YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|229343532, gi...
Organism:	Vibrio cholerae RC9
Length:	204 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for gi|229343532, gi....

Description	E-value	Query Range	Subject Range
RUVA_VIBVU - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio vulnificus GN=ruvA PE=3 SV=1 RUVA_VIBVY - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio vulnificus (strain YJ016) GN=ruvA PE=3 S... RUVA_VIBVU - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio vulnificus (strain CMCP6) GN=ruvA PE=3 S...	267.0	[0..1]	[204..1]
gi\|91188507, gi\|... - gi\|91227614\|ref\|ZP_01261918.1\| Holliday junction DNA helicase motor protein [Vibrio alginolyticus 12...	267.0	[0..1]	[204..1]
gi\|37199217, gi\|... - gi\|37680469\|ref\|NP_935078.1\| Holliday junction DNA helicase motor protein [Vibrio vulnificus YJ016],...	264.0	[0..2]	[204..4]
gi\|86146483, gi\|... - gi\|86146483\|ref\|ZP_01064806.1\| Holliday junction DNA helicase motor protein [Vibrio sp. MED222], gi\|... RUVA_VIBTL - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio tasmaniensis (strain LGP32) GN=ruvA PE=3...	263.0	[0..1]	[204..1]
gi\|84377068, gi\|... - gi\|84388519\|ref\|ZP_00991066.1\| Holliday junction DNA helicase motor protein [Vibrio splendidus 12B01...	262.0	[0..1]	[204..1]
RUVA_VIBPA - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio parahaemolyticus serotype O3:K6 (strain ... RUVA_VIBPA - Holliday junction ATP-dependent DNA helicase RuvA OS=Vibrio parahaemolyticus GN=ruvA PE=3 SV=1	261.0	[0..1]	[204..1]
RUVA_PSEU2 - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas syringae pv. syringae (strain B728a...	258.0	[0..1]	[203..1]
RUVA_PSESM - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas syringae pv. tomato (strain DC3000)... RUVA_PSESM - Holliday junction ATP-dependent DNA helicase ruvA OS=Pseudomonas syringae pv. tomato GN=ruvA PE=3 SV... gi\|213926183, gi... - gi\|213969185\|ref\|ZP_03397324.1\| Holliday junction DNA helicase RuvA [Pseudomonas syringae pv. tomato...	258.0	[0..1]	[203..1]
RUVA_PSEAE - Holliday junction ATP-dependent DNA helicase ruvA OS=Pseudomonas aeruginosa GN=ruvA PE=3 SV=1 gi\|194556234, gi... - gi\|84322552\|ref\|ZP_00970637.1\| COG0632: Holliday junction resolvasome, DNA-binding subunit [Pseudomo... gi\|254239314, gi... - gi\|84316457\|ref\|ZP_00964931.1\| COG0632: Holliday junction resolvasome, DNA-binding subunit [Pseudomo... RUVA_PSEAB - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas aeruginosa (strain UCBPP-PA14) GN=r... RUVA_PSEAE - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas aeruginosa (strain ATCC 15692 / PAO... gi\|107100423 - gi\|107100423\|ref\|ZP_01364341.1\| hypothetical protein PaerPA_01001448 [Pseudomonas aeruginosa PACS2] RUVA_PSEA8 - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas aeruginosa (strain LESB58) GN=ruvA ... RUVA_PSEA7 - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas aeruginosa (strain PA7) GN=ruvA PE=...	258.0	[0..1]	[204..1]
RUVA_PSE14 - Holliday junction ATP-dependent DNA helicase RuvA OS=Pseudomonas savastanoi pv. phaseolicola (strain...	258.0	[0..1]	[203..1]

Back

Predicted Domain #1

Region A:
Residues: [1-204]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MIGRLRGTLI EKLPPQILIE VGGIGYEVQM PMSCIYELPN IGEEAIIYTH FVVREDAQLL  60
   61 YGFNTVSERA LFREVIKANG VGPKMGLAIL SGMTANQFVT CVEKEDISTL IKLPGVGKKT 120
  121 AERLVVEMKD RLKGWGAGDL FTPATDAAPV DSTPVIAQNA QEEAMSALLA LGYKPPQASK 180
  181 AVSQVAKAGM SSEELIREAL KSMV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	68.69897
Match:	1bdxA
Description:	DNA helicase RuvA subunit, C-terminal domain; DNA helicase RuvA subunit, middle domain; DNA helicase RuvA subunit, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
four-way junction helicase activity	6.5377357736202	bayes_pls_golite062009
DNA helicase activity	4.17140899815273	bayes_pls_golite062009
endodeoxyribonuclease activity	3.43738564958931	bayes_pls_golite062009
helicase activity	3.41619150983834	bayes_pls_golite062009
deoxyribonuclease activity	3.18777140839084	bayes_pls_golite062009
excinuclease ABC activity	2.75922711242844	bayes_pls_golite062009
nucleic acid binding	1.99569639221804	bayes_pls_golite062009
structure-specific DNA binding	1.68542948433544	bayes_pls_golite062009
binding	1.60192408330567	bayes_pls_golite062009
single-stranded DNA binding	1.58506920916947	bayes_pls_golite062009
DNA binding	1.33645375386113	bayes_pls_golite062009
endonuclease activity	1.07194065760938	bayes_pls_golite062009
damaged DNA binding	1.01799678384131	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.01626429465845	bayes_pls_golite062009
structural constituent of ribosome	0.83740886071361	bayes_pls_golite062009
structural molecule activity	0.53636537261201	bayes_pls_golite062009
nuclease activity	0.29926900436997	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.0954216620147701	bayes_pls_golite062009
exonuclease activity	0.0152988330656798	bayes_pls_golite062009

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: