YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|20908082, gi\|...
Organism:	Arabidopsis thaliana
Length:	423 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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|20908082, gi|....

Description	E-value	Query Range	Subject Range
gi\|56552023, gi\|... - gi\|56552023\|ref\|YP_162862.1\| tRNA-dihydrouridine synthase [Zymomonas mobilis subsp. mobilis ZM4], gi...	283.0	[0..70]	[401..7]
gi\|52346439, gi\|... - gi\|52783937\|ref\|YP_089766.1\| YacF [Bacillus licheniformis ATCC 14580], gi\|52346439\|gb\|AAU39073.1\| Ya...	283.0	[0..79]	[412..2]
DUS1_BACSU - Probable tRNA-dihydrouridine synthase 1 OS=Bacillus subtilis GN=dus1 PE=3 SV=1 gi\|221321409 - gi\|221321409\|ref\|ZP_03602703.1\| hypothetical protein BsubsS_00410 [Bacillus subtilis subsp. subtilis... gi\|221317146 - gi\|221317146\|ref\|ZP_03598440.1\| hypothetical protein BsubsJ_00410 [Bacillus subtilis subsp. subtilis... DUS1_BACSU - Probable tRNA-dihydrouridine synthase 1 OS=Bacillus subtilis (strain 168) GN=dus1 PE=3 SV=1 gi\|221312213 - gi\|221312213\|ref\|ZP_03594018.1\| hypothetical protein BsubsN3_00410 [Bacillus subtilis subsp. subtili...	281.0	[0..79]	[396..2]
gi\|88775590, gi\|... - gi\|88793018\|ref\|ZP_01108735.1\| tRNA-dihydrouridine synthase B [Alteromonas macleodii 'Deep ecotype']...	280.0	[0..80]	[411..2]
gi\|5834292 - gi\|5834292\|gb\|AAD53896.1\|AF176314_6 NifR3-like protein [Zymomonas mobilis] gi\|5834292\|gb\|AA... - NifR3-like protein [Zymomonas mobilis]	279.0	[0..70]	[409..7]
gi\|255652101 - gi\|255652101\|ref\|ZP_05399003.1\| tRNA-dihydrouridine synthase [Clostridium difficile QCD-37x79] gi\|145952352, gi... - gi\|90572713\|ref\|ZP_01229237.1\| hypothetical protein CdifQ_02003914 [Clostridium difficile QCD-32g58]... gi\|255102766 - gi\|255102766\|ref\|ZP_05331743.1\| tRNA-dihydrouridine synthase [Clostridium difficile QCD-63q42] gi\|255308587 - gi\|255308587\|ref\|ZP_05352758.1\| tRNA-dihydrouridine synthase [Clostridium difficile ATCC 43255] gi\|255316261 - gi\|255316261\|ref\|ZP_05357844.1\| tRNA-dihydrouridine synthase [Clostridium difficile QCD-76w55] gi\|255518922 - gi\|255518922\|ref\|ZP_05386598.1\| tRNA-dihydrouridine synthase [Clostridium difficile QCD-97b34] gi\|254977180 - gi\|254977180\|ref\|ZP_05273652.1\| tRNA-dihydrouridine synthase [Clostridium difficile QCD-66c26] gi\|255094510 - gi\|255094510\|ref\|ZP_05323988.1\| tRNA-dihydrouridine synthase [Clostridium difficile CIP 107932] gi\|115252617, gi... - gi\|126701180\|ref\|YP_001090077.1\| tRNA-dihydrouridine synthase [Clostridium difficile 630], gi\|115252...	279.0	[0..80]	[397..2]
gi\|114773260 - gi\|114773260\|ref\|ZP_01450495.1\| tRNA-dihydrouridine synthase B [alpha proteobacterium HTCC2255] gi\|114773260, gi... - gi\|114773260\|ref\|ZP_01450495.1\| tRNA-dihydrouridine synthase B [alpha proteobacterium HTCC2255], gi\|...	279.0	[0..75]	[404..1]
gi\|82409331, gi\|... - gi\|82701266\|ref\|YP_410832.1\| dihydrouridine synthase TIM-barrel protein nifR3 [Nitrosospira multifor...	279.0	[0..80]	[415..2]
gi\|52424587, gi\|... - gi\|52424587\|ref\|YP_087724.1\| hypothetical protein MS0532 [Mannheimia succiniciproducens MBEL55E], gi...	277.0	[0..61]	[403..2]
gi\|28807910, gi\|... - gi\|28899658\|ref\|NP_799263.1\| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633], gi\|28... gi\|28807910 - gi\|28807910\|dbj\|BAC61147.1\| NifR3/Smm1 family protein [Vibrio parahaemolyticus RIMD 2210633]	277.0	[0..70]	[404..1]

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Predicted Domain #1

Region A:
Residues: [1-69]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKLNLSNLRF LRTRKSLISQ TRAMTQNPDP KPDPSQVLDD ILCSEQRDGQ IEETVDTAPA  60
   61 SLGSPSRVL

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.598	a.47.2	t-snare proteins
View	Download	0.598	a.47.2	t-snare proteins
View	Download	0.565	d.52.5	Probable GTPase Der, C-terminal domain
View	Download	0.565	d.52.5	Probable GTPase Der, C-terminal domain
View	Download	0.552	a.58.1	Chemotaxis receptor methyltransferase CheR, N-terminal domain
View	Download	0.547	a.24.28	Description not found.
View	Download	0.546	a.118.23	Description not found.
View	Download	0.513	d.58.17	Metal-binding domain
View	Download	0.497	a.7.7	BAG domain
View	Download	0.395	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.350	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.310	a.126.1	Serum albumin-like
View	Download	0.232	a.16.1	S15/NS1 RNA-binding domain

Predicted Domain #2

Region A:
Residues: [70-423]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SIDTRVERAW AHWKKLGRPK YIVAPMVDNS ELPFRLLCQK YGAQAAYTPM LHSRIFTETE  60
   61 KYRNQEFTTC KEDRPLFVQF CANDPDTLLE AAKRVEPYCD YVDINLGCPQ RIARRGNYGA 120
  121 FLMDNLPLVK SLVEKLAQNL NVPVSCKIRI FPNLEDTLKY AKMLEDAGCS LLAVHGRTRD 180
  181 EKDGKKFRAD WSAIKEVKNA MRIPVLANGN VRCIEDVDNC IKETGVEGVL SAETLLENPA 240
  241 AFAGFRTAEW AKDNEEEGFV DGGLDQGDLV VEYLKLCEKH PVPWRMIRSH VHKMLGEWFR 300
  301 IHPQVREQLN AQNILTFEFL YGLVDQLREL GGRVPLYKKK KIDTLTPQDS PQRV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	53.69897
Match:	1vhnA
Description:	Crystal structure of a putative flavin oxidoreductase with flavin
Matching Structure (courtesy of the PDB):

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