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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|238922433|ref|YP_002935946.1| chromosomal replication initiation protein (EUBREC_0001) [Eubacterium rectale ATCC 33656] 453 COG0113 3-452 -118.000 33  [L] COG0593 ATPase involved in DNA replication initiation
PDB0113 7-453 -118.000 34  2z4r_A mol:protein length:440 Chromosomal replication initiator protein dna
PfamA26U 5-71 -13.700 20  PF11638.3; DNAA_LAWIP/5-67; DnaA N-terminal domain
113-334 -100.000 60  PF00308.13; DNAA_STRCO/317-535; Bacterial dnaA protein
360-429 -38.600 42  PF08299.6; DNAA_PSEPU/414-483; Bacterial dnaA protein helix-turn-helix
SCOP175 111-329 -93.400 38  d1l8qa2 c.37.1.20 (A:77-289) Chromosomal replication initiation factor DnaA {Aquifex aeolicus [TaxId: 63363]}
346-453 -46.900 24  d1l8qa1 a.4.12.2 (A:290-399) Chromosomal replication initiation factor DnaA C-terminal domain IV {Aquifex aeolicus [TaxId: 63363]}
2 gi|238922434|ref|YP_002935947.1| DNA polymerase III, beta subunit (EUBREC_0002) [Eubacterium rectale ATCC 33656] 370 COG0113 1-368 -103.000 22  [L] COG0592 DNA polymerase sliding clamp subunit (PCNA homolog)
PDB0113 1-370 -115.000 100  3t0p_A mol:protein length:371 DNA polymerase III, beta subunit
PfamA26U 1-119 -50.400 40  PF00712.14; DPO3B_BACSU/1-127; DNA polymerase III beta subunit, N-terminal domain
128-243 -56.400 30  PF02767.11; DPO3B_PROMI/129-244; DNA polymerase III beta subunit, central domain
245-364 -46.100 30  PF02768.10; DPO3B_BACSU/253-376; DNA polymerase III beta subunit, C-terminal domain
SCOP175 1-120 -51.700 21  d1ok7a1 d.131.1.1 (A:1-122) DNA polymerase III, beta subunit {Escherichia coli [TaxId: 562]}
122-244 -54.700 17  d1vpka2 d.131.1.1 (A:121-243) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]}
245-366 -48.900 27  d1vpka3 d.131.1.1 (A:244-366) DNA polymerase III, beta subunit {Thermotoga maritima [TaxId: 2336]}
3 gi|238922435|ref|YP_002935948.1| hypothetical protein (EUBREC_0003) [Eubacterium rectale ATCC 33656] 71 COG0113 3-70 -44.000 39  [S] COG2501 Uncharacterized conserved protein
PDB0113 8-70 -42.500 34  1p9k_A mol:protein length:79 orf, hypothetical protein
PfamA26U 6-70 -42.900 56  PF13275.1; D4IXS8_BUTFI/4-68; S4 domain
SCOP175 8-70 -42.500 34  d1p9ka_ d.66.1.6 (A:) Hypothetical protein YbcJ {Escherichia coli [TaxId: 562]}
4 gi|238922436|ref|YP_002935949.1| DNA replication and repair protein RecF (EUBREC_0004) [Eubacterium rectale ATCC 33656] 362 COG0113 1-359 -108.000 23  [L] COG1195 Recombinational DNA repair ATPase (RecF pathway)
PDB0113 1-362 -103.000 28  2o5v_A mol:protein length:359 DNA replication and repair protein recF
PfamA26U 1-358 -26.100 16  PF11398.3; Q6D3T4_ERWCT/1-377; Protein of unknown function (DUF2813 topsan)
SCOP175 1-341 -27.800 20  g1f2t.1 c.37.1.12 (A:,B:) Rad50 {Archaeon Pyrococcus furiosus [TaxId: 2261]}
5 gi|238922437|ref|YP_002935950.1| DNA gyrase, B subunit (EUBREC_0005) [Eubacterium rectale ATCC 33656] 645 COG0113 5-645 -145.000 53  [L] COG0187 Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), B subunit
PDB0113 7-640 -104.000 24  4gfh_A mol:protein length:1177 DNA topoisomerase 2
11-401 -116.000 48  1kij_A mol:protein length:390 DNA GYRASE SUBUNIT B
PfamA26U 45-145 -9.550 15  PF13589.1; A5G4D8_GEOUR/22-165; Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
230-400 -78.100 48  PF00204.20; Q9R3E4_ACISP/115-285; DNA gyrase B
568-634 -43.100 49  PF00986.16; Q6MRR8_BDEBA/731-795; DNA gyrase B subunit, carboxyl terminus
SCOP175 9-229 -86.400 53  d1ei1a2 d.122.1.2 (A:2-220) DNA gyrase B {Escherichia coli [TaxId: 562]}
230-401 -80.100 47  d1ei1a1 d.14.1.3 (A:221-392) DNA gyrase B {Escherichia coli [TaxId: 562]}
415-635 -27.800 30  d1bjta_ e.11.1.1 (A:) DNA topoisomerase II, C-terminal fragment (residues 410-1202) {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
6 gi|238922438|ref|YP_002935951.1| DNA gyrase, A subunit (EUBREC_0006) [Eubacterium rectale ATCC 33656] 852 COG0113 4-828 -196.000 43  [L] COG0188 Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit
PDB0113 1-492 -142.000 61  2xco_A mol:protein length:726 DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
31-750 -139.000 37  1zvu_A mol:protein length:716 Topoisomerase IV subunit A
505-811 -60.800 38  1zi0_A mol:protein length:307 DNA gyrase subunit A
PfamA26U 33-468 -93.100 30  PF00521.15; A1ZXC5_9BACT/29-447; DNA gyrase/topoisomerase IV, subunit A
614-659 -11.800 47  PF03989.8; GYRA_HAEIN/641-686; DNA gyrase C-terminal domain, beta-propeller
SCOP175 31-492 -132.000 56  d1ab4a_ e.11.1.1 (A:) DNA Gyrase A {Escherichia coli [TaxId: 562]}
507-809 -58.100 31  d1suua_ b.68.10.1 (A:) DNA gyrase A C-terminal domain {Lyme disease spirochete (Borrelia burgdorferi) [TaxId: 139]}
7 gi|238922439|ref|YP_002935952.1| hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit (EUBREC_0007) [Eubacterium rectale ATCC 33656] 281 COG0113 7-281 -98.900 28  [C] COG1951 Tartrate dehydratase alpha subunit/Fumarate hydratase class I, N-terminal domain
PDB0113 38-170 -6.410 15  1y4h_A mol:protein length:188 cysteine protease
PfamA26U 10-281 -110.000 54  PF05681.9; A7VNZ1_9CLOT/21-293; Fumarate hydratase (Fumerase)
SCOP175 188-274 -7.570 11  d2aa4a1 c.55.1.10 (A:1-119) N-acetylmannosamine kinase NanK {Escherichia coli [TaxId: 562]}
8 gi|238922440|ref|YP_002935953.1| hypothetical protein (EUBREC_0008) [Eubacterium rectale ATCC 33656] 47 COG0113 1-46 -4.610 17  [R] COG0705 Uncharacterized membrane protein (homolog of Drosophila rhomboid)
PDB0113 10-47 -5.750 22  2lsm_A mol:protein length:61 DNA-packaging protein FI
PfamA26U 3-47 -5.000 28  PF04502.8; Q803C6_DANRE/1-340; Family of unknown function (DUF572 topsan)
SCOP175 3-47 -4.180 25  d2r6gf1 e.70.1.1 (F:13-260) Maltose transport system permease protein MalF {Escherichia coli [TaxId: 562]}
9 gi|238922441|ref|YP_002935954.1| fumarate hydratase subunit B (EUBREC_0009) [Eubacterium rectale ATCC 33656] 183 COG0113 1-182 -92.500 37  [C] COG1838 Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain
PDB0113 1-175 -84.300 42  2isb_A mol:protein length:192 Fumarase
PfamA26U 7-178 -86.900 43  PF05683.7; A0KKZ8_AERHH/379-585; Fumarase C-terminus
SCOP175 1-174 -84.000 42  d2isba1 c.8.9.1 (A:2-179) Fumarate hydratase class I beta subunit {Archaeoglobus fulgidus [TaxId: 2234]}
10 gi|238922442|ref|YP_002935955.1| putative oxidoreductase (EUBREC_0016) [Eubacterium rectale ATCC 33656] 329 COG0113 1-329 -91.500 19  [GQ] KOG2741 Dimeric dihydrodiol dehydrogenase
PDB0113 3-329 -113.000 24  2o48_X mol:protein length:334 Dimeric dihydrodiol dehydrogenase
PfamA26U 4-121 -52.700 22  PF01408.17; CBAC_COMTE/1-120; Oxidoreductase family, NAD-binding Rossmann fold
125-242 -20.200 PF08635.5; Q4PF44_USTMA/241-382; Putative oxidoreductase C terminal
SCOP175 3-185 -72.200 24  d1ydwa1 c.2.1.3 (A:6-133,A:305-360) Probable oxidoreductase At4g09670 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}
127-290 -45.800 17  d1ydwa2 d.81.1.5 (A:134-304) Probable oxidoreductase At4g09670 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}
11 gi|238922443|ref|YP_002935956.1| transcription repressor of fructose operon FruR (EUBREC_0017) [Eubacterium rectale ATCC 33656] 247 COG0113 1-247 -79.700 27  [KG] COG1349 Transcriptional regulators of sugar metabolism
PDB0113 7-79 -22.500 11  2htj_A mol:protein length:81 P fimbrial regulatory protein KS71A
79-212 -12.600 17  1uj4_A mol:protein length:227 ribose 5-phosphate isomerase
PfamA26U 1-113 -33.900 11  PF06163.6; Q8XAE8_ECO57/1-127; Bacterial protein of unknown function (DUF977 topsan)
75-232 -59.600 25  PF00455.17; A9CFA5_AGRT5/77-236; DeoR C terminal sensor domain
SCOP175 7-56 -19.800 16  d2htja1 a.4.5.73 (A:1-73) P fimbrial regulatory protein PapI {Escherichia coli [TaxId: 562]}
79-212 -14.700 17  d1uj4a1 c.124.1.4 (A:3-131,A:206-227) D-ribose-5-phosphate isomerase (RpiA), catalytic domain {Thermus thermophilus [TaxId: 274]}
12 gi|238922444|ref|YP_002935957.1| fructose-1-phosphate kinase (EUBREC_0018) [Eubacterium rectale ATCC 33656] 305 COG0113 1-304 -87.300 24  [G] COG1105 Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB)
PDB0113 1-304 -92.200 42  2jg5_A mol:protein length:306 FRUCTOSE 1-PHOSPHATE KINASE
PfamA26U 11-286 -28.900 14  PF00294.19; ADK_YEAST/21-336; pfkB family carbohydrate kinase
SCOP175 1-304 -92.100 44  d2abqa1 c.72.1.1 (A:1-306) Fructose 1-phosphate kinase FruB {Bacillus halodurans [TaxId: 86665]}
13 gi|238922445|ref|YP_002935958.1| PTS system, fructose-specific, IIABC component (EUBREC_0019) [Eubacterium rectale ATCC 33656] 642 COG0113 6-263 -49.200 21  [G] COG4668 Mannitol/fructose-specific phosphotransferase system, IIA domain
172-295 -57.700 49  [G] COG1445 Phosphotransferase system fructose-specific component IIB
302-641 -110.000 54  [G] COG1299 Phosphotransferase system, fructose-specific IIC component
PDB0113 1-150 -52.600 22  3urr_A mol:protein length:153 PTS IIA-like nitrogen-regulatory protein PtsN
173-278 -55.700 51  2r4q_A mol:protein length:106 Phosphotransferase system (PTS) fructose-spec
298-642 -10.500 16  3qnq_A mol:protein length:442 PTS system, cellobiose-specific IIC component
PfamA26U 5-146 -42.600 20  PF00359.17; A8AYR4_STRGC/491-627; Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2
317-642 -61.900 17  PF13303.1; Q1J8T2_STRPF/28-337; Phosphotransferase system, EIIC
SCOP175 1-150 -51.000 27  d1a6ja_ d.112.1.1 (A:) Nitrogen regulatory bacterial protein IIa-ntr {Escherichia coli [TaxId: 562]}
176-278 -55.400 53  d2r4qa1 c.44.2.2 (A:171-273) Fructose-specific enzyme IIABC component FruA, middle domain {Bacillus subtilis [TaxId: 1423]}
14 gi|238922446|ref|YP_002935959.1| chaperone protein DnaK (EUBREC_0020) [Eubacterium rectale ATCC 33656] 586 COG0113 1-585 -174.000 53  [O] COG0443 Molecular chaperone
PDB0113 1-585 -174.000 52  2kho_A mol:protein length:605 Heat shock protein 70
PfamA26U 4-585 -175.000 52  PF00012.15; HSP77_YEAST/32-633; Hsp70 protein
SCOP175 2-160 -75.000 58  d1bupa1 c.55.1.1 (A:4-188) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]}
160-354 -75.700 42  d1bupa2 c.55.1.1 (A:189-381) Heat shock protein 70kDa, ATPase fragment {Cow (Bos taurus) [TaxId: 9913]}
366-483 -75.900 65  d1dkza2 b.130.1.1 (A:389-506) DnaK {Escherichia coli [TaxId: 562]}
484-585 -31.300 19  d1dkza1 a.8.4.1 (A:507-603) DnaK {Escherichia coli [TaxId: 562]}
15 gi|238922447|ref|YP_002935960.1| hypothetical protein (EUBREC_0021) [Eubacterium rectale ATCC 33656] 290 COG0113 4-285 -16.000 [YU] KOG4460 Nuclear pore complex, Nup88/rNup84 component
PDB0113 1-290 -10.500 1bf5_A mol:protein length:575 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPT
3-260 -15.200 1jch_A mol:protein length:551 COLICIN E3
PfamA26U 4-285 -14.700 10  PF10168.4; Q707M9_XENLA/4-726; Nuclear pore component
SCOP175 3-141 -7.010 10  d1gs9a_ a.24.1.1 (A:) Apolipoprotein E {Human (Homo sapiens), E4 [TaxId: 9606]}
16 gi|238922448|ref|YP_002935961.1| DNA-binding response regulator (EUBREC_0022) [Eubacterium rectale ATCC 33656] 230 COG0113 2-229 -93.400 35  [TK] COG0745 Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain
PDB0113 2-228 -103.000 32  2oqr_A mol:protein length:230 Sensory transduction protein regX3
PfamA26U 1-212 -9.790 PF07688.7; KAIA_SYNY3/5-288; KaiA domain
3-112 -51.600 32  PF00072.19; ZRAR_SALTY/8-118; Response regulator receiver domain
150-226 -38.300 32  PF00486.23; O85058_PROST/114-189; Transcriptional regulatory protein, C terminal
SCOP175 2-117 -63.500 39  d1zesa1 c.23.1.1 (A:3-123) PhoB receiver domain {Escherichia coli [TaxId: 562]}
130-228 -51.800 34  d1p2fa1 a.4.6.1 (A:121-217) Response regulator DrrB {Thermotoga maritima [TaxId: 2336]}
17 gi|238922449|ref|YP_002935962.1|(removed signalp:1-29) hypothetical protein (EUBREC_0023) [Eubacterium rectale ATCC 33656] 428 COG0113 120-427 -59.500 17  [T] COG0642 Signal transduction histidine kinase
PDB0113 141-428 -30.400 10  1jm6_A mol:protein length:407 Pyruvate dehydrogenase kinase, isozyme 2
192-427 -51.600 22  2c2a_A mol:protein length:258 SENSOR HISTIDINE KINASE
PfamA26U 145-409 -17.600 PF03882.9; MUKF_SHIFL/1-440; KicB killing factor
221-422 -17.700 12  PF10090.4; A4YN87_BRASO/37-219; Uncharacterized protein conserved in bacteria (DUF2328 topsan)
SCOP175 192-273 -23.700 23  d2c2aa1 a.30.2.1 (A:232-320) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]}
274-427 -35.200 22  d1bxda_ d.122.1.3 (A:) Histidine kinase domain of the osmosensor EnvZ {Escherichia coli [TaxId: 562]}
18 gi|238922450|ref|YP_002935963.1| hypothetical protein (EUBREC_0024) [Eubacterium rectale ATCC 33656] 761 COG0113 33-761 -125.000 21  [CE] KOG0453 Aconitase/homoaconitase (aconitase superfamily)
PDB0113 17-761 -130.000 21  1aco_A mol:protein length:754 ACONITASE
PfamA26U 1-475 -27.600 14  PF04412.8; Q1M4S5_RHIL3/165-568; Protein of unknown function (DUF521 topsan)
44-479 -80.600 22  PF00330.15; LEUC_YEAST/11-471; Aconitase family (aconitate hydratase)
547-695 -40.000 24  PF00694.14; ACON_BOVIN/582-712; Aconitase C-terminal domain
552-761 -20.700 17  PF06434.8; Q0YRL9_9CHLB/171-373; Aconitate hydratase 2 N-terminus
SCOP175 17-513 -99.200 22  d1acoa2 c.83.1.1 (A:2-528) Aconitase A, N-terminal domain {Cow (Bos taurus) [TaxId: 9913]}
520-761 -44.000 20  d1acoa1 c.8.2.1 (A:529-754) Aconitase A, C-terminal domain {Cow (Bos taurus) [TaxId: 9913]}
19 gi|238922451|ref|YP_002935964.1| hypothetical protein (EUBREC_0025) [Eubacterium rectale ATCC 33656] 437 COG0113 50-426 -52.700 17  [R] COG0628 Predicted permease
PDB0113 139-230 -7.360 1xq8_A mol:protein length:140 Alpha-synuclein
PfamA26U 53-404 -55.400 18  PF01594.11; Y338_HAEIN/10-332; Domain of unknown function DUF20 topsan
SCOP175 42-420 -6.190 11  d1pv7a_ f.38.1.2 (A:) Lactose permease {Escherichia coli [TaxId: 562]}
20 gi|238922452|ref|YP_002935965.1| hypothetical protein (EUBREC_0026) [Eubacterium rectale ATCC 33656] 877 COG0113 2-199 -16.100 14  [R] COG4105 DNA uptake lipoprotein
9-232 -13.100 12  [DO] KOG1174 Anaphase-promoting complex (APC), subunit 7
9-871 -9.720 [R] COG5271 AAA ATPase containing von Willebrand factor type A (vWA) domain
277-840 -11.000 10  [L] KOG1968 Replication factor C, subunit RFC1 (large subunit)
519-876 -11.900 10  [LD] KOG2227 Pre-initiation complex, subunit CDC6, AAA+ superfamily ATPase
662-863 -16.600 12  [U] COG3267 Type II secretory pathway, component ExeA (predicted ATPase)
PDB0113 1-208 -15.000 13  3qky_A mol:protein length:261 Outer membrane assembly lipoprotein YfiO
16-169 -15.400 14  3asd_A mol:protein length:200 MamA
605-877 -45.300 17  3syk_A mol:protein length:309 Protein CbbX
PfamA26U 4-283 -11.500 10  PF12569.3; A9SDC6_PHYPA/187-705; NMDA receptor-regulated protein 1
5-190 -13.100 11  PF04910.9; O80734_ARATH/225-566; Transcriptional repressor TCF25
39-187 -13.200 15  PF13525.1; A6D3Q4_9VIBR/26-235; Outer membrane lipoprotein
631-845 -11.800 14  PF05496.7; RUVB_SOLUE/5-238; Holliday junction DNA helicase ruvB N-terminus
644-877 -9.870 13  PF05621.6; Q48383_KLEAE/1-302; Bacterial TniB protein
SCOP175 2-169 -10.900 11  d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}
643-876 -11.900 10  d1fnna2 c.37.1.20 (A:1-276) CDC6, N-domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}
644-846 -12.100 14  d1iqpa2 c.37.1.20 (A:2-232) Replication factor C {Archaeon Pyrococcus furiosus [TaxId: 2261]}


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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, Godzik A. Database searching by flexible protein structure alignment. Protein Sci. 2004 Jul;13(7):1841-50.