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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|15894240|ref|NP_347589.1| hypothetical protein (CA_C0953) [Clostridium acetobutylicum ATCC 824] (Range: 1-132) 132 COG0113 8-130 -6.390 13  [U] KOG4072 Signal peptidase complex, subunit SPC25
PDB0113 26-132 -7.820 10  3kwt_A mol:protein length:148 Munc13-1
PfamA26U 44-117 -8.060 12  PF00168.25; Q9LS53_ARATH/577-655; C2 domain
SCOP175 42-130 -6.690 11  d2nq3a1 b.7.1.1 (A:13-145) E3 ubiquitin-protein ligase Itchy {Human (Homo sapiens) [TaxId: 9606]}
2 gi|15895268|ref|NP_348617.1| ABC-type transport system, ATPase component (CA_C1998) [Clostridium acetobutylicum ATCC 824] (Range: 1-224) 224 COG0113 2-224 -108.000 40  [Q] COG4181 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, ATPase component
PDB0113 4-224 -109.000 48  3tif_A mol:protein length:235 Uncharacterized ABC transporter ATP-binding p
PfamA26U 18-224 -30.200 14  PF09818.4; Q2C6W1_9GAMM/1-438; Predicted ATPase of the ABC class
48-173 -34.400 27  PF00005.22; YTFR_ECOLI/49-174; ABC transporter
SCOP175 4-224 -109.000 49  d1l2ta_ c.37.1.12 (A:) MJ0796 {Archaeon Methanococcus jannaschii [TaxId: 2190]}
3 gi|15895079|ref|NP_348428.1| ribosome-binding factor A (CA_C1803) [Clostridium acetobutylicum ATCC 824] (Range: 1-121) 121 COG0113 2-121 -62.500 30  [J] COG0858 Ribosome-binding factor A
PDB0113 1-118 -63.800 19  1pa4_A mol:protein length:116 Probable ribosome-binding factor A
PfamA26U 5-109 -59.800 33  PF02033.13; A3Y8H6_9GAMM/7-113; Ribosome-binding factor A
SCOP175 1-113 -58.000 18  d2e7ga1 d.52.7.1 (A:86-201) Ribosome-binding factor A, RbfA {Human (Homo sapiens) [TaxId: 9606]}
4 gi|15896238|ref|NP_349587.1| dimethyladenosine transferase (CA_C2986) [Clostridium acetobutylicum ATCC 824] (Range: 1-276) 276 COG0113 2-276 -97.900 29  [A] KOG0821 Predicted ribosomal RNA adenine dimethylase
PDB0113 8-276 -108.000 32  3tpz_A mol:protein length:273 Ribosomal RNA small subunit methyltransferase
PfamA26U 15-269 -96.300 25  PF00398.15; DIM1_YEAST/27-282; Ribosomal RNA adenine dimethylase
SCOP175 23-276 -105.000 34  d1qyra_ c.66.1.24 (A:) High level kasugamycin resistance protein KsgA {Escherichia coli [TaxId: 562]}
5 gi|15894673|ref|NP_348022.1| phosphoribosylglycinamide formyltransferase (CA_C1394) [Clostridium acetobutylicum ATCC 824] (Range: 1-204) 204 COG0113 2-204 -87.600 34  [F] COG0299 Folate-dependent phosphoribosylglycinamide formyltransferase PurN
PDB0113 1-204 -89.500 35  3tqr_A mol:protein length:215 Phosphoribosylglycinamide formyltransferase
PfamA26U 4-174 -29.300 23  PF00551.14; AL1L1_RAT/1-180; Formyl transferase
SCOP175 2-204 -87.500 34  d1jkxa_ c.65.1.1 (A:) Glycinamide ribonucleotide transformylase, GART {Escherichia coli [TaxId: 562]}
6 gi|15894664|ref|NP_348013.1| Alpha-ribazole-5'-phosphate phosphatase, CobC (CA_C1385) [Clostridium acetobutylicum ATCC 824] (Range: 1-191) 191 COG0113 1-191 -67.800 18  [G] COG0406 Fructose-2,6-bisphosphatase
PDB0113 2-191 -88.400 25  1h2e_A mol:protein length:207 PHOSPHATASE
PfamA26U 3-152 -44.100 25  PF00300.17; Q756M6_ASHGO/9-242; Histidine phosphatase superfamily (branch 1)
SCOP175 2-191 -88.400 25  d1h2ea_ c.60.1.1 (A:) Broad specificity phosphatase PhoE (YhfR) {Bacillus stearothermophilus [TaxId: 1422]}
7 gi|15894369|ref|NP_347718.1| Beta-glucosidase family protein (CA_C1084) [Clostridium acetobutylicum ATCC 824] (Range: 1-474) 474 COG0113 1-470 -139.000 40  [G] COG2723 Beta-glucosidase/6-phospho-beta-glucosidase/beta-galactosidase
PDB0113 2-471 -138.000 40  3pn8_A mol:protein length:480 Putative phospho-beta-glucosidase
PfamA26U 1-469 -143.000 39  PF00232.13; ARBB_ERWCH/1-461; Glycosyl hydrolase family 1
SCOP175 1-470 -132.000 34  d1pbga_ c.1.8.4 (A:) 6-phospho-beta-D-galactosidase, PGAL {Lactococcus lactis [TaxId: 1358]}
8 gi|15896898|ref|NP_350247.1| alpha/beta fold family hydrolase (CA_C3665) [Clostridium acetobutylicum ATCC 824] (Range: 1-265) 265 COG0113 4-264 -57.700 28  [I] KOG4667 Predicted esterase
PDB0113 2-263 -69.700 32  3pf8_A mol:protein length:270 Cinnamoyl esterase
PfamA26U 7-263 -51.700 15  PF02273.10; LUXD2_PHOLU/8-301; Acyl transferase
SCOP175 6-264 -51.000 19  d2fuka1 c.69.1.36 (A:3-220) XC6422 protein {Xanthomonas campestris [TaxId: 339]}
9 gi|15895531|ref|NP_348880.1| ATP-dependent exonuclease synthesis protein AddB (CA_C2263) [Clostridium acetobutylicum ATCC 824] (Range: 1-500) 500 COG0113 1-500 -100.000 29  [L] COG3857 ATP-dependent nuclease, subunit B
PDB0113 1-500 -102.000 30  3u44_B mol:protein length:1166 ATP-dependent helicase/deoxyribonuclease subu
PfamA26U 1-500 -50.900 12  PF04257.9; C4ZZX4_ECOBW/1-836; Exodeoxyribonuclease V, gamma subunit
SCOP175 5-489 -34.200 16  g1qhh.1 c.37.1.19 (A:,B:,C:,D:) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}
10 gi|15895531|ref|NP_348880.1| ATP-dependent exonuclease synthesis protein AddB (CA_C2263) [Clostridium acetobutylicum ATCC 824] (Range: 251-750) 500 COG0113 1-500 -91.900 30  [L] COG3857 ATP-dependent nuclease, subunit B
PDB0113 1-500 -96.400 30  3u44_B mol:protein length:1166 ATP-dependent helicase/deoxyribonuclease subu
PfamA26U 19-497 -70.800 12  PF04257.9; C4ZZX4_ECOBW/1-836; Exodeoxyribonuclease V, gamma subunit
SCOP175 26-488 -74.600 12  d1w36c2 c.37.1.19 (C:348-817) Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain {Escherichia coli [TaxId: 562]}
11 gi|15895531|ref|NP_348880.1| ATP-dependent exonuclease synthesis protein AddB (CA_C2263) [Clostridium acetobutylicum ATCC 824] (Range: 501-1000) 500 COG0113 1-500 -115.000 32  [L] COG3857 ATP-dependent nuclease, subunit B
PDB0113 1-500 -119.000 32  3u44_B mol:protein length:1166 ATP-dependent helicase/deoxyribonuclease subu
PfamA26U 1-201 -28.800 13  PF04257.9; C4ZZX4_ECOBW/1-836; Exodeoxyribonuclease V, gamma subunit
275-495 -61.100 17  PF12705.2; B5D322_9BACE/660-959; PD-(D/E)XK nuclease superfamily
SCOP175 1-197 -33.800 13  d1w36c2 c.37.1.19 (C:348-817) Exodeoxyribonuclease V gamma chain (RecC), N-terminal domain {Escherichia coli [TaxId: 562]}
281-497 -19.300 14  d1w36b3 c.52.1.24 (B:899-1174) Exodeoxyribonuclease V beta chain (RecB), C-terminal domain {Escherichia coli [TaxId: 562]}
12 gi|15895531|ref|NP_348880.1| ATP-dependent exonuclease synthesis protein AddB (CA_C2263) [Clostridium acetobutylicum ATCC 824] (Range: 751-1153) 403 COG0113 1-396 -98.500 35  [L] COG3857 ATP-dependent nuclease, subunit B
PDB0113 1-398 -104.000 35  3u44_B mol:protein length:1166 ATP-dependent helicase/deoxyribonuclease subu
PfamA26U 22-403 -26.000 12  PF10926.3; B0K6Q0_THEPX/4-363; Protein of unknown function (DUF2800 topsan)
25-364 -69.700 18  PF12705.2; B5D322_9BACE/660-959; PD-(D/E)XK nuclease superfamily
SCOP175 31-292 -15.100 15  d1w36b3 c.52.1.24 (B:899-1174) Exodeoxyribonuclease V beta chain (RecB), C-terminal domain {Escherichia coli [TaxId: 562]}
13 gi|15895492|ref|NP_348841.1| chemotaxis protein CheW (CA_C2224) [Clostridium acetobutylicum ATCC 824] (Range: 1-147) 147 COG0113 2-143 -57.300 20  [NT] COG0835 Chemotaxis signal transduction protein
PDB0113 2-147 -73.500 32  2ho9_A mol:protein length:167 Chemotaxis protein cheW
PfamA26U 8-143 -19.600 16  PF01584.14; Q8XQ78_RALSO/559-691; CheW-like domain
SCOP175 3-141 -60.900 30  d2ch4w1 b.40.7.1 (W:9-147) Chemotaxis protein CheW {Thermotoga maritima [TaxId: 2336]}
14 gi|15894672|ref|NP_348021.1| phosphoribosylaminoimidazole synthetase (CA_C1393) [Clostridium acetobutylicum ATCC 824] (Range: 1-332) 332 COG0113 2-328 -114.000 52  [F] COG0150 Phosphoribosylaminoimidazole (AIR) synthetase
PDB0113 2-331 -114.000 49  1cli_A mol:protein length:345 PROTEIN (PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHE
PfamA26U 38-136 -13.200 20  PF00586.19; A0LIX8_SYNFM/31-128; AIR synthase related protein, N-terminal domain
SCOP175 2-165 -88.200 53  d1clia1 d.79.4.1 (A:5-170) Aminoimidazole ribonucleotide synthetase (PurM) N-terminal domain {Escherichia coli [TaxId: 562]}
166-331 -68.800 45  d1clia2 d.139.1.1 (A:171-345) Aminoimidazole ribonucleotide synthetase (PurM) C-terminal domain {Escherichia coli [TaxId: 562]}
15 gi|15893880|ref|NP_347229.1| riboflavin synthase subunit alpha (CA_C0591) [Clostridium acetobutylicum ATCC 824] (Range: 1-213) 213 COG0113 1-201 -96.800 35  [H] KOG3310 Riboflavin synthase alpha chain
PDB0113 1-201 -96.800 35  1kzl_A mol:protein length:208 Riboflavin Synthase
PfamA26U 97-179 -42.000 34  PF00677.12; RISA_HAEIN/3-87; Lumazine binding domain
SCOP175 1-94 -42.200 36  d1hzea_ b.43.4.3 (A:) Riboflavin synthase {Escherichia coli [TaxId: 562]}
90-198 -55.300 33  d1kzla2 b.43.4.3 (A:93-202) Riboflavin synthase {Fission yeast (Schizosaccharomyces pombe) [TaxId: 4896]}
16 gi|15893578|ref|NP_346927.1| hypothetical protein (CA_C0286) [Clostridium acetobutylicum ATCC 824] (Range: 1-244) 244 COG0113 1-244 -82.300 18  [S] COG4200 Uncharacterized protein conserved in bacteria
PDB0113 63-244 -7.080 13  3v2w_A mol:protein length:520 Sphingosine 1-phosphate receptor 1, Lysozyme
PfamA26U 7-238 -64.200 15  PF12730.2; B6FXG5_9CLOT/10-245; ABC-2 family transporter protein
SCOP175 2-172 -5.310 10  d1u19a_ f.13.1.2 (A:) Rhodopsin {Cow (Bos taurus) [TaxId: 9913]}
17 gi|15896862|ref|NP_350211.1| oligopeptide ABC transporter, ATPase component (CA_C3628) [Clostridium acetobutylicum ATCC 824] (Range: 1-322) 322 COG0113 7-322 -134.000 52  [E] COG4608 ABC-type oligopeptide transport system, ATPase component
PDB0113 2-258 -61.200 32  3tui_C mol:protein length:366 Methionine import ATP-binding protein MetN
11-307 -43.300 29  2d62_A mol:protein length:375 multiple sugar-binding transport ATP-binding
PfamA26U 28-264 -24.000 11  PF09818.4; Q2C6W1_9GAMM/1-438; Predicted ATPase of the ABC class
234-301 -38.700 32  PF08352.7; A4D7W3_PROAC/243-312; Oligopeptide/dipeptide transporter, C-terminal region
SCOP175 10-254 -63.700 34  d3dhwc1 c.37.1.12 (C:1-240) Methionine import ATP-binding protein MetN {Escherichia coli [TaxId: 562]}
39-290 -10.900 12  d1a7ja_ c.37.1.6 (A:) Phosphoribulokinase {Rhodobacter sphaeroides [TaxId: 1063]}
18 gi|15895331|ref|NP_348680.1| segregation and condensation protein A (CA_C2061) [Clostridium acetobutylicum ATCC 824] (Range: 1-249) 249 COG0113 2-249 -87.300 29  [S] COG1354 Uncharacterized conserved protein
PDB0113 180-247 -12.600 22  1w1w_E mol:protein length:121 SISTER CHROMATID COHESION PROTEIN 1
PfamA26U 20-245 -80.500 38  PF02616.9; SCPA_BACSU/21-245; ScpA/B protein
SCOP175 180-243 -11.400 21  d1w1we_ a.4.5.57 (E:) Sister chromatid cohesion protein 1 (SCC1), C-terminal domain {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
19 gi|15894096|ref|NP_347445.1| hydrogenase formation factor (hypE) (CA_C0809) [Clostridium acetobutylicum ATCC 824] (Range: 1-335) 335 COG0113 2-335 -97.500 51  [O] COG0309 Hydrogenase maturation factor
PDB0113 2-335 -95.500 46  2z1t_A mol:protein length:343 Hydrogenase expression/formation protein HypE
PfamA26U 36-127 -37.700 22  PF00586.19; A0LIX8_SYNFM/31-128; AIR synthase related protein, N-terminal domain
162-311 -19.400 18  PF02769.17; PURL_STRCO/213-370; AIR synthase related protein, C-terminal domain
SCOP175 4-153 -32.800 11  d2zoda1 d.79.4.1 (A:3-154) Selenide, water dikinase SelD {Aquifex aeolicus [TaxId: 63363]}
38-151 -55.200 50  d2z1ea1 d.79.4.1 (A:43-155) Hydrogenase expression/formation protein HypE {Thermococcus kodakaraensis [TaxId: 311400]}
155-331 -56.000 41  d2z1ea2 d.139.1.1 (A:156-334) Hydrogenase expression/formation protein HypE {Thermococcus kodakaraensis [TaxId: 311400]}
20 gi|15895945|ref|NP_349294.1| DNA helicase (CA_C2687) [Clostridium acetobutylicum ATCC 824] (Range: 1-714) 714 COG0113 1-593 -155.000 39  [L] COG0514 Superfamily II DNA helicase
1-639 -59.700 14  [R] COG1202 Superfamily II helicase, archaea-specific
407-711 -27.400 15  [S] COG4955 Uncharacterized protein conserved in bacteria
PDB0113 1-517 -134.000 37  1oyw_A mol:protein length:523 ATP-dependent DNA helicase
14-625 -25.500 13  2p6r_A mol:protein length:702 afUHEL308 HELICASE
508-595 -37.900 33  1wud_A mol:protein length:89 ATP-dependent DNA helicase recQ
591-713 -24.400 16  3iuo_A mol:protein length:122 ATP-dependent DNA helicase RecQ
PfamA26U 3-714 -13.900 11  PF02399.10; OBP_EHV1V/51-880; Origin of replication binding protein
19-185 -72.300 40  PF00270.24; SGS1_YEAST/680-854; DEAD/DEAH box helicase
73-356 -14.400 13  PF06862.7; Q8H1E7_ARATH/308-753; Protein of unknown function (DUF1253 topsan)
247-324 -25.900 29  PF00271.26; O01378_BOMMO/449-526; Helicase conserved C-terminal domain
406-509 -39.300 29  PF09382.5; Q9ZHY4_NEIGO/406-509; RQC domain
518-585 -34.400 38  PF00570.18; Q8G567_BIFLO/575-642; HRDC domain
SCOP175 1-199 -82.900 46  d1oywa2 c.37.1.19 (A:1-206) RecQ helicase domain {Escherichia coli [TaxId: 562]}
200-401 -84.200 38  d1oywa3 c.37.1.19 (A:207-406) RecQ helicase domain {Escherichia coli [TaxId: 562]}
398-541 -39.200 16  d2axla1 a.4.5.43 (A:1-144) Werner syndrome ATP-dependent helicase WRN {Human (Homo sapiens) [TaxId: 9606]}
402-509 -39.500 24  d1oywa1 a.4.5.43 (A:407-516) DNA helicase RecQ DNA-binding domain {Escherichia coli [TaxId: 562]}
516-592 -37.500 37  d1wuda1 a.60.8.1 (A:530-606) HRDC domain from RecQ helicase {Escherichia coli [TaxId: 562]}


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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.

Ye Y, Li Z, and Godzik A. Modeling and Analyzing Three-Dimensional Structures of Human Disease Proteins Pacific Symposium on Biocomputing 11:439-450(2006) [PDF]