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

Results: 1-20 of 2301next page >

# Query Length Result vs. Range Score %id Covered by template(s)
1 VFG0865 aap/aspU - Dispersin [Escherichia coli 17-2] (VF0215) 116 COG0113 1-86 -6.600 19  [R] COG3942 Surface antigen
PDB0113 22-115 -45.600 95  2jvu_A mol:protein length:104 DISPERSIN
PfamA26U 1-60 -8.220 19  PF06607.6; PROK1_HUMAN/1-97; Prokineticin
SCOP175 19-56 -7.200 15  d1ly2a1 g.18.1.1 (A:0-66) Complement receptor 2, cr2 {Human (Homo sapiens) [TaxId: 9606]}
2 VFG2285 (gi:110800384) nanH - sialidase [Clostridium perfringens ATCC 13124] (VF0391) 382 COG0113 3-373 -56.300 21  [G] COG4409 Neuraminidase (sialidase)
PDB0113 4-381 -79.100 33  1dil_A mol:protein length:381 SIALIDASE
PfamA26U 38-362 -47.100 20  PF13859.1; Q4E5U1_TRYCR/92-446; BNR repeat-like domain
SCOP175 4-381 -79.400 33  d3sila_ b.68.1.1 (A:) Salmonella sialidase {Salmonella typhimurium, strain lt2 [TaxId: 90371]}
3 VFG2286 (gi:110801889) cpe - enterotoxin Cpe [Clostridium perfringens SM101] (VF0383) 319 COG0113 235-307 -4.650 12  [J] COG0023 Translation initiation factor 1 (eIF-1/SUI1) and related proteins
PDB0113 1-319 -152.000 100  3am2_A mol:protein length:328 Heat-labile enterotoxin B chain
PfamA26U 55-240 -70.700 19  PF03505.9; Q45877_CLOBO/230-426; Clostridium enterotoxin
SCOP175 214-318 -5.490 17  d1nqja_ b.23.2.1 (A:) Class 1 collagenase {Bacteria (Clostridium histolyticum) [TaxId: 1498]}
4 VFG1640 (gi:11322959) sfaC - SfaC protein [Escherichia coli 536] 73 COG0113 2-51 -22.800 18  [S] COG3388 Uncharacterized protein conserved in archaea
PDB0113 1-73 -29.500 90  2htj_A mol:protein length:81 P fimbrial regulatory protein KS71A
PfamA26U 2-51 -23.000 18  PF10007.4; A4YIE5_METS5/9-101; Uncharacterized protein conserved in archaea (DUF2250 topsan)
SCOP175 1-73 -31.900 90  d2htja1 a.4.5.73 (A:1-73) P fimbrial regulatory protein PapI {Escherichia coli [TaxId: 562]}
5 VFG1643 (gi:11322961) sfaD - SfaD protein [Escherichia coli 536] 179 COG0113 4-151 -30.500 13  [NU] COG3539 P pilus assembly protein, pilin FimA
PDB0113 9-178 -62.600 17  2j2z_B mol:protein length:173 PAP FIMBRIAL MINOR PILIN PROTEIN
PfamA26U 30-178 -39.100 13  PF00419.15; C0ARF8_9ENTR/245-441; Fimbrial protein
SCOP175 31-178 -58.400 18  d2j2zb1 b.2.3.2 (B:24-173) PAP fimbrial minor pilin protein PapH {Escherichia coli [TaxId: 562]}
6 VFG0772 (gi:11527908) espC - enterotoxin EspC [Escherichia coli E2348/69] (VF0173) 1305 COG0113 1-783 -13.700 11  [U] COG3210 Large exoproteins involved in heme utilization or adhesion
73-1305 -48.100 12  [S] COG4625 Uncharacterized protein with a C-terminal OMP (outer membrane protein) domain
412-1305 -74.900 13  [MU] COG3468 Type V secretory pathway, adhesin AidA
PDB0113 2-485 -9.510 12  2wan_A mol:protein length:921 PULLULANASE
54-1028 -136.000 40  3sze_A mol:protein length:968 Serine protease espP
999-1305 -73.200 75  3slj_A mol:protein length:313 Serine protease espP
PfamA26U 46-724 -109.000 43  PF02395.11; ESPP_ECO57/47-730; Immunoglobulin A1 protease
1011-1305 -15.300 10  PF09381.5; Q1RC46_ECOUT/18-318; Outer membrane protein G (OmpG)
1042-1296 -32.300 12  PF03797.14; Q87E01_XYLFT/468-724; Autotransporter beta-domain
SCOP175 79-284 -9.790 16  d1elva1 b.47.1.2 (A:410-668) Complement C1S protease, catalytic domain {Human (Homo sapiens) [TaxId: 9606]}
380-1003 -13.400 13  d1daba_ b.80.1.7 (A:) Virulence factor P.69 pertactin {Bordetella pertussis [TaxId: 520]}
1011-1305 -41.400 15  d1uynx_ f.4.5.1 (X:) Translocator domain of NalP {Neisseria meningitidis [TaxId: 487]}
7 VFG0767 (gi:11527909) orf1 - unknown [Escherichia coli E2348/69] 66 COG0113 3-49 -6.800 17  [S] COG4924 Uncharacterized protein conserved in bacteria
PDB0113 27-54 -6.120 10  2rnl_A mol:protein length:50 Amphiregulin
PfamA26U 22-45 -5.880 29  PF12424.3; B3N0M2_DROAN/1054-1109; Plasma membrane calcium transporter ATPase C terminal
SCOP175 7-53 -4.800 23  d2gg2a1 d.127.1.1 (A:3-264) Methionine aminopeptidase {Escherichia coli [TaxId: 562]}
8 VFG0770 (gi:11527910) orf2 - unknown [Escherichia coli E2348/69] 54 COG0113 1-34 -5.190 20  [K] COG3636 Predicted transcriptional regulator
PDB0113 36-51 -6.400 43  3oak_C mol:protein length:31 Transcription elongation factor SPT6
PfamA26U 1-51 -5.910 17  PF04771.7; Q96671_9CIRC/1-121; Chicken anaemia virus VP-3 protein
SCOP175 16-34 -5.450 31  d1imta2 g.3.10.1 (A:37-80) Intestinal toxin 1 {Black mamba (Dendroaspis polylepis polylepis) [TaxId: 8620]}
9 VFG0771 (gi:11527911) orf3 - unknown [Escherichia coli E2348/69] 390 COG0113 90-147 -7.390 17  [J] KOG3499 60S ribosomal protein L38
PDB0113 36-390 -138.000 44  3pcr_A mol:protein length:357 EspG
PfamA26U 9-390 -141.000 43  PF06872.6; Q5WMC0_ECOLX/15-397; EspG protein
SCOP175 52-206 -5.500 11  d1k28d1 b.106.1.1 (D:4-200) Baseplate structural protein gp27 {Bacteriophage T4 [TaxId: 10665]}
10 VFG0773 (gi:11527912) orf5 - unknown [Escherichia coli E2348/69] 57 COG0113 1-29 -5.430 24  [S] KOG4816 Uncharacterized conserved protein
PDB0113 1-57 -4.970 27  3khp_A mol:protein length:311 MaoC family protein
PfamA26U 1-50 -6.890 29  PF07418.6; Q4YUM7_PLABA/1-292; Acidic phosphoprotein precursor PCEMA1
SCOP175 12-51 -4.910 12  d1an4a_ a.38.1.1 (A:) Usf B/HLH domain {Human (Homo sapiens) [TaxId: 9606]}
11 VFG0777 (gi:11527914) orf6.2 - unknown [Escherichia coli E2348/69] 51 COG0113 1-46 -9.520 15  [L] COG3316 Transposase and inactivated derivatives
PDB0113 1-50 -11.900 12  1c6v_A mol:protein length:164 PROTEIN (SIV INTEGRASE)
PfamA26U 1-46 -11.300 17  PF13610.1; B5WJN4_9BURK/77-216; DDE domain
SCOP175 1-50 -11.000 12  d1exqa_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Human immunodeficiency virus type 1 [TaxId: 11676]}
12 VFG0778 (gi:11527915) orf6.3 - unknown [Escherichia coli E2348/69] 46 COG0113 13-44 -4.620 15  [G] COG4806 L-rhamnose isomerase
PDB0113 15-45 -5.640 25  3n97_A mol:protein length:72 RNA polymerase sigma factor
PfamA26U 15-28 -7.130 21  PF12752.2; B0CU27_LACBS/192-272; SUZ domain
SCOP175 15-40 -4.750 23  d1ku3a_ a.4.13.2 (A:) Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 271]}
13 VFG0780 (gi:11527916) orf7 - unknown [Escherichia coli E2348/69] 463 COG0113 1-346 -106.000 41  [L] COG4584 Transposase and inactivated derivatives
PDB0113 2-130 -20.600 10  1u78_A mol:protein length:141 transposable element tc3 transposase
4-395 -19.900 11  4fcy_A mol:protein length:529 Transposase
64-300 -23.600 11  4FW2 Entity 1(prereleased)
114-277 -24.600 14  1vsd_A mol:protein length:152 INTEGRASE
395-463 -10.200 17  2w58_A mol:protein length:202 PRIMOSOME COMPONENT (HELICASE LOADER)
PfamA26U 2-102 -15.900 20  PF00292.13; PAX6_DANRE/23-147; `Paired box` domain
4-309 -9.640 PF07592.6; B3EJR4_CHLPB/96-407; Rhodopirellula transposase DDE domain
119-295 -18.800 PF02914.10; TRA_HAEIN/267-485; Bacteriophage Mu transposase
120-244 -19.300 16  PF00665.21; O89811_FLV/1485-1601; Integrase core domain
396-463 -18.300 32  PF01695.12; Y4IQ_RHISN/60-238; IstB-like ATP binding protein
SCOP175 1-42 -13.500 14  d1tc3c_ a.4.1.2 (C:) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}
119-292 -18.200 13  d1exqa_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Human immunodeficiency virus type 1 [TaxId: 11676]}
120-244 -23.700 16  d1cxqa_ c.55.3.2 (A:) Retroviral integrase, catalytic domain {Rous sarcoma virus RSV [TaxId: 11886]}
14 VFG0781 (gi:11527917) orf8 - unknown [Escherichia coli E2348/69] 83 COG0113 2-83 -13.400 20  [L] COG1484 DNA replication protein
PDB0113 1-81 -31.000 22  3ecc_A mol:protein length:185 DNA replication protein DnaC
PfamA26U 2-73 -42.300 35  PF01695.12; Y4IQ_RHISN/60-238; IstB-like ATP binding protein
SCOP175 16-81 -6.730 d1no1a_ a.179.1.1 (A:) Replisome organizer (g39p helicase loader/inhibitor protein) {Bacteriophage Spp1 [TaxId: 10724]}
15 VFG0776 (gi:11527918) orf6.1 - unknown [Escherichia coli E2348/69] 80 COG0113 1-74 -22.400 17  [L] COG2801 Transposase and inactivated derivatives
PDB0113 1-78 -12.000 13  1pdn_C mol:protein length:128 PROTEIN (PRD PAIRED)
2-35 -12.200 2jrt_A mol:protein length:95 Uncharacterized protein
PfamA26U 1-74 -29.900 18  PF13551.1; B2T8S8_BURPP/9-115; Winged helix-turn helix
SCOP175 2-33 -11.700 15  d2oa4a1 a.4.12.3 (A:1-93) Uncharacterized protein SPO1678 {Silicibacter pomeroyi [TaxId: 89184]}
16 VFG0766 (gi:11527918) rorf1 - unknown [Escherichia coli E2348/69] 126 COG0113 13-108 -6.380 16  [S] COG2098 Uncharacterized protein conserved in archaea
PDB0113 12-125 -8.880 20  1aqh_A mol:protein length:453 ALPHA-AMYLASE
PfamA26U 2-100 -8.350 18  PF03010.9; Q9QKG0_EAV/1-152; GP4
SCOP175 24-116 -12.700 22  d1ua7a1 b.71.1.1 (A:348-425) Bacterial alpha-Amylase {Bacillus subtilis [TaxId: 1423]}
17 VFG0768 (gi:11527919) rorf2 - unknown [Escherichia coli E2348/69] 56 COG0113 5-45 -4.800 28  [AR] KOG0109 RNA-binding protein LARK, contains RRM and retroviral-type Zn-finger domains
PDB0113 10-47 -6.990 28  2eqp_A mol:protein length:50 Tumor necrosis factor receptor superfamily me
PfamA26U 11-56 -6.360 26  PF11093.3; A5DP09_PICGU/1-94; Mitochondrial export protein Som1
SCOP175 1-53 -6.300 13  d2hqya2 d.108.1.4 (A:1-134) Hypothetical protein BT3689 {Bacteroides thetaiotaomicron [TaxId: 818]}
18 VFG0769 (gi:11527920) rorf3 - unknown [Escherichia coli E2348/69] 161 COG0113 4-119 -6.410 15  [L] COG0338 Site-specific DNA methylase
PDB0113 9-121 -6.400 17  1uuz_A mol:protein length:137 INHIBITOR OF VERTEBRATE LYSOZYME
PfamA26U 12-121 -6.850 14  PF08816.6; A0KMD6_AERHH/30-145; Inhibitor of vertebrate lysozyme (Ivy)
SCOP175 11-153 -7.270 12  d2ebfx2 c.150.1.2 (X:875-1093) Dermonecrotic toxin, ToxA {Pasteurella multocida [TaxId: 747]}
19 VFG0774 (gi:11527921) rorf4 - unknown [Escherichia coli E2348/69] 126 COG0113 19-126 -15.800 10  [S] COG4891 Uncharacterized conserved protein
PDB0113 13-126 -17.200 3ijt_A mol:protein length:155 Putative uncharacterized protein
PfamA26U 27-123 -12.700 15  PF03364.15; Q82RS2_STRAW/11-133; Polyketide cyclase / dehydrase and lipid transport
SCOP175 19-118 -17.400 d2b79a1 d.129.3.9 (A:1-137) Hypothetical protein SMU440 {Streptococcus mutans [TaxId: 1309]}
20 VFG0775 (gi:11527922) rorf5 - unknown [Escherichia coli E2348/69] 62 COG0113 27-62 -6.230 11  [S] KOG3869 Uncharacterized conserved protein
PDB0113 1-61 -34.200 32  3oxn_A mol:protein length:241 Putative transcriptional regulator, LysR fami
PfamA26U 34-62 -6.440 13  PF10197.4; Q9VQF5_DROME/11-47; N-terminal domain of CBF1 interacting co-repressor CIR
SCOP175 1-58 -33.400 32  d1utha_ c.94.1.1 (A:) LysR-type regulatory protein DntR {Burkholderia sp. [TaxId: 36773]}


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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. Database searching by flexible protein structure alignment. Protein Sci. 2004 Jul;13(7):1841-50.