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# Query Length Result vs. Range Score %id Covered by template(s)
1 CE21227 CE21227 1315 PDB-2004-06-11 525 COG0312 6-521 -144.000 50  [I] KOG0693 Myo-inositol-1-phosphate synthase
PDB0312 1-525 -158.000 100  1vko_A mol:protein length:537 inositol-3-phosphate synthase
PfamA26U 65-498 -118.000 56  PF07994.7; Q6CFS3_YARLI/75-512; Myo-inositol-1-phosphate synthase
SCOP175 11-427 -93.400 39  d1p1ja1 c.2.1.3 (A:9-322,A:438-533) Myo-inositol 1-phosphate synthase {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
2 TM0001 TM0001 281882 Purified-2001-08-24 41 COG0312 6-41 -3.330 13  [A] KOG1780 Small Nuclear ribonucleoprotein G
PDB0312 10-39 -6.690 26  2jxc_B mol:protein length:45 Stonin-2
PfamA26U 13-33 -4.810 38  PF07660.9; A6C2R4_9PLAN/303-351; Secretin and TonB N terminus short domain
SCOP175 9-39 -4.890 32  d1skza1 g.3.15.1 (A:7-58) Factor Xa inhibitor antistasin {Mexican leech (Haementeria officinalis) [TaxId: 6410]}
3 TM0002 TM0002 281883 Purified-2001-08-29 41 COG0312 8-35 -4.100 28  [J] COG0256 Ribosomal protein L18
PDB0312 8-29 -4.610 31  2cmy_B mol:protein length:34 VERONICA HEDERIFOLIA TRYPSIN INHIBITOR
PfamA26U 3-35 -5.790 PF03004.9; Q9M9D8_ARATH/153-297; Plant transposase (Ptta/En/Spm family)
SCOP175 1-27 -4.440 34  d1k0ra4 d.202.1.1 (A:-4-99) Transcription factor NusA, N-terminal domain {Mycobacterium tuberculosis [TaxId: 1773]}
4 TM0003 TM0003 281884 Purified-2001-12-06 40 COG0312 1-37 -3.840 13  [E] COG4401 Chorismate mutase
PDB0312 1-24 -4.600 12  1vry_A mol:protein length:76 Glycine receptor alpha-1 chain
PfamA26U 23-39 -4.180 35  PF01840.12; TCL1A_MOUSE/1-111; TCL1/MTCP1 family
SCOP175 8-36 -4.550 24  d1ufya_ d.79.1.2 (A:) Chorismate mutase {Thermus thermophilus [TaxId: 274]}
5 TM0004 TM0004 281885 Purified-2004-07-19 31 COG0312 12-28 -2.820 17  [UR] KOG4677 Golgi integral membrane protein
PDB0312 4-31 -4.230 10  2yue_A mol:protein length:168 Protein neuralized
PfamA26U 6-31 -4.540 15  PF02791.12; Q7RXP4_NEUCR/357-420; DDT domain
SCOP175 2-26 -3.060 16  d1ngka_ a.1.1.1 (A:) Protozoan/bacterial hemoglobin {Mycobacterium tuberculosis, HbO [TaxId: 1773]}
6 TM0005 TM0005 281886 Purified-2001-01-30 650 COG0312 2-649 -122.000 24  [L] KOG1803 DNA helicase
PDB0312 1-649 -118.000 26  2wjv_A mol:protein length:800 REGULATOR OF NONSENSE TRANSCRIPTS 1
PfamA26U 170-419 -58.600 30  PF13086.1; B6HQI4_PENCW/1305-1589; AAA domain
424-626 -71.000 33  PF13087.1; D3ZG52_RAT/805-1017; AAA domain
SCOP175 161-650 -14.200 14  g1qhh.1 c.37.1.19 (A:,B:,C:,D:) DEXX box DNA helicase {Bacillus stearothermophilus, PcrA [TaxId: 1422]}
170-448 -15.000 18  d1w36d1 c.37.1.19 (D:2-360) Exodeoxyribonuclease V alpha chain (RecD) {Escherichia coli [TaxId: 562]}
7 TM0006 TM0006 281887 Diffraction|HSQC-2004-07-13 345 COG0312 4-345 -65.600 19  [H] COG1441 O-succinylbenzoate synthase
PDB0312 1-345 -99.400 100  2zad_A mol:protein length:345 Muconate cycloisomerase
PfamA26U 6-123 -42.500 22  PF02746.11; CLCB_PSEPU/5-125; Mandelate racemase / muconate lactonizing enzyme, N-terminal domain
141-311 -33.500 17  PF07476.6; O66145_CITAM/161-411; Methylaspartate ammonia-lyase C-terminus
241-345 -26.700 15  PF13378.1; DGOD_VEREI/234-351; Enolase C-terminal domain-like
SCOP175 2-124 -51.500 26  d1jpma2 d.54.1.1 (A:1-125) L-Ala-D/L-Glu epimerase {Bacillus subtilis [TaxId: 1423]}
126-345 -65.800 38  d1jpma1 c.1.11.2 (A:126-359) L-Ala-D/L-Glu epimerase {Bacillus subtilis [TaxId: 1423]}
8 TM0007 TM0007 281888 Purified-2004-07-19 438 COG0312 12-437 -31.700 11  [O] KOG0909 Peptide:N-glycanase
39-394 -39.700 11  [D] KOG4575 TGc (transglutaminase/protease-like) domain-containing protein involved in cytokinesis
147-395 -51.500 15  [E] COG1305 Transglutaminase-like enzymes, putative cysteine proteases
PDB0312 6-371 -30.100 11  3kd4_A mol:protein length:506 Putative protease
137-394 -54.500 19  3isr_A mol:protein length:293 Transglutaminase-like enzymes, putative cyste
196-435 -35.000 15  2f4m_A mol:protein length:295 peptide N-glycanase
PfamA26U 229-364 -31.500 11  PF14381.1; B9SY16_RICCO/70-280; Ethylene-responsive protein kinase Le-CTR1
259-363 -56.300 18  PF01841.14; Q0W040_UNCMA/73-192; Transglutaminase-like superfamily
316-418 -15.400 13  PF14402.1; A4SPP0_AERS4/186-501; 7 transmembrane helices usually fused to an inactive transglutaminase
SCOP175 196-435 -35.600 15  d2f4ma1 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {Mouse (Mus musculus) [TaxId: 10090]}
9 TM0008 TM0008 281889 Crystal|NMR-2001-04-01 224 COG0312 1-224 -82.100 31  [R] COG1878 Predicted metal-dependent hydrolase
PDB0312 1-224 -81.800 27  1r61_A mol:protein length:207 metal-dependent hydrolase
PfamA26U 2-158 -69.300 20  PF04199.8; A8MEU2_ALKOO/9-169; Putative cyclase
SCOP175 1-224 -83.000 27  d1r61a_ c.8.8.1 (A:) Unnamed protein {Bacillus stearothermophilus [TaxId: 1422]}
10 TM0009 TM0009 281890 Purified-2001-02-14 142 COG0312 1-141 -45.600 20  [S] COG1633 Uncharacterized conserved protein
PDB0312 1-141 -53.000 32  1vjx_A mol:protein length:157 putative ferritin-like diiron-carboxylate pro
PfamA26U 3-141 -44.800 13  PF13668.1; A3XPH6_LEEBM/59-205; Ferritin-like domain
SCOP175 2-141 -53.300 32  d1vjxa_ a.25.1.1 (A:) Hypothetical protein TM1526 {Thermotoga maritima [TaxId: 2336]}
11 TM0010 TM0010 281891 Purified-2005-03-03 607 COG0312 24-570 -48.200 15  [C] COG4656 Predicted NADH:ubiquinone oxidoreductase, subunit RnfC
46-537 -115.000 35  [C] KOG2658 NADH:ubiquinone oxidoreductase, NDUFV1/51kDa subunit
405-604 -30.400 25  [C] COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB
PDB0312 3-103 -24.600 30  1f37_A mol:protein length:110 FERREDOXIN [2FE-2S]
103-536 -109.000 44  2fug_1 mol:protein length:438 NADH-quinone oxidoreductase chain 1
540-598 -24.200 25  2vkr_A mol:protein length:103 ZINC-CONTAINING FERREDOXIN
PfamA26U 2-81 -10.300 21  PF01257.14; Q1HPR5_BOMMO/56-203; Respiratory-chain NADH dehydrogenase 24 Kd subunit
158-329 -40.700 27  PF01512.12; A1U014_MARAV/14-154; Respiratory-chain NADH dehydrogenase 51 Kd subunit
415-589 -10.300 14  PF00757.15; INSR_XENLA/189-350; Furin-like cysteine rich region
439-484 -23.100 65  PF10589.4; A7ALS7_9PORP/404-449; NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
547-593 -21.800 42  PF13187.1; Q8PZV2_METMA/251-319; 4Fe-4S dicluster domain
SCOP175 5-96 -24.500 31  d1m2da_ c.47.1.11 (A:) Thioredoxin-like 2Fe-2S ferredoxin {Aquifex aeolicus [TaxId: 63363]}
110-349 -86.500 49  d2fug12 c.142.1.1 (1:7-249) NADH-quinone oxidoreductase chain 1, Nqo1 {Thermus thermophilus [TaxId: 274]}
351-434 -34.800 44  d2fug13 d.15.13.1 (1:250-333) NADH-quinone oxidoreductase chain 1, Nqo1 {Thermus thermophilus [TaxId: 274]}
435-536 -46.900 42  d2fug11 a.29.12.1 (1:334-438) NADH-quinone oxidoreductase chain 1, Nqo1 {Thermus thermophilus [TaxId: 274]}
518-598 -34.300 31  d1hfel2 d.58.1.5 (L:2-86) Fe-only hydrogenase larger subunit, N-domain {Desulfovibrio desulfuricans [TaxId: 876]}
12 TM0011 TM0011 281892 Purified-2004-02-02 128 COG0312 1-127 -49.700 23  [C] COG3411 Ferredoxin
PDB0312 30-128 -48.900 28  1f37_A mol:protein length:110 FERREDOXIN [2FE-2S]
PfamA26U 3-110 -29.900 20  PF01257.14; Q1HPR5_BOMMO/56-203; Respiratory-chain NADH dehydrogenase 24 Kd subunit
SCOP175 3-117 -27.400 15  d2fug21 c.47.1.21 (2:3-180) NADH-quinone oxidoreductase chain 2, NQO2 {Thermus thermophilus [TaxId: 274]}
33-125 -46.400 28  d1m2da_ c.47.1.11 (A:) Thioredoxin-like 2Fe-2S ferredoxin {Aquifex aeolicus [TaxId: 63363]}
13 TM0012 TM0012 281893 Purified-2001-08-29 176 COG0312 1-172 -85.300 26  [C] COG1905 NADH:ubiquinone oxidoreductase 24 kD subunit
PDB0312 16-175 -87.200 27  2fug_2 mol:protein length:181 NADH-quinone oxidoreductase chain 2
PfamA26U 26-173 -82.700 34  PF01257.14; Q1HPR5_BOMMO/56-203; Respiratory-chain NADH dehydrogenase 24 Kd subunit
SCOP175 18-175 -87.900 27  d2fug21 c.47.1.21 (2:3-180) NADH-quinone oxidoreductase chain 2, NQO2 {Thermus thermophilus [TaxId: 274]}
14 TM0013 TM0013 281894 Purified-2001-08-24 253 COG0312 1-252 -69.700 15  [C] COG0426 Uncharacterized flavoproteins
PDB0312 1-242 -82.300 13  3hnn_A mol:protein length:262 Putative diflavin flavoprotein A 5
PfamA26U 28-238 -18.700 14  PF14234.1; B4VMX6_9CYAN/40-360; Domain of unknown function (DUF4336 topsan)
SCOP175 1-242 -81.500 17  d1e5da2 d.157.1.3 (A:2-250) Rubredoxin oxygen:oxidoreductase (ROO), N-terminal domain {Desulfovibrio gigas [TaxId: 879]}
15 TM0014 TM0014 281895 Purified-2001-01-30 278 COG0312 2-277 -41.300 22  [NT] COG0840 Methyl-accepting chemotaxis protein
PDB0312 4-277 -53.500 19  2ch7_A mol:protein length:309 METHYL-ACCEPTING CHEMOTAXIS PROTEIN
42-253 -62.400 100  3g67_A mol:protein length:213 Methyl-accepting chemotaxis protein
PfamA26U 1-263 -32.600 10  PF03532.8; O50963_BORBU/3-255; OMS28 porin
82-277 -39.900 22  PF00015.16; MCPC_SALTY/323-517; Methyl-accepting chemotaxis protein (MCP) signalling domain
SCOP175 39-188 -8.670 14  d1qkra_ a.24.9.1 (A:) Vinculin {Chicken (Gallus gallus) [TaxId: 9031]}
16 TM0015 TM0015 281896 PDB-2007-09-14 192 COG0312 7-192 -51.400 22  [C] COG1014 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit
PDB0312 1-192 -95.300 100  2raa_A mol:protein length:204 Pyruvate synthase subunit porC
PfamA26U 16-186 -59.200 20  PF01558.13; Q31EX2_THICR/20-185; Pyruvate ferredoxin/flavodoxin oxidoreductase
SCOP175 6-192 -62.400 18  d2c42a4 c.64.1.1 (A:416-668) Pyruvate-ferredoxin oxidoreductase, PFOR, domain III {Desulfovibrio africanus [TaxId: 873]}
17 TM0016 TM0016 281897 Purified-2001-08-24 101 COG0312 1-100 -36.000 25  [C] KOG3256 NADH:ubiquinone oxidoreductase, NDUFS8/23 kDa subunit
PDB0312 1-100 -32.400 30  2fug_9 mol:protein length:182 NADH-quinone oxidoreductase chain 9
PfamA26U 42-88 -20.900 31  PF13187.1; Q8PZV2_METMA/251-319; 4Fe-4S dicluster domain
SCOP175 16-100 -33.700 31  d2fug91 d.58.1.5 (9:26-179) NADH-quinone oxidoreductase chain 9, Nqo9 {Thermus thermophilus [TaxId: 274]}
18 TM0017 TM0017 281898 Purified-2003-03-05 394 COG0312 6-393 -104.000 32  [C] COG0674 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit
PDB0312 7-393 -66.100 29  1b0p_A mol:protein length:1231 PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
PfamA26U 20-197 -41.700 28  PF01855.14; KORA_ARCFU/14-229; Pyruvate flavodoxin/ferredoxin oxidoreductase, thiamine diP-bdg
265-365 -12.700 17  PF02780.15; O16144_ASCSU/223-346; Transketolase, C-terminal domain
SCOP175 7-256 -83.200 28  d2c42a1 c.36.1.8 (A:2-258) Pyruvate-ferredoxin oxidoreductase, PFOR, domain I {Desulfovibrio africanus [TaxId: 873]}
257-393 -47.900 31  d2c42a3 c.48.1.3 (A:259-415) Pyruvate-ferredoxin oxidoreductase, PFOR, domain II {Desulfovibrio africanus [TaxId: 873]}
19 TM0018 TM0018 281899 Purified-2001-08-24 324 COG0312 13-308 -60.600 18  [C] COG1013 Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit
PDB0312 4-322 -51.400 27  1b0p_A mol:protein length:1231 PROTEIN (PYRUVATE-FERREDOXIN OXIDOREDUCTASE)
PfamA26U 55-224 -10.400 16  PF02775.16; Q6LZH8_METMP/393-541; Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
SCOP175 5-318 -70.000 27  d2c42a2 c.36.1.12 (A:786-1232) Pyruvate-ferredoxin oxidoreductase, PFOR, domains VI {Desulfovibrio africanus [TaxId: 873]}
20 TM0019 TM0019 281900 Crystal|NMR-2004-03-31 256 COG0312 5-252 -92.000 29  [R] KOG0725 Reductases with broad range of substrate specificities
PDB0312 1-254 -94.500 39  2d1y_A mol:protein length:256 hypothetical protein TT0321
PfamA26U 13-249 -57.200 13  PF13561.1; A1ZQI0_9BACT/15-256; Enoyl-(Acyl carrier protein) reductase
SCOP175 1-252 -94.800 40  d2d1ya1 c.2.1.2 (A:2-249) Hypothetical protein TTHA0369 {Thermus thermophilus [TaxId: 274]}


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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.

Plewczynski D, Rychlewski L, Ye Y, Jaroszewski L, Godzik A. Integrated web service for improving alignment quality based on segments comparison. BMC Bioinformatics. 2004 Jul 22;5(1):98.