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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|15644635|ref|NP_206803.1| transcription antitermination protein NusB (HP0001) [Helicobacter pylori 26695] 138 COG0113 1-135 -71.600 27  [K] COG0781 Transcription termination factor
PDB0113 1-136 -72.000 28  3d3b_A mol:protein length:141 N utilization substance protein B
PfamA26U 3-129 -66.500 21  PF09185.5; Y027_MYCGE/12-151; Domain of unknown function (DUF1948 topsan)
SCOP175 1-136 -72.400 28  d1ey1a_ a.79.1.1 (A:) Antitermination factor NusB {Escherichia coli [TaxId: 562]}
2 gi|15644636|ref|NP_206804.1| 6,7-dimethyl-8-ribityllumazine synthase (HP0002) [Helicobacter pylori 26695] 156 COG0113 1-156 -89.200 48  [H] COG0054 Riboflavin synthase beta-chain
PDB0113 1-156 -93.300 44  1c2y_A mol:protein length:156 PROTEIN (LUMAZINE SYNTHASE)
PfamA26U 11-154 -88.500 38  PF00885.14; Q5FS93_GLUOX/14-155; 6,7-dimethyl-8-ribityllumazine synthase
SCOP175 1-155 -93.300 50  d1nqua_ c.16.1.1 (A:) Lumazine synthase {Aquifex aeolicus [TaxId: 63363]}
3 gi|15644637|ref|NP_206805.1| 2-dehydro-3-deoxyphosphooctonate aldolase (HP0003) [Helicobacter pylori 26695] 276 COG0113 1-276 -111.000 41  [M] COG2877 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase
PDB0113 9-276 -117.000 50  2ef9_A mol:protein length:267 2-dehydro-3-deoxyphosphooctonate aldolase
PfamA26U 8-243 -12.900 16  PF00793.15; AROG_HAEIN/32-347; DAHP synthetase I family
73-276 -11.500 15  PF03102.9; A4Y8R3_SHEPC/37-279; NeuB family
SCOP175 9-276 -118.000 51  d2a21a1 c.1.10.4 (A:1002-1264) 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase) {Aquifex aeolicus [TaxId: 63363]}
4 gi|15644638|ref|NP_206806.1| carbonic anhydrase (icfA) (HP0004) [Helicobacter pylori 26695] 221 COG0113 2-219 -94.300 23  [P] KOG1578 Predicted carbonic anhydrase involved in protection against oxidative damage
PDB0113 2-209 -96.500 28  1ekj_A mol:protein length:221 BETA-CARBONIC ANHYDRASE
PfamA26U 33-195 -85.000 26  PF00484.14; Q28W87_JANSC/42-203; Carbonic anhydrase
SCOP175 2-209 -96.100 28  d1ekja_ c.53.2.1 (A:) beta-carbonic anhydrase {Pea (Pisum sativum) [TaxId: 3888]}
5 gi|15644639|ref|NP_206807.1| orotidine 5'-phosphate decarboxylase (HP0005) [Helicobacter pylori 26695] 227 COG0113 2-227 -103.000 33  [F] COG0284 Orotidine-5`-phosphate decarboxylase
PDB0113 2-227 -104.000 35  1dbt_A mol:protein length:239 OROTIDINE 5`-PHOSPHATE DECARBOXYLASE
PfamA26U 2-223 -101.000 34  PF00215.19; PYRF_STRP1/5-224; Orotidine 5`-phosphate decarboxylase / HUMPS family
SCOP175 2-227 -104.000 35  d1dbta_ c.1.2.3 (A:) Orotidine 5`-monophosphate decarboxylase (OMP decarboxylase) {Bacillus subtilis [TaxId: 1423]}
6 gi|15644640|ref|NP_206808.1| pantoate--beta-alanine ligase (HP0006) [Helicobacter pylori 26695] 276 COG0113 1-276 -120.000 39  [H] COG0414 Panthothenate synthetase
PDB0113 1-276 -121.000 42  1ufv_A mol:protein length:276 Pantoate-beta-alanine ligase
PfamA26U 3-276 -119.000 39  PF02569.10; PANC_ECOLI/2-280; Pantoate-beta-alanine ligase
SCOP175 1-276 -117.000 38  d2a84a1 c.26.1.4 (A:3-288) Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC) {Mycobacterium tuberculosis [TaxId: 1773]}
7 gi|15646197|ref|NP_206811.1| outer membrane protein (HP0009) [Helicobacter pylori 26695] 634 COG0113 3-634 -10.200 [G] COG4409 Neuraminidase (sialidase)
PDB0113 463-634 -10.600 15  2lhf_A mol:protein length:179 Outer membrane protein H1
PfamA26U 465-634 -61.300 38  PF01856.12; O26005_HELPY/59-248; Helicobacter outer membrane protein
SCOP175 453-634 -9.550 14  d1qjpa_ f.4.1.1 (A:) Outer membrane protein A (OMPA) transmembrane domain {Escherichia coli [TaxId: 562]}
8 gi|15644643|ref|NP_206812.1| chaperonin GroEL (HP0010) [Helicobacter pylori 26695] 546 COG0113 1-539 -156.000 61  [O] COG0459 Chaperonin GroEL (HSP60 family)
PDB0113 1-546 -158.000 60  1grl_A mol:protein length:548 GROEL (HSP60 CLASS)
PfamA26U 22-519 -30.900 15  PF00118.19; A2FL92_TRIVA/36-522; TCP-1/cpn60 chaperonin family
SCOP175 8-257 -19.700 19  d1q3qa1 a.129.1.2 (A:9-145,A:406-526) Thermosome, E domain {Archaeon Thermococcus sp. ks-1, alpha chain [TaxId: 79679]}
184-375 -86.400 63  d1kida_ c.8.5.1 (A:) GroEL, A domain {Escherichia coli [TaxId: 562]}
274-523 -68.300 32  d1kp8a1 a.129.1.1 (A:2-136,A:410-526) GroEL, E domain {Escherichia coli [TaxId: 562]}
9 gi|15644644|ref|NP_206813.1| co-chaperonin GroES (HP0011) [Helicobacter pylori 26695] 118 COG0113 1-90 -50.300 40  [O] COG0234 Co-chaperonin GroES (HSP10)
PDB0113 1-90 -53.400 47  1we3_O mol:protein length:100 cpn10(GroES)
PfamA26U 2-89 -51.300 43  PF00166.16; CH10_CORGL/5-97; Chaperonin 10 Kd subunit
SCOP175 1-90 -52.600 47  d1we3o_ b.35.1.1 (O:) Chaperonin-10 (GroES) {Thermus thermophilus [TaxId: 274]}
10 gi|15644645|ref|NP_206814.1| DNA primase (HP0012) [Helicobacter pylori 26695] 559 COG0113 1-558 -114.000 26  [L] COG0358 DNA primase (bacterial type)
PDB0113 3-415 -98.200 31  2au3_A mol:protein length:407 DNA primase
PfamA26U 2-99 -57.900 46  PF01807.15; PRIM_PSEPU/5-102; CHC2 zinc finger
117-239 -51.900 38  PF08275.6; Q64P92_BACFR/123-254; DNA primase catalytic core, N-terminal domain
249-334 -48.100 44  PF13155.1; C5EJG0_9FIRM/258-343; Toprim-like
352-409 -10.600 10  PF10410.4; Q5QVK4_IDILO/371-429; DnaB-helicase binding domain of primase
SCOP175 1-100 -57.400 40  d1d0qa_ g.41.3.2 (A:) Zinc-binding domain of DNA primase {Bacillus stearothermophilus [TaxId: 1422]}
106-411 -81.100 28  d1dd9a_ e.13.1.1 (A:) DNA primase DnaG catalytic core {Escherichia coli [TaxId: 562]}
11 gi|15644646|ref|NP_206815.1| hypothetical protein (HP0013) [Helicobacter pylori 26695] 350 COG0113 2-341 -67.700 15  [J] COG0482 Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain
PDB0113 2-341 -67.700 16  2hma_A mol:protein length:376 Probable tRNA (5-methylaminomethyl-2-thiourid
PfamA26U 4-341 -68.300 16  PF03054.11; MNMA_HAEIN/25-379; tRNA methyl transferase
SCOP175 2-248 -38.800 14  d2c5sa1 c.26.2.6 (A:174-391) Thiamine biosynthesis protein ThiI, C-terminal domain {Bacillus anthracis [TaxId: 1392]}
12 gi|15644647|ref|NP_206816.1| hypothetical protein (HP0014) [Helicobacter pylori 26695] 275 COG0113 3-263 -12.400 12  [S] COG3802 Uncharacterized protein conserved in bacteria
PDB0113 7-246 -13.500 15  3lzk_A mol:protein length:359 Fumarylacetoacetate hydrolase family protein
PfamA26U 7-239 -9.880 13  PF01557.13; Q1LF48_RALME/58-257; Fumarylacetoacetate (FAA) hydrolase family
SCOP175 7-239 -10.700 15  d1sawa_ d.177.1.1 (A:) FAHD1 (Flj36880, YISKL) {Human (Homo sapiens) [TaxId: 9606]}
13 gi|15644648|ref|NP_206817.1| hypothetical protein (HP0015) [Helicobacter pylori 26695] 93 COG0113 25-91 -9.290 18  [U] COG3838 Type IV secretory pathway, VirB2 components (pilins)
PDB0113 35-92 -5.250 17  3rpj_A mol:protein length:134 Curlin genes transcriptional regulator
PfamA26U 4-93 -7.910 PF04147.7; A4QVL9_MAGO7/41-869; Nop14-like family
SCOP175 46-92 -4.980 15  d2hg7a1 d.186.2.1 (A:1-60) Phage-like element PbsX protein XkdW {Bacillus subtilis [TaxId: 1423]}
14 gi|15644649|ref|NP_206818.1| hypothetical protein (HP0016) [Helicobacter pylori 26695] 87 COG0113 11-86 -15.900 [U] COG3702 Type IV secretory pathway, VirB3 components
PDB0113 65-87 -6.770 26  1ejp_A mol:protein length:28 SYNDECAN-4
PfamA26U 3-80 -11.300 11  PF05101.8; A5I9X1_LEGPC/1-87; Type IV secretory pathway, VirB3-like protein
SCOP175 14-80 -6.860 20  d1h6va2 c.3.1.5 (A:171-292) Mammalian thioredoxin reductase {Rat (Rattus norvegicus) [TaxId: 10116]}
15 gi|15644650|ref|NP_206819.1| virB4 homolog (virB4) (HP0017) [Helicobacter pylori 26695] 787 COG0113 257-786 -75.200 16  [U] COG3451 Type IV secretory pathway, VirB4 components
PDB0113 410-764 -44.200 13  4ag5_A mol:protein length:392 TYPE IV SECRETORY PATHWAY VIRB4 COMPONENTS-LI
PfamA26U 175-375 -43.800 15  PF03135.9; Q9ZE45_RICPR/194-399; CagE, TrbE, VirB family, component of type IV transporter system
406-733 -20.700 12  PF05872.7; Q8YFZ2_BRUME/11-503; Bacterial protein of unknown function (DUF853 topsan)
439-772 -15.100 16  PF02534.9; Q9ZDN4_RICPR/120-569; Type IV secretory system Conjugative DNA transfer
441-717 -33.500 16  PF12846.2; A4JVD5_BURVG/498-898; AAA-like domain
SCOP175 439-787 -19.600 15  d1e9ra_ c.37.1.11 (A:) Bacterial conjugative coupling protein TrwB {Escherichia coli [TaxId: 562]}
16 gi|15644651|ref|NP_206820.1| hypothetical protein (HP0018) [Helicobacter pylori 26695] 469 COG0113 1-469 -146.000 98  [S] COG3014 Uncharacterized protein conserved in bacteria
PDB0113 21-246 -30.300 3u4t_A mol:protein length:272 TPR repeat-containing protein
23-335 -22.600 10  1w3b_A mol:protein length:388 UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUC
35-405 -21.100 10  4abn_A mol:protein length:474 TETRATRICOPEPTIDE REPEAT PROTEIN 5
PfamA26U 20-160 -26.900 11  PF12968.2; Q8KAL8_CHLTE/2-145; Domain of Unknown Function (DUF3856 topsan)
20-240 -24.500 10  PF13429.1; Q39U81_GEOMG/198-480; Tetratricopeptide repeat
21-469 -24.200 12  PF12569.3; A9SDC6_PHYPA/187-705; NMDA receptor-regulated protein 1
SCOP175 23-335 -22.600 10  d1w3ba_ a.118.8.1 (A:) O-GlcNAc transferase p110 subunit, OGT {Human (Homo sapiens) [TaxId: 9606]}
24-258 -31.000 10  d1xnfa_ a.118.8.1 (A:) Lipoprotein NlpI {Escherichia coli [TaxId: 562]}
28-391 -16.600 d1hz4a_ a.118.8.2 (A:) Transcription factor MalT domain III {Escherichia coli [TaxId: 562]}
17 gi|15644652|ref|NP_206821.1| chemotaxis protein (cheV) (HP0019) [Helicobacter pylori 26695] 321 COG0113 1-198 -46.000 23  [NT] COG0835 Chemotaxis signal transduction protein
183-321 -32.000 13  [TK] COG4567 Response regulator consisting of a CheY-like receiver domain and a Fis-type HTH domain
PDB0113 195-318 -43.300 22  4HNR Entity 1(prereleased)
PfamA26U 25-173 -24.300 11  PF01584.14; Q8XQ78_RALSO/559-691; CheW-like domain
199-315 -36.200 22  PF00072.19; ZRAR_SALTY/8-118; Response regulator receiver domain
SCOP175 18-176 -33.900 18  d2ch4w1 b.40.7.1 (W:9-147) Chemotaxis protein CheW {Thermotoga maritima [TaxId: 2336]}
196-320 -41.400 24  d1mb3a_ c.23.1.1 (A:) Cell division response regulator DivK {Caulobacter crescentus [TaxId: 155892]}
18 gi|15644653|ref|NP_206822.1| carboxynorspermidine decarboxylase (nspC) (HP0020) [Helicobacter pylori 26695] 405 COG0113 1-405 -76.100 13  [E] COG0019 Diaminopimelate decarboxylase
PDB0113 1-405 -110.000 48  3n29_A mol:protein length:418 Carboxynorspermidine decarboxylase
PfamA26U 15-264 -35.300 13  PF02784.11; DCOR2_DROME/37-273; Pyridoxal-dependent decarboxylase, pyridoxal binding domain
267-385 -33.600 19  PF00278.17; Q5LXE4_SILPO/280-393; Pyridoxal-dependent decarboxylase, C-terminal sheet domain
SCOP175 15-265 -47.100 16  d1twia2 c.1.6.1 (A:50-313) Diaminopimelate decarboxylase LysA {Archaeon Methanococcus jannaschii [TaxId: 2190]}
250-405 -54.300 18  d1twia1 b.49.2.3 (A:15-49,A:314-448) Diaminopimelate decarboxylase LysA {Archaeon Methanococcus jannaschii [TaxId: 2190]}
19 gi|15644654|ref|NP_206823.1| lipid A 1-phosphatase (HP0021) [Helicobacter pylori 26695] 190 COG0113 9-190 -54.400 14  [S] KOG4268 Uncharacterized conserved protein containing PAP2 domain
PDB0113 26-186 -42.600 14  1d2t_A mol:protein length:231 ACID PHOSPHATASE
PfamA26U 69-189 -44.200 15  PF01569.16; A7N7S4_VIBHB/78-234; PAP2 superfamily
SCOP175 26-186 -44.100 13  d1d2ta_ a.111.1.1 (A:) Bacterial acid phosphatase {Escherichia blattae [TaxId: 563]}
20 gi|15644655|ref|NP_206824.1| lipid A phosphoethanolamine transferase (HP0022) [Helicobacter pylori 26695] 521 COG0113 1-521 -93.500 25  [R] COG2194 Predicted membrane-associated, metal-dependent hydrolase
PDB0113 190-521 -32.000 11  3lxq_A mol:protein length:450 Uncharacterized protein VP1736
PfamA26U 5-226 -10.200 PF11893.3; A4SP91_AERS4/1-253; Domain of unknown function (DUF3413 topsan)
56-207 -23.500 21  PF08019.7; A8FYE5_SHESH/59-214; Domain of unknown function (DUF1705 topsan)
192-517 -28.700 13  PF02995.12; Q9VIP6_DROME/62-563; Protein of unknown function (DUF229 topsan)
SCOP175 218-517 -24.700 13  d1p49a_ c.76.1.2 (A:) Steryl-sulfatase {Human (Homo sapiens) [TaxId: 9606]}


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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.

Reed JC, Doctor K, Rojas A, Zapata JM, Stehlik C, Fiorentino L, Damiano J, Roth W, Matsuzawa S, Newman R, Takayama S, Marusawa H, Xu F, Salvesen G, Godzik A.; RIKEN GER Group; GSL Members. Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res. 2003 Jun;13(6B):1376-88.