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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|60680547|ref|YP_210691.1| hypothetical protein (BF1003) [Bacteroides fragilis NCTC 9343] (Range:1-117) 117 COG0113 58-111 -9.130 16  [R] COG4797 Predicted regulatory domain of a methyltransferase
PDB0113 24-113 -30.000 17  3g2b_A mol:protein length:95 Coenzyme PQQ synthesis protein D
PfamA26U 33-112 -30.300 18  PF05402.7; A3KTI3_PSEAE/11-90; Coenzyme PQQ synthesis protein D (PqqD)
SCOP175 61-117 -7.430 21  d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}
2 gi|60680256|ref|YP_210400.1| hypothetical protein (BF0697) [Bacteroides fragilis NCTC 9343] (Range:1-74) 74 COG0113 46-73 -7.570 10  [UR] KOG4677 Golgi integral membrane protein
PDB0113 39-73 -6.050 17  2wwb_C mol:protein length:96 PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
PfamA26U 20-74 -6.500 20  PF10961.3; Q179T4_AEDAE/2-92; Protein of unknown function (DUF2763 topsan)
SCOP175 31-66 -6.150 30  d1ppje2 f.23.12.1 (E:1-69) Iron-sulfur subunit (ISP) of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane region {Cow (Bos taurus) [TaxId: 9913]}
3 gi|60681449|ref|YP_211593.1| MatE family transmembrane protein (BF1960) [Bacteroides fragilis NCTC 9343] (Range:1-447) 447 COG0113 14-440 -77.000 19  [V] COG0534 Na+-driven multidrug efflux pump
PDB0113 13-446 -63.500 17  3mkt_A mol:protein length:460 Multi antimicrobial extrusion protein (Na(+)/
PfamA26U 4-336 -36.100 PF07260.6; Q6NS07_XENLA/1-345; Progressive ankylosis protein (ANKH)
40-434 -21.400 11  PF03023.9; MVIN_ECOLI/28-479; MviN-like protein
SCOP175 37-313 -4.850 d1vk4a_ c.72.1.1 (A:) Hypothetical protein TM0415 {Thermotoga maritima [TaxId: 2336]}
4 gi|60683425|ref|YP_213569.1| 30S ribosomal protein S14 (BF3990) [Bacteroides fragilis NCTC 9343] (Range:1-99) 99 COG0113 1-99 -72.100 55  [J] COG0199 Ribosomal protein S14
PDB0113 1-99 -72.300 44  3bbn_N mol:protein length:100 Ribosomal Protein S14
PfamA26U 44-97 -42.700 35  PF00253.16; Q6FQ77_CANGA/59-113; Ribosomal protein S14p/S29e
SCOP175 2-99 -70.400 55  d2qaln1 g.39.1.7 (N:1-100) Ribosomal protein S14 {Escherichia coli [TaxId: 562]}
5 gi|60682385|ref|YP_212529.1| putative CTP pyrophosphohydrolase (BF2916) [Bacteroides fragilis NCTC 9343] (Range:1-130) 130 COG0113 7-130 -39.700 19  [F] COG1051 ADP-ribose pyrophosphatase
PDB0113 1-130 -85.000 99  3gwy_A mol:protein length:140 Putative CTP pyrophosphohydrolase
PfamA26U 6-130 -24.100 21  PF00293.23; NUDC_ECOLI/127-247; NUDIX domain
SCOP175 1-129 -77.900 25  d1puna_ d.113.1.1 (A:) Nucleoside triphosphate pyrophosphorylase (MutT) {Escherichia coli [TaxId: 562]}
6 gi|60680762|ref|YP_210906.1| putative transmembrane conjugate transposon protein (BF1242) [Bacteroides fragilis NCTC 9343] (Range:1-110) 110 COG0113 1-58 -12.200 10  [U] COG3702 Type IV secretory pathway, VirB3 components
PDB0113 10-75 -6.400 2i68_A mol:protein length:137 Protein emrE
PfamA26U 6-101 -62.700 71  PF13571.1; B6W538_9BACE/6-101; Domain of unknown function (DUF4133 topsan)
SCOP175 1-69 -7.030 14  d2h8aa1 f.56.1.1 (A:9-147) Microsomal glutathione S-transferase 1 {Rat (Rattus norvegicus) [TaxId: 10116]}
7 gi|60683330|ref|YP_213474.1| ATP-dependent protease ATP-binding subunit ClpX (BF3893) [Bacteroides fragilis NCTC 9343] (Range:1-415) 415 COG0113 2-415 -131.000 53  [O] COG1219 ATP-dependent protease Clp, ATPase subunit
PDB0113 2-57 -25.400 32  1ovx_A mol:protein length:67 ATP-dependent Clp protease ATP-binding subuni
57-414 -123.000 50  1um8_A mol:protein length:376 ATP-dependent Clp protease ATP-binding subuni
PfamA26U 8-47 -20.400 40  PF06689.8; CLPX_RHOFD/12-51; ClpX C4-type zinc finger
52-381 -11.300 23  PF05496.7; RUVB_SOLUE/5-238; Holliday junction DNA helicase ruvB N-terminus
79-243 -12.800 22  PF01078.16; Q8EJV7_SHEON/193-396; Magnesium chelatase, subunit ChlI
SCOP175 9-45 -19.000 45  d2ds5a1 g.39.1.11 (A:11-48) ClpX chaperone zinc binding domain {Escherichia coli [TaxId: 562]}
62-409 -124.000 52  d1um8a_ c.37.1.20 (A:) ClpX {Helicobacter pylori [TaxId: 210]}
8 gi|60682477|ref|YP_212621.1|(removed signalp:1-23) hypothetical protein (BF3007) [Bacteroides fragilis NCTC 9343] (Range:24-588) 565 COG0113 4-556 -29.200 [U] KOG2376 Signal recognition particle, subunit Srp72
5-342 -31.800 13  [DO] KOG1173 Anaphase-promoting complex (APC), Cdc16 subunit
24-320 -32.200 15  [T] KOG1130 Predicted G-alpha GTPase interaction protein, contains GoLoco domain
55-328 -34.100 [U] KOG1586 Protein required for fusion of vesicles in vesicular transport, alpha-SNAP
PDB0113 1-565 -17.900 4gns_B mol:protein length:754 Chitin biosynthesis protein CHS6
24-273 -39.600 17  3ulq_A mol:protein length:383 Response regulator aspartate phosphatase F
24-311 -39.300 15  3ro2_A mol:protein length:338 G-protein-signaling modulator 2
34-347 -28.800 1hz4_A mol:protein length:373 MALT REGULATORY PROTEIN
PfamA26U 4-549 -24.000 11  PF12569.3; A9SDC6_PHYPA/187-705; NMDA receptor-regulated protein 1
5-310 -27.200 10  PF13429.1; Q39U81_GEOMG/198-480; Tetratricopeptide repeat
SCOP175 4-310 -25.600 13  d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}
19-553 -9.810 d1ya0a1 a.118.8.1 (A:1-497) SMG-7 {Human (Homo sapiens) [TaxId: 9606]}
34-347 -29.000 d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}
63-330 -36.200 11  d1qqea_ a.118.8.1 (A:) Vesicular transport protein sec17 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
506-564 -16.400 13  d1p4wa_ a.4.6.2 (A:) Transcriptional regulator RcsB {Erwinia amylovora [TaxId: 552]}
9 gi|60681243|ref|YP_211387.1| hypothetical protein (BF1751) [Bacteroides fragilis NCTC 9343] (Range:1-157) 157 COG0113 3-132 -7.540 [M] COG3056 Uncharacterized lipoprotein
PDB0113 7-118 -7.140 10  1usu_B mol:protein length:170 AHA1
PfamA26U 10-132 -39.100 15  PF14137.1; A6LYB2_CLOB8/32-182; Domain of unknown function (DUF4304 topsan)
SCOP175 7-118 -7.520 10  d1usub_ d.83.2.1 (B:) Activator of Hsp90 ATPase, Aha1 {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
10 gi|60682315|ref|YP_212459.1| hypothetical protein (BF2845) [Bacteroides fragilis NCTC 9343] (Range:1-207) 207 COG0113 9-206 -5.590 17  [C] KOG4009 NADH-ubiquinone oxidoreductase, subunit NDUFB10/PDSW
PDB0113 23-204 -6.690 12  3u9l_A mol:protein length:324 3-oxoacyl-[acyl-carrier-protein] reductase
PfamA26U 30-140 -7.220 16  PF06232.6; Q2HVW6_MEDTR/41-164; Embryo-specific protein 3, (ATS3)
SCOP175 42-109 -7.150 14  d1kb0a1 a.3.1.6 (A:579-675) Quinoprotein alcohol dehydrogenase, C-terminal domain {Comamonas testosteroni [TaxId: 285]}
11 gi|60680924|ref|YP_211068.1| putative anti-sigma factor (BF1413) [Bacteroides fragilis NCTC 9343] (Range:1-311) 311 COG0113 4-311 -56.400 18  [PT] COG3712 Fe2+-dicitrate sensor, membrane component
PDB0113 1-199 -7.920 2z2s_B mol:protein length:203 Anti-Sigma factor ChrR, transcriptional activ
PfamA26U 100-196 -34.500 21  PF04773.8; Q2YA72_NITMU/40-132; FecR protein
SCOP175 104-268 -6.800 15  d2f20a1 d.303.1.1 (A:2-232) Hypothetical protein BT1218 {Bacteroides thetaiotaomicron [TaxId: 818]}
12 gi|60683563|ref|YP_213707.1| putative SufE Fe/S-cluster-related protein (BF4142) [Bacteroides fragilis NCTC 9343] (Range:1-142) 142 COG0113 1-138 -80.300 34  [R] COG2166 SufE protein probably involved in Fe-S center assembly
PDB0113 1-138 -80.100 32  1mzg_A mol:protein length:146 SufE Protein
PfamA26U 10-133 -73.800 31  PF02657.10; YGDK_ECOLI/20-145; Fe-S metabolism associated domain
SCOP175 3-141 -78.400 31  d1mzga_ d.224.1.1 (A:) SufE (YhnA) {Escherichia coli [TaxId: 562]}
13 gi|60682225|ref|YP_212369.1| putative two component system response regulator (BF2753) [Bacteroides fragilis NCTC 9343] (Range:1-225) 225 COG0113 2-225 -84.300 25  [TK] COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain
PDB0113 1-225 -98.100 30  1ys6_A mol:protein length:233 Transcriptional regulatory protein prrA
PfamA26U 1-216 -12.300 11  PF07688.7; KAIA_SYNY3/5-288; KaiA domain
3-113 -52.200 27  PF00072.19; ZRAR_SALTY/8-118; Response regulator receiver domain
145-222 -35.400 23  PF00486.23; O85058_PROST/114-189; Transcriptional regulatory protein, C terminal
SCOP175 1-121 -65.300 38  d1kgsa2 c.23.1.1 (A:2-123) PhoB receiver domain {Thermotoga maritima [TaxId: 2336]}
121-225 -44.700 23  d1gxqa_ a.4.6.1 (A:) PhoB {Escherichia coli [TaxId: 562]}
14 gi|60682801|ref|YP_212945.1| nicotinate phosphoribosyltransferase (BF3334) [Bacteroides fragilis NCTC 9343] (Range:1-388) 388 COG0113 4-384 -61.000 21  [H] COG1488 Nicotinic acid phosphoribosyltransferase
PDB0113 2-388 -126.000 48  2im5_A mol:protein length:394 Nicotinate phosphoribosyltransferase
PfamA26U 160-383 -53.600 21  PF04095.11; O23191_ARATH/174-402; Nicotinate phosphoribosyltransferase (NAPRTase) family
SCOP175 2-135 -60.200 29  d1vlpa1 d.41.2.2 (A:1-149) Nicotinate phosphoribosyltransferase, N-terminal domain {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
137-387 -79.000 33  d1vlpa2 c.1.17.2 (A:150-415) Nicotinate phosphoribosyltransferase, C-terminal domain {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
15 gi|60680875|ref|YP_211019.1| hypothetical protein (BF1359) [Bacteroides fragilis NCTC 9343] (Range:1-245) 245 COG0113 4-245 -36.500 14  [M] COG3209 Rhs family protein
PDB0113 10-244 -42.900 2oy7_A mol:protein length:320 Outer surface protein A
PfamA26U 3-245 -39.100 10  PF06788.8; Q57PD7_SALCH/4-239; Uncharacterised protein family (UPF0257 topsan)
SCOP175 31-242 -10.100 d2biba1 b.109.1.1 (A:309-541) Teichoic acid phosphorylcholine esterase Pce (LytD), C-terminal domain {Streptococcus pneumoniae [TaxId: 1313]}
16 gi|60682029|ref|YP_212173.1| putative bifunctional CbiF/CbiG cobalamin biosynthesis protein (BF2549) [Bacteroides fragilis NCTC 9343] (Range:1-599) 599 COG0113 1-346 -71.500 26  [H] COG2073 Cobalamin biosynthesis protein CbiG
357-599 -69.100 45  [H] COG2875 Precorrin-4 methylase
PDB0113 1-346 -63.400 20  3eeq_A mol:protein length:336 putative Cobalamin biosynthesis protein G hom
348-598 -68.100 44  4e16_A mol:protein length:253 precorrin-4 C(11)-methyltransferase
PfamA26U 43-126 -51.500 45  PF11760.3; Q6ARS3_DESPS/35-118; Cobalamin synthesis G N-terminal
130-228 -26.600 13  PF11761.3; A8FV20_SHESH/134-234; Cobalamin biosynthesis central region
226-344 -39.000 29  PF01890.11; A1AU03_PELPD/230-350; Cobalamin synthesis G C-terminus
353-559 -31.800 16  PF00590.15; A1AUS5_PELPD/5-191; Tetrapyrrole (Corrin/Porphyrin) Methylases
SCOP175 1-224 -56.200 20  d3eeqa2 c.152.1.1 (A:8-214) Cobalamin biosynthesis protein G, CbiG {Sulfolobus solfataricus [TaxId: 2287]}
221-346 -37.800 26  d2w6ka1 c.151.1.1 (A:1-139) Cobalamin biosynthesis protein CobE {Pseudomonas aeruginosa [TaxId: 287]}
350-580 -63.700 44  d1cbfa_ c.90.1.1 (A:) Cobalt precorrin-4 methyltransferase CbiF {Bacillus megaterium [TaxId: 1404]}
17 gi|60681247|ref|YP_211391.1| hypothetical protein (BF1755) [Bacteroides fragilis NCTC 9343] (Range:1-299) 299 COG0113 3-299 -20.700 [MOT] KOG1550 Extracellular protein SEL-1 and related proteins
80-299 -29.300 11  [R] COG0790 FOG: TPR repeat, SEL1 subfamily
PDB0113 87-290 -40.300 3rjv_A mol:protein length:212 Putative Sel1 repeat protein
PfamA26U 243-277 -22.200 22  PF08238.7; Q5PFP4_SALPA/166-201; Sel1 repeat
SCOP175 89-299 -34.600 10  d1ouva_ a.118.18.1 (A:) Cysteine rich protein C (HcpC) {Helicobacter pylori [TaxId: 210]}
172-299 -39.800 18  d1klxa_ a.118.18.1 (A:) Cysteine rich protein B (HcpB) {Helicobacter pylori [TaxId: 210]}
18 gi|60681605|ref|YP_211749.1| hypothetical protein (BF2124) [Bacteroides fragilis NCTC 9343] (Range:1-361) 361 COG0113 281-345 -8.180 15  [J] COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation
PDB0113 313-357 -10.100 15  2co8_A mol:protein length:82 NEDD9 interacting protein with calponin homol
PfamA26U 292-352 -8.390 11  PF05495.7; A7TR54_VANPO/18-100; CHY zinc finger
SCOP175 298-347 -8.150 16  d1vd4a_ g.41.3.1 (A:) Transcription initiation factor TFIIE-alpha {Human (Homo sapiens) [TaxId: 9606]}
19 gi|60681337|ref|YP_211481.1| hypothetical protein (BF1846) [Bacteroides fragilis NCTC 9343] (Range:1-71) 71 COG0113 5-67 -5.890 [S] COG5458 Uncharacterized conserved protein
PDB0113 4-56 -7.770 13  2w9p_A mol:protein length:87 MULTICYSTATIN
PfamA26U 5-67 -6.050 11  PF07370.6; A4EER5_9RHOB/7-143; Protein of unknown function (DUF1489 topsan)
SCOP175 1-71 -5.060 21  d1ybea2 d.41.2.2 (A:8-167) Nicotinate phosphoribosyltransferase, N-terminal domain {Agrobacterium tumefaciens [TaxId: 358]}
20 gi|60680681|ref|YP_210825.1| hypothetical protein (BF1156) [Bacteroides fragilis NCTC 9343] (Range:1-221) 221 COG0113 15-216 -55.700 15  [R] KOG1665 AFH1-interacting protein FIP2, contains BTB/POZ domain and pentapeptide repeats
PDB0113 1-220 -55.800 16  3du1_X mol:protein length:257 All3740 protein
33-219 -72.200 25  2w7z_A mol:protein length:214 PENTAPEPTIDE REPEAT FAMILY PROTEIN
PfamA26U 56-220 -12.700 12  PF12541.3; C4ZDA1_EUBR3/4-281; Protein of unknown function (DUF3737 topsan)
75-172 -28.800 28  PF13599.1; A5FH08_FLAJ1/44-123; Pentapeptide repeats (9 copies)
SCOP175 41-219 -66.200 21  d2bm5a1 b.80.8.1 (A:2-182) Hypothetical protein Rv3361c (MT3469) {Mycobacterium tuberculosis [TaxId: 1773]}


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Selected papers from Godzik Lab
Ying Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley Deacon, John Wooley, Scott Lesley, Ian Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik. Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima. Science. 2009 Sep 18;325(5947):1544-9.

Alexey M. Eroshkin, Andrew LeBlanc, Dana Weekes, Kai Post, Zhanwen Li, Akhil Rajput, Sal T. Butera, Dennis R. Burton, Adam Godzik. bNAber: database of broadly neutralizing HIV antibodies. Nucl. Acids Res. 2013; published on November 7, 2013.

Li W, Godzik A. cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 May 26;