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# Query Length Result vs. Range Score %id Covered by template(s)
1 gi|29345411|ref|NP_808914.1| hypothetical protein BT_0001 [Bacteroides thetaiotaomicron VPI-5482] 205 COG0113 185-205 -5.710 23  [J] COG3130 Ribosome modulation factor
PDB0113 1-205 -7.620 1sg3_A mol:protein length:349 Allantoicase
PfamA26U 44-126 -6.030 10  PF05048.8; A0B9A8_METTP/209-441; Periplasmic copper-binding protein (NosD)
SCOP175 4-143 -6.230 15  d1bhea_ b.80.1.3 (A:) Polygalacturonase {Erwinia carotovora, subsp. carotovora [TaxId: 554]}
2 gi|29345412|ref|NP_808915.1|(removed signal:1-19) hypothetical protein BT_0002 [Bacteroides thetaiotaomicron VPI-5482] 312 COG0113 90-275 -5.970 12  [O] KOG1193 Arginyl-tRNA-protein transferase
PDB0113 46-214 -6.450 13  3mc0_B mol:protein length:239 Enterotoxin SEG
PfamA26U 17-211 -6.870 10  PF09365.5; A5GE98_GEOUR/13-224; Conserved hypothetical protein (DUF2461 topsan)
SCOP175 46-139 -7.450 11  d1dfca2 b.42.5.1 (A:1141-1259) Fascin {Human (Homo sapiens) [TaxId: 9606]}
3 gi|29345413|ref|NP_808916.1| hypothetical protein BT_0003 [Bacteroides thetaiotaomicron VPI-5482] 258 COG0113 31-117 -16.200 12  [L] COG0776 Bacterial nucleoid DNA-binding protein
PDB0113 2-258 -105.000 53  4fmr_A mol:protein length:265 uncharacterized hypothetical protein
PfamA26U 32-116 -12.500 11  PF00216.16; A1VGI8_DESVV/5-94; Bacterial DNA-binding protein
SCOP175 32-116 -15.300 16  d1owfb_ a.55.1.1 (B:) Integration host factor beta subunit (IHFB) {Escherichia coli [TaxId: 562]}
4 gi|29345414|ref|NP_808917.1| hypothetical protein BT_0004 [Bacteroides thetaiotaomicron VPI-5482] 222 COG0113 34-185 -6.150 13  [S] COG5352 Uncharacterized protein conserved in bacteria
PDB0113 41-191 -7.860 13  3ltq_A mol:protein length:171 Interleukin-1 beta
PfamA26U 26-159 -7.030 17  PF08664.5; A8FHF3_BACP2/157-299; YcbB domain
SCOP175 64-209 -6.560 21  d1uyla_ d.122.1.1 (A:) HSP90 {Human (Homo sapiens) [TaxId: 9606]}
5 gi|29345415|ref|NP_808918.1| 30S ribosomal protein S17 BT_0005 [Bacteroides thetaiotaomicron VPI-5482] 178 COG0113 29-177 -82.300 18  [J] KOG1728 40S ribosomal protein S11
PDB0113 29-177 -85.600 16  3iz6_P mol:protein length:161 40S ribosomal protein S11 (S17p)
PfamA26U 108-176 -52.300 55  PF00366.15; RS17_THEMA/8-76; Ribosomal protein S17
SCOP175 104-177 -55.000 43  d2gy9q1 b.40.4.5 (Q:5-82) Ribosomal protein S17 {Escherichia coli [TaxId: 562]}
6 gi|29345416|ref|NP_808919.1| hypothetical protein BT_0006 [Bacteroides thetaiotaomicron VPI-5482] 148 COG0113 5-140 -7.210 19  [G] COG3732 Phosphotransferase system sorbitol-specific component IIBC
PDB0113 2-73 -9.500 19  1wwx_A mol:protein length:107 E74-like factor 5 ESE-2b
PfamA26U 4-54 -7.380 13  PF02950.12; CO16A_CONPL/1-79; Conotoxin
SCOP175 2-66 -7.380 21  d1yo5c1 a.4.5.21 (C:247-334) Sam pointed domain containing ets transcription SPDEF {Human (Homo sapiens) [TaxId: 9606]}
7 gi|29345417|ref|NP_808920.1| hypothetical protein BT_0007 [Bacteroides thetaiotaomicron VPI-5482] 130 COG0113 45-122 -8.130 28  [K] COG5450 Transcription regulator of the Arc/MetJ class
PDB0113 47-80 -6.890 26  2gjv_A mol:protein length:175 putative cytoplasmic protein
PfamA26U 21-116 -6.930 13  PF06232.6; Q2HVW6_MEDTR/41-164; Embryo-specific protein 3, (ATS3)
SCOP175 24-79 -6.660 23  d1hrua_ d.115.1.1 (A:) Hypothetical protein YrdC {Escherichia coli [TaxId: 562]}
8 gi|29345418|ref|NP_808921.1| hypothetical protein BT_0008 [Bacteroides thetaiotaomicron VPI-5482] 181 COG0113 1-177 -32.200 10  [R] KOG4144 Arylalkylamine N-acetyltransferase
PDB0113 1-175 -34.400 13  2pr1_A mol:protein length:163 Uncharacterized N-acetyltransferase ylbP
PfamA26U 1-163 -25.000 PF02474.10; A5A959_9BRAD/14-210; Nodulation protein A (NodA)
26-157 -25.800 10  PF13673.1; Q7V9H3_PROMA/20-139; Acetyltransferase (GNAT) domain
SCOP175 1-177 -33.800 11  d1cjwa_ d.108.1.1 (A:) Serotonin N-acetyltranferase {Sheep (Ovis aries) [TaxId: 9940]}
9 gi|29345419|ref|NP_808922.1|(removed signal:1-26) phosphate-binding periplasmic protein precursor, putative ABC transporter BT_0009 [Bacteroides thetaiotaomicron VPI-5482] 343 COG0113 1-343 -107.000 29  [P] COG0226 ABC-type phosphate transport system, periplasmic component
PDB0113 5-336 -109.000 24  1pc3_A mol:protein length:350 Phosphate-binding protein 1
PfamA26U 16-306 -15.300 11  PF12849.2; A1EKQ7_VIBCH/24-252; PBP superfamily domain
SCOP175 16-336 -110.000 24  d1pc3a_ c.94.1.1 (A:) Phosphate-binding protein {Mycobacterium tuberculosis [TaxId: 1773]}
10 gi|29345420|ref|NP_808923.1| hypothetical protein BT_0010 [Bacteroides thetaiotaomicron VPI-5482] 357 COG0113 21-197 -5.920 19  [O] KOG1635 Peptide methionine sulfoxide reductase
PDB0113 72-343 -6.870 14  2ghi_A mol:protein length:260 transport protein
PfamA26U 62-174 -6.110 20  PF05836.7; CH16_DROME/29-138; Chorion protein S16
SCOP175 1-203 -6.840 18  d1fvga_ d.58.28.1 (A:) Peptide methionine sulfoxide reductase {Cow (Bos taurus) [TaxId: 9913]}
11 gi|29345421|ref|NP_808924.1| hypothetical protein BT_0011 [Bacteroides thetaiotaomicron VPI-5482] 282 COG0113 182-276 -10.000 23  [K] KOG3248 Transcription factor TCF-4
PDB0113 195-278 -8.890 26  1mv3_A mol:protein length:213 Myc box dependent interacting protein 1
PfamA26U 198-279 -7.440 26  PF04998.12; RPB1_CAEEL/820-1416; RNA polymerase Rpb1, domain 5
SCOP175 193-282 -6.860 22  d1b3ta_ d.58.8.1 (A:) Epstein barr virus nuclear antigen-1 (ebna1) {Epstein-Barr virus [TaxId: 10376]}
12 gi|29345422|ref|NP_808925.1|(removed signal:1-34) hypothetical protein BT_0012 [Bacteroides thetaiotaomicron VPI-5482] 354 COG0113 1-276 -11.100 10  [M] COG5434 Endopolygalacturonase
PDB0113 2-354 -14.400 1ru4_A mol:protein length:400 Pectate lyase
PfamA26U 2-347 -9.830 PF03718.8; P77813_ARTGO/20-620; Glycosyl hydrolase family 49
SCOP175 2-354 -14.400 d1ru4a_ b.80.1.9 (A:) Pectate transeliminase {Erwinia chrysanthemi [TaxId: 556]}
13 gi|29345423|ref|NP_808926.1| hypothetical protein BT_0013 [Bacteroides thetaiotaomicron VPI-5482] 180 COG0113 1-162 -6.340 15  [H] COG0259 Pyridoxamine-phosphate oxidase
PDB0113 23-168 -7.880 16  2apl_A mol:protein length:157 hypothetical protein PG0816
PfamA26U 5-113 -5.800 13  PF02611.10; A8GL49_SERP5/44-265; CDP-diacylglycerol pyrophosphatase
SCOP175 23-167 -7.980 16  d2apla1 a.258.1.1 (A:2-150) Hypothetical protein PG0816 {Porphyromonas gingivalis [TaxId: 837]}
14 gi|29345424|ref|NP_808927.1| two-component system histidine kinase with response regulator receiver domain BT_0014 [Bacteroides thetaiotaomicron VPI-5482] 807 COG0113 120-570 -43.800 17  [T] COG5000 Signal transduction histidine kinase involved in nitrogen fixation and metabolism regulation
176-556 -49.400 20  [T] COG5002 Signal transduction histidine kinase
558-694 -31.700 15  [T] COG4999 Uncharacterized domain of BarA-like signal transduction histidine kinases
576-788 -29.300 10  [T] COG2198 FOG: HPt domain
PDB0113 181-550 -41.200 21  3a0r_A mol:protein length:349 Sensor protein
295-555 -65.300 25  4ew8_A mol:protein length:268 Sensor protein divL
414-801 -27.500 10  2zbk_B mol:protein length:530 Type 2 DNA topoisomerase 6 subunit B
450-694 -57.200 19  2ayx_A mol:protein length:254 Sensor kinase protein rcsC
PfamA26U 302-538 -23.000 11  PF03882.9; MUKF_SHIFL/1-440; KicB killing factor
327-391 -24.600 30  PF00512.20; Q55783_SYNY3/185-253; His Kinase A (phospho-acceptor) domain
570-682 -28.200 29  PF00072.19; ZRAR_SALTY/8-118; Response regulator receiver domain
SCOP175 295-394 -21.400 28  d2c2aa1 a.30.2.1 (A:232-320) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]}
395-548 -47.200 30  d2c2aa2 d.122.1.3 (A:321-481) Sensor histidine kinase TM0853 {Thermotoga maritima [TaxId: 2336]}
563-694 -37.500 26  d2ayxa1 c.23.1.1 (A:817-949) Sensor kinase protein RcsC, C-terminal domain {Escherichia coli [TaxId: 562]}
567-750 -19.600 19  d1s8na_ c.23.1.1 (A:) Probable two-component system transcriptional regulator Rv1626 {Mycobacterium tuberculosis [TaxId: 1773]}
675-788 -12.200 d1sr2a_ a.24.10.4 (A:) Sensor-like histidine kinase YojN, C-terminal domain {Escherichia coli [TaxId: 562]}
15 gi|29345425|ref|NP_808928.1| rteB, two-component system response regulator BT_0015 [Bacteroides thetaiotaomicron VPI-5482] 432 COG0113 2-432 -120.000 35  [T] COG2204 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains
PDB0113 2-363 -109.000 39  3dzd_A mol:protein length:368 Transcriptional regulator (NtrC family)
125-428 -103.000 43  1ojl_A mol:protein length:304 TRANSCRIPTIONAL REGULATORY PROTEIN ZRAR
PfamA26U 4-114 -41.900 30  PF00072.19; ZRAR_SALTY/8-118; Response regulator receiver domain
5-350 -28.200 10  PF08298.6; YEAG_ECOLI/19-380; PrkA AAA domain
127-293 -81.000 46  PF00158.21; Q8E8E7_SHEON/154-320; Sigma-54 interaction domain
388-429 -12.800 31  PF02954.14; Q52200_PSEPU/518-559; Bacterial regulatory protein, Fis family
SCOP175 2-121 -44.900 28  d1krwa_ c.23.1.1 (A:) NTRC receiver domain {Salmonella typhimurium [TaxId: 90371]}
126-373 -97.800 44  d1ny5a2 c.37.1.20 (A:138-384) Transcriptional activator sigm54 (NtrC1), C-terminal domain {Aquifex aeolicus [TaxId: 63363]}
339-432 -25.700 27  d1ntca_ a.4.1.12 (A:) DNA-binding domain of NTRC {Salmonella typhimurium [TaxId: 90371]}
16 gi|29345426|ref|NP_808929.1| hypothetical protein BT_0016 [Bacteroides thetaiotaomicron VPI-5482] 212 COG0113 1-212 -6.310 [Z] KOG3565 Cdc42-interacting protein CIP4
PDB0113 133-212 -7.120 15  1hfe_S mol:protein length:123 PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1)
PfamA26U 2-211 -56.800 14  PF09357.5; Q64WJ7_BACFR/81-300; RteC protein
SCOP175 129-211 -5.630 13  d1jr8a_ a.24.15.1 (A:) Thiol oxidase Erv2p {Baker`s yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
17 gi|29345427|ref|NP_808930.1| hypothetical protein BT_0017 [Bacteroides thetaiotaomicron VPI-5482] 315 COG0113 33-234 -6.540 [P] COG3256 Nitric oxide reductase large subunit
PDB0113 33-234 -7.080 10  3ayf_A mol:protein length:800 Nitric oxide reductase
PfamA26U 193-313 -6.390 15  PF06936.6; SELS_MOUSE/1-188; Selenoprotein S (SelS)
SCOP175 9-81 -6.760 d1ukfa_ d.3.1.10 (A:) Avirulence protein Avrpph3 {Pseudomonas syringae pv. phaseolicola [TaxId: 319]}
18 gi|29345428|ref|NP_808931.1| hypothetical protein BT_0018 [Bacteroides thetaiotaomicron VPI-5482] 238 COG0113 89-238 -5.660 [O] COG0652 Peptidyl-prolyl cis-trans isomerase (rotamase) - cyclophilin family
PDB0113 1-146 -7.700 1ukf_A mol:protein length:188 Avirulence protein AVRPPH3
PfamA26U 45-209 -7.140 11  PF12000.3; A4F0P0_9RHOB/24-194; Gkycosyl transferase family 4 group
SCOP175 1-146 -7.700 d1ukfa_ d.3.1.10 (A:) Avirulence protein Avrpph3 {Pseudomonas syringae pv. phaseolicola [TaxId: 319]}
19 gi|29345429|ref|NP_808932.1| hypothetical protein BT_0019 [Bacteroides thetaiotaomicron VPI-5482] 106 COG0113 4-77 -7.230 12  [B] KOG3844 Predicted component of NuA3 histone acetyltransferase complex
PDB0113 52-104 -7.580 17  2vt1_B mol:protein length:93 SURFACE PRESENTATION OF ANTIGENS PROTEIN SPAS
PfamA26U 7-84 -9.200 17  PF06857.6; CITD_ERWCT/2-87; Malonate decarboxylase delta subunit (MdcD)
SCOP175 52-104 -6.690 17  g2vt1.1 d.367.1.1 (A:237-257,B:258-338) Surface presentation of antigens protein SpaS {Shigella flexneri [TaxId: 623]}
20 gi|29345430|ref|NP_808933.1| hypothetical protein BT_0020 [Bacteroides thetaiotaomicron VPI-5482] 152 COG0113 43-151 -6.290 10  [P] COG2156 K+-transporting ATPase, c chain
PDB0113 35-151 -7.490 1nfp_A mol:protein length:228 LUXF GENE PRODUCT
PfamA26U 46-89 -6.570 PF09201.5; A7TFS7_VANPO/1-148; SRX
SCOP175 35-151 -7.490 d1nfpa_ c.1.16.2 (A:) Non-fluorescent flavoprotein (luxF, FP390) {Photobacterium leiognathi [TaxId: 553611]}


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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.

Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A. FFAS03: a server for profile--profile sequence alignments. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W284-8.