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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|60680547|ref|YP_210691.1| hypothetical protein (BF1003) [Bacteroides fragilis NCTC 9343] (Range: 1-117) 117 VFDB 61-112 -5.030 23  VFG000880(gi:26249428) (papI) regulatory protein PapI [P fimbriae (VF0220)] [Escherichia coli CFT073]
2 gi|60680256|ref|YP_210400.1| hypothetical protein (BF0697) [Bacteroides fragilis NCTC 9343] (Range: 1-74) 74 VFDB 26-73 -5.570 20  VFG043465(gi:15903694) (pfbA) cell wall surface anchor family protein, Plasminogen- and Fibronectin-binding protein A [PfbA (VF0525)] [Streptococcus pneumoniae R6]
3 gi|60681449|ref|YP_211593.1| MatE family transmembrane protein (BF1960) [Bacteroides fragilis NCTC 9343] (Range: 1-447) 447 VFDB 12-432 -24.800 11  VFG001339(gi:22537320) (cpsL) polysaccharide biosynthesis protein CpsL [Capsule (VF0274)] [Streptococcus agalactiae 2603V/R]
4 gi|60683425|ref|YP_213569.1| 30S ribosomal protein S14 (BF3990) [Bacteroides fragilis NCTC 9343] (Range: 1-99) 99 VFDB 12-98 -4.520 21  VFG007154(gi:28898438) (vscX) type III secretion system C-ring protein VscX for secretion specificity [T3SS1 (VF0408)] [Vibrio parahaemolyticus RIMD 2210633]
5 gi|60682385|ref|YP_212529.1| putative CTP pyrophosphohydrolase (BF2916) [Bacteroides fragilis NCTC 9343] (Range: 1-130) 130 VFDB 1-72 -5.140 VFG020318(gi:16760658) (cdtB) cytolethal distending toxin B [CdtB (VF0407)] [Salmonella enterica subsp. enterica serovar Typhi str. CT18]
6 gi|60680762|ref|YP_210906.1| putative transmembrane conjugate transposon protein (BF1242) [Bacteroides fragilis NCTC 9343] (Range: 1-110) 110 VFDB 1-58 -13.200 17  VFG002232(gi:49476011) (virB3) type IV secretion system virB3 protein homolog [VirB/VirD4 type IV secretion system (VF0369)] [Bartonella henselae str. Houston-1]
7 gi|60683330|ref|YP_213474.1| ATP-dependent protease ATP-binding subunit ClpX (BF3893) [Bacteroides fragilis NCTC 9343] (Range: 1-415) 415 VFDB 46-385 -14.000 25  VFG000080(gi:16803037) (clpE) ATP-dependent protease [ClpE (VF0073)] [Listeria monocytogenes EGD-e]
8 gi|60682477|ref|YP_212621.1|(removed signalp:1-23) hypothetical protein (BF3007) [Bacteroides fragilis NCTC 9343] (Range: 24-588) 565 VFDB 4-557 -26.900 VFG006662(gi:15645888) (pflA) paralysed flagella protein (pflA) [Flagella (CVF223)] [Helicobacter pylori 26695]
42-347 -27.700 12  VFG045530(gi:52841882) (lpg1654) Dot/Icm type IV secretion system effector [Dot/Icm (VF0156)] [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]
75-324 -31.100 13  VFG042869(gi:52841776) (pilF) type IV pilus biogenesis protein PilF [type IV pili (AI111)] [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]
9 gi|60681243|ref|YP_211387.1| hypothetical protein (BF1751) [Bacteroides fragilis NCTC 9343] (Range: 1-157) 157 VFDB 1-133 -6.320 VFG044455(gi:15604762) (slc1) chaperone for TARP, CT875 [T3SS (SS001)] [Chlamydia trachomatis D/UW-3/CX]
10 gi|60682315|ref|YP_212459.1| hypothetical protein (BF2845) [Bacteroides fragilis NCTC 9343] (Range: 1-207) 207 VFDB 10-164 -4.730 11  VFG043338(gi:52841916) (fliK) flagellar hook-length control protein FliK [polar flagella (AI149)] [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]
11 gi|60680924|ref|YP_211068.1| putative anti-sigma factor (BF1413) [Bacteroides fragilis NCTC 9343] (Range: 1-311) 311 VFDB 86-293 -6.270 11  VFG002346(gi:123442782) (flgG) flagellar basal-body rod protein FlgG [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
12 gi|60683563|ref|YP_213707.1| putative SufE Fe/S-cluster-related protein (BF4142) [Bacteroides fragilis NCTC 9343] (Range: 1-142) 142 VFDB 74-127 -4.540 24  VFG000180(gi:15598297) (xcpT) general secretion pathway protein G [xcp secretion system (VF0084)] [Pseudomonas aeruginosa PAO1]
13 gi|60682225|ref|YP_212369.1| putative two component system response regulator (BF2753) [Bacteroides fragilis NCTC 9343] (Range: 1-225) 225 VFDB 1-224 -88.000 28  VFG001386(gi:15607897) (phoP) Possible two component system response transcriptional positive regulator PhoP [PhoP (VF0286)] [Mycobacterium tuberculosis H37Rv]
14 gi|60682801|ref|YP_212945.1| nicotinate phosphoribosyltransferase (BF3334) [Bacteroides fragilis NCTC 9343] (Range: 1-388) 388 VFDB 9-367 -4.760 12  VFG000630(gi:24114232) (sigA) serine protease, autotransporter SigA [SigA (VF0119)] [Shigella flexneri 2a str. 301]
15 gi|60680875|ref|YP_211019.1| hypothetical protein (BF1359) [Bacteroides fragilis NCTC 9343] (Range: 1-245) 245 VFDB 123-239 -7.790 13  VFG000457(gi:16764499) (csgB) minor curlin subunit precursor, curli nucleator protein CsgB [Agf (VF0103)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]
16 gi|60682029|ref|YP_212173.1| putative bifunctional CbiF/CbiG cobalamin biosynthesis protein (BF2549) [Bacteroides fragilis NCTC 9343] (Range: 1-599) 599 VFDB 2-575 -4.740 VFG010682(gi:52840530) (sdbA) Dot/Icm type IV secretion system effector SdbA [Dot/Icm (SS047)] [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]
17 gi|60681247|ref|YP_211391.1| hypothetical protein (BF1755) [Bacteroides fragilis NCTC 9343] (Range: 1-299) 299 VFDB 89-299 -29.600 VFG041321(gi:52842435) (lpnE) Dot/Icm type IV secretion system effector LpnE [Dot/Icm (SS047)] [Legionella pneumophila subsp. pneumophila str. Philadelphia 1]
18 gi|60681605|ref|YP_211749.1| hypothetical protein (BF2124) [Bacteroides fragilis NCTC 9343] (Range: 1-361) 361 VFDB 107-350 -5.800 VFG002358(gi:123442806) (flhC) flagellar biosynthesis transcription activator FlhC [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
19 gi|60681337|ref|YP_211481.1| hypothetical protein (BF1846) [Bacteroides fragilis NCTC 9343] (Range: 1-71) 71 VFDB 45-70 -4.210 23  VFG002353(gi:123442789) (flgM) negative regulator of flagellin synthesis [Flagella (VF0394)] [Yersinia enterocolitica subsp. enterocolitica 8081]
20 gi|60680681|ref|YP_210825.1| hypothetical protein (BF1156) [Bacteroides fragilis NCTC 9343] (Range: 1-221) 221 VFDB 5-209 -41.000 14  VFG002483(gi:53722527) (tagB-5) Type VI secretion system protein [T6SS-1 (VF0429)] [Burkholderia pseudomallei K96243]

FFAS is supported by the NIH grant R01-GM087218-01
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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.

Friedberg I, Jaroszewski L, Ye Y, Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol. 2004 Jun;14(3):307-12.