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Shows best template from each database, and all templates with significant scores covering different query fragments

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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 PfamA30U 5-71 -9.870 20  PF11638.6; DNAA_LAWIP/5-67; DnaA N-terminal domain
113-334 -107.000 60  PF00308.16; DNAA_STRCO/317-535; Bacterial dnaA protein
361-429 -34.600 42  PF08299.9; D9QS97_ACEAZ/358-426; Bacterial dnaA protein helix-turn-helix
2 gi|238922434|ref|YP_002935947.1| DNA polymerase III, beta subunit (EUBREC_0002) [Eubacterium rectale ATCC 33656] 370 PfamA30U 1-118 -39.800 33  PF00712.17; DPO3B_CAUCR/1-121; DNA polymerase III beta subunit, N-terminal domain
128-243 -43.600 28  PF02767.14; DPO3B_PSEPK/129-244; DNA polymerase III beta subunit, central domain
245-364 -48.100 30  PF02768.13; DPO3B_BACSU/253-376; DNA polymerase III beta subunit, C-terminal domain
3 gi|238922435|ref|YP_002935948.1| hypothetical protein (EUBREC_0003) [Eubacterium rectale ATCC 33656] 71 PfamA30U 6-70 -46.300 56  PF13275.4; D4IXS8_BUTFI/4-68; S4 domain
4 gi|238922436|ref|YP_002935949.1| DNA replication and repair protein RecF (EUBREC_0004) [Eubacterium rectale ATCC 33656] 362 PfamA30U 1-335 -19.700 15  PF13175.4; I1YS32_PREI7/1-378; AAA ATPase domain
5 gi|238922437|ref|YP_002935950.1| DNA gyrase, B subunit (EUBREC_0005) [Eubacterium rectale ATCC 33656] 645 PfamA30U 230-399 -84.500 46  PF00204.23; A9KS52_CLOPH/226-396; DNA gyrase B
540-640 -23.100 19  PF16898.3; K5XBZ3_PHACS/641-767; C-terminal associated domain of TOPRIM
571-634 -43.200 59  PF00986.19; M9X0E0_MANHA/738-800; DNA gyrase B subunit, carboxyl terminus
6 gi|238922438|ref|YP_002935951.1| DNA gyrase, A subunit (EUBREC_0006) [Eubacterium rectale ATCC 33656] 852 PfamA30U 33-476 -62.000 21  PF00521.18; A0A0D1DXS4_USTMA/785-1232; DNA gyrase/topoisomerase IV, subunit A
614-659 -13.100 47  PF03989.11; GYRA_HAEIN/641-686; DNA gyrase C-terminal domain, beta-propeller
7 gi|238922439|ref|YP_002935952.1| hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit (EUBREC_0007) [Eubacterium rectale ATCC 33656] 281 PfamA30U 11-278 -119.000 56  PF05681.12; D4KEY3_9FIRM/11-279; Fumarate hydratase (Fumerase)
8 gi|238922440|ref|YP_002935953.1| hypothetical protein (EUBREC_0008) [Eubacterium rectale ATCC 33656] 47 PfamA30U 22-41 -5.770 20  PF10659.7; Q57TR4_TRYB2/411-523; Trypanosome variant surface glycoprotein C-terminal domain
9 gi|238922441|ref|YP_002935954.1| fumarate hydratase subunit B (EUBREC_0009) [Eubacterium rectale ATCC 33656] 183 PfamA30U 1-175 -84.500 39  PF05683.10; W4Y8Y1_STRPU/30-236; Fumarase C-terminus
10 gi|238922442|ref|YP_002935955.1| putative oxidoreductase (EUBREC_0016) [Eubacterium rectale ATCC 33656] 329 PfamA30U 4-119 -26.300 15  PF01408.20; YEAH_SCHPO/36-187; Oxidoreductase family, NAD-binding Rossmann fold
125-245 -17.100 PF08635.8; A0A0D1E5T6_USTMA/241-382; Putative oxidoreductase C terminal
11 gi|238922443|ref|YP_002935956.1| transcription repressor of fructose operon FruR (EUBREC_0017) [Eubacterium rectale ATCC 33656] 247 PfamA30U 4-126 -27.200 12  PF06163.9; A0A070SGS2_ECOLX/1-127; Bacterial protein of unknown function (DUF977 topsan)
76-232 -55.300 26  PF00455.20; A9CFA5_AGRFC/78-235; DeoR C terminal sensor domain
12 gi|238922444|ref|YP_002935957.1| fructose-1-phosphate kinase (EUBREC_0018) [Eubacterium rectale ATCC 33656] 305 PfamA30U 24-279 -19.200 16  PF00294.22; ADK_YEAST/21-336; pfkB family carbohydrate kinase
13 gi|238922445|ref|YP_002935958.1| PTS system, fructose-specific, IIABC component (EUBREC_0019) [Eubacterium rectale ATCC 33656] 642 PfamA30U 5-146 -41.100 20  PF00359.20; A8AYR4_STRGC/491-627; Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2
319-641 -46.200 18  PF13303.4; Q9A1Q9_STRP1/29-336; Phosphotransferase system, EIIC
14 gi|238922446|ref|YP_002935959.1| chaperone protein DnaK (EUBREC_0020) [Eubacterium rectale ATCC 33656] 586 PfamA30U 4-585 -179.000 52  PF00012.18; HSP7E_DROME/54-653; Hsp70 protein
15 gi|238922447|ref|YP_002935960.1| hypothetical protein (EUBREC_0021) [Eubacterium rectale ATCC 33656] 290 PfamA30U 2-172 -10.200 PF05478.9; F1S5C8_PIG/18-820; Prominin
16 gi|238922448|ref|YP_002935961.1| DNA-binding response regulator (EUBREC_0022) [Eubacterium rectale ATCC 33656] 230 PfamA30U 3-108 -48.400 28  PF00072.22; RSSB_ECOLI/10-121; Response regulator receiver domain
150-226 -27.200 32  PF00486.26; I0DPC2_PROSM/145-220; Transcriptional regulatory protein, C terminal
17 gi|238922449|ref|YP_002935962.1|(removed signalp:1-29) hypothetical protein (EUBREC_0023) [Eubacterium rectale ATCC 33656] 428 PfamA30U 206-270 -14.200 24  PF00512.23; Q55783_SYNY3/185-253; His Kinase A (phospho-acceptor) domain
223-422 -10.600 12  PF10090.7; V5SF53_9RHIZ/32-212; Histidine phosphotransferase
318-428 -20.400 27  PF02518.24; O52937_9CYAN/626-739; Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
18 gi|238922450|ref|YP_002935963.1| hypothetical protein (EUBREC_0024) [Eubacterium rectale ATCC 33656] 761 PfamA30U 47-479 -51.600 21  PF00330.18; D2R1Y9_PIRSD/11-461; Aconitase family (aconitate hydratase)
549-759 -12.900 13  PF06434.11; Q01EA0_OSTTA/235-442; Aconitate hydratase 2 N-terminus
550-696 -44.700 23  PF00694.17; ACON_BOVIN/582-712; Aconitase C-terminal domain
19 gi|238922451|ref|YP_002935964.1| hypothetical protein (EUBREC_0025) [Eubacterium rectale ATCC 33656] 437 PfamA30U 62-403 -36.200 18  PF01594.14; Y338_HAEIN/10-332; AI-2E family transporter
20 gi|238922452|ref|YP_002935965.1| hypothetical protein (EUBREC_0026) [Eubacterium rectale ATCC 33656] 877 PfamA30U 10-194 -12.000 15  PF13429.4; Q39U81_GEOMG/198-480; Tetratricopeptide repeat
16-283 -11.200 PF12569.6; A9SDC6_PHYPA/187-705; NMDA receptor-regulated protein 1


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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.

Li W, Godzik A. cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006 May 26;