog sensitivity 'acrA' 'acridine efflux pump(1st module)' ecoli464 - 1,3,1 Cell processes Folding and ushering proteins Chaperones 'htpG' 'chaperone Hsp90 heat shock protein C 62.5' ecoli2673 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'mutS' 'methyl-directed mismatch repair(2nd module)' Test Accuracy: 1/4 (25.00%) Test Frequency class 'Surface structures': 22/712 (3.09%) Test Significance: dev(2.53) ; prob(1.179842E-01) Application to new data (2167 items): ecoli2068 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yehB' 'paral putative outer membrane protein (2nd module)' ecoli3519 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yibH' 'paral putative membrane protein' ecoli534 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0544' 'orf' ecoli3932 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjbI' 'orf' ecoli1803 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1835' 'paral putative rRNA methyltransferase (2nd module)' 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' ecoli916 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0941' 'paral putative fimbrial-like protein' ecoli701 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0718' 'paral putative outer membrane protein (2nd module)' ecoli1422 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1451' 'paral putative outer membrane receptor' ecoli2486 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'csiE' 'stationary phase inducible protein' ecoli1476 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1505' 'paral putative outer membrane protein (2nd module)' ecoli4143 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yjgL' 'orf' ecoli1225 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciB' 'orf' ecoli1824 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yebA' 'orf(1st module)' ecoli3314 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'hofQ' 'orf (2nd module)' ecoli3436 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhiU' 'paral putative membrane protein' Frequency rule on new data: 17/2167 (0.78%) 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)' ecoli1847 4,1,5 Structural elements Cell envelop Surface structures 'flhA' 'flagellar biosynthesis; possible export of flagellar proteins(2nd module)' ecoli1906 4,1,5 Structural elements Cell envelop Surface structures 'fliI' 'flagellum-specific ATP synthase(2nd module)' 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): ecoli3885 - 2,2,11 Macromolecule metabolism Macromolecule synthesis, modification RNA synthesis, modification, DNA transcription 'rpoB' 'RNA polymerase beta subunit' 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: 1/2 (50.00%) Validation Frequency class 'Surface structures': 12/471 (2.55%) Validation Significance: dev(4.26) ; prob(4.965719E-02) ------------------ Rule 54: (6, lift 27.4) [ss_coil( A ,gt,3),nss_coil( A , B ,lteq,6),nss_coil( B , C ,gt,6)] = 1 [ss_coil( A ,lteq,3),nss_coil( A , B ,lteq,10),nss_coil( B , C ,gt,6)] = 1 [ss_coil( A ,gt,1),nss_coil( A , B ,gt,3),nss_coil( B , C ,gt,5),nss_coil( C , D ,lteq,6),nss_coil( D , E ,gt,3)] = 0 [hom( A ),species( A ,mycoplasma_pneumoniae),mol_wt_lteq( A ,32892)] = 0 [hom( A ),species( A ,cricetulus_griseus__chinese_hamster_),mol_wt_lteq( A ,77359)] = 0 [hom( A ),mol_wt_gt( A ,55220),keyword( A ,inner_membrane)] = 1 [hom( A ),keyword( A ,transmembrane),classification( A ,rhodobacter)] = 0 -> class 'Global regulatory functions' [0.875] Evaluation on test data (712 items): ecoli2120 - 1,5,7 Cell processes Transport/binding proteins CNT family 'yeiJ' 'CNT family of transport protein' ecoli357 - 1,5,3 Cell processes Transport/binding proteins ABC superfamily (peri_perm) 'b0365' 'ABC superfamily (peri_perm) taurine transport system periplasmic protein' ecoli2223 - 3,2,8 Metabolism of small molecules Biosynthesis of cofactors, carriers Menaquinone, ubiquinone 'menF' 'isochorismate hydroxymutase 2/isochorismate synthase menaquinone biosynthesis' ecoli2851 - 2,2,3 Macromolecule metabolism Macromolecule synthesis, modification DNA - replication, repair, restraction/modification 'iciA' 'replication initiation inhibitor binds to 13-mers at oriC(1st module)' ecoli1364 - 3,4,3 Metabolism of small molecules Degradation of small molecules Carbon compounds 'b1393' 'phenylacetic acid degradation protein probable enoyl-CoA hydratase-isomerase' ecoli2123 - 1,5,7 Cell processes Transport/binding proteins CNT family 'yeiM' 'CNT family of transport protein' Test Accuracy: 0/6 (0.00%) Test Frequency class 'Global regulatory functions': 16/712 (2.25%) Test Significance: dev(-0.37) ; prob(1.000000E+00) Application to new data (2167 items): ecoli2859 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yggB' 'involved in stability of MscS mechanosensitive channel paral putative transport protein' ecoli1933 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1969' 'paral putative regulator protein' ecoli2761 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ygdB' 'orf' ecoli2326 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'evgA' 'multicopy on plasmid in envZ-deleted strain induces ompC expression(1st module)' ecoli2959 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b3025' 'paral putative regulator protein' ecoli1187 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ychA' 'orf' ecoli4216 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yjiE' 'paral putative regulator' ecoli1565 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1595' 'paral putative regulator' ecoli3443 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yhjB' 'putative regulator' ecoli562 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b0572' 'orf' ecoli1500 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'ydeB' 'orf' ecoli1013 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'csgD' 'paral putative regulator protein' ecoli1578 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'rstA' 'response transcriptional regulatory protein (rstb sensor) (2nd module)' ecoli55 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yabH' 'DnaJ like protein chaperone' ecoli1225 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yciB' 'orf' ecoli2769 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2832' 'putative transport protein' ecoli1614 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b1644' 'paral putative membrane protein' ecoli3499 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yiaM' 'orf' ecoli3300 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yhfT' 'orf (2nd module)' Frequency rule on new data: 19/2167 (0.88%) Evaluation on training data (939 items): ecoli2038 6,1,1 Global functions Global regulatory functions Global regulatory functions 'baeR' 'suppresses envZ and phoR/creC mutations(1st module)' ecoli3867 6,1,1 Global functions Global regulatory functions Global regulatory functions 'oxyR' 'bifunctional regulatory protein sensor for oxidative stress(1st module)' ecoli1103 6,1,1 Global functions Global regulatory functions Global regulatory functions 'phoP' 'regulatory protein in two-component system with PhoQ transcribes genes expressed under low Mg+ concentration (mgrB mgtA)(1st module)' ecoli3328 6,1,1 Global functions Global regulatory functions Global regulatory functions 'ompR' 'response regulator (sensor EnvZ) affecting transcription of ompC and ompF: outer membrane protein synthesis(1st module)' ecoli4284 6,1,1 Global functions Global regulatory functions Global regulatory functions 'creB' 'catabolic regulation response regulator(1st module)' ecoli3280 6,1,1 Global functions Global regulatory functions Global regulatory functions 'crp' 'cyclic AMP receptor protein (interacts with RNAP)' Training Accuracy: 6/6 (100.00%) Training Frequency class 'Global regulatory functions': 30/939 (3.19%) Training Significance: dev(13.48) ; prob(1.063491E-09) Evaluation on validation data (471 items): ecoli677 6,1,1 Global functions Global regulatory functions Global regulatory functions 'kdpE' 'cytoplasmic response regulator of kdp operon (transcriptional effector) (2nd module DNA binding)' 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)' Validation Accuracy: 1/2 (50.00%) Validation Frequency class 'Global regulatory functions': 8/471 (1.70%) Validation Significance: dev(5.29) ; prob(3.339329E-02) ------------------ Rule 95: (2, lift 352.1) [ss_beta( A ,lteq,1),nss_beta( A , B ,lteq,3)] = 0 [ss_coil( A ,lteq,6),nss_coil( A , B ,lteq,1),nss_coil( B , C ,gt,6)] = 1 [ss_beta( A ,lteq,830),nss_beta( A , B ,lteq,6),nss_beta( B , C ,gt,10)] = 1 [hom( A ),species( A ,pseudomonas_putida)] = 0 [hom( A ),species( A ,leishmania_tarentolae__sauroleishmania_tarentolae_),mol_wt_gt( A ,55220)] = 1 -> class 'STP family' [0.750] Evaluation on test data (712 items): ecoli252 - 1,5,42 Cell processes Transport/binding proteins APC family of transport protein 'ykfD' 'APC family of transport protein S-methylmethionine permease' ecoli3961 - 1,5,35 Cell processes Transport/binding proteins SSS family 'yjcG' 'SSS family transport protein' Test Accuracy: 0/2 (0.00%) Test Frequency class 'STP family': 2/712 (0.28%) Test Significance: dev(-0.08) ; prob(1.000000E+00) Application to new data (2167 items): ecoli3606 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'yidE' 'paral putative transport protein(1st module)' ecoli2444 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b2493' 'paral putative transport protein' ecoli4009 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b4115' 'putative amino acid/amine transport protein cryptic' ecoli2821 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2885' 'orf' ecoli1042 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'mviN' 'putative virulence factor' ecoli2454 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2503' 'orf' ecoli2352 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'yfeA' 'orf(2nd module)' ecoli784 - 7,0,0 Miscellaneous Some information, but not classifiable Not classified (included putative assignments) 'b0808' 'pral putative transport protein (2nd module)' ecoli2212 - 0,0,0 Open reading frames Unknown proteins, no known homologs Unknown function 'b2254' 'orf(1st module)' Frequency rule on new data: 9/2167 (0.42%) Evaluation on training data (939 items): ecoli2736 1,5,36 Cell processes Transport/binding proteins STP family 'sdaC' 'STP family of transport protein serine transporter' ecoli3049 1,5,36 Cell processes Transport/binding proteins STP family 'tdcC' 'STP family of transport protein anaerobically inducible L-threonine/ L-serine permease' Training Accuracy: 2/2 (100.00%) Training Frequency class 'STP family': 2/939 (0.21%) Training Significance: dev(30.61) ; prob(4.536582E-06) Evaluation on validation data (471 items): 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)' ecoli2782 1,5,36 Cell processes Transport/binding proteins STP family 'b2845' 'STP family of transport protein' Validation Accuracy: 1/2 (50.00%) Validation Frequency class 'STP family': 1/471 (0.21%) Validation Significance: dev(15.30) ; prob(4.237269E-03) ------------------