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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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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.

Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003 Oct;19 Suppl 2:II246-II255.