YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|11358905, gi\|...
Organism:	Arabidopsis thaliana
Length:	540 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|11358905, gi|....

Description	E-value	Query Range	Subject Range
gi\|110741670, gi... - gi\|186522847\|ref\|NP_196950.2\| pseudouridine synthase/ transporter [Arabidopsis thaliana], gi\|1107416...	841.0	[0..1]	[540..1]
gi\|52353567, gi\|... - gi\|52353567\|gb\|AAU44133.1\| putative tRNA synthase [Oryza sativa Japonica Group], gi\|255675942\|dbj\|BA...	478.0	[0..147]	[540..108]
gi\|14719313 - gi\|14719313\|gb\|AAK73131.1\|AC079022_4 putative tRNA synthase [Oryza sativa]	476.0	[0..147]	[540..145]
gi\|28195117, gi\|... - gi\|28195117\|gb\|AAO33771.1\| putative tRNA pseudouridine synthase [Oryza sativa (indica cultivar-group...	432.0	[0..147]	[504..108]
gi\|90422006, gi\|... - gi\|90422006\|ref\|YP_530376.1\| tRNA pseudouridine synthase B [Rhodopseudomonas palustris BisB18], gi\|9...	318.0	[0..266]	[537..14]
TRUB_VIBCH - tRNA pseudouridine synthase B OS=Vibrio cholerae GN=truB PE=3 SV=1 gi\|121587869, gi... - gi\|121587869\|ref\|ZP_01677626.1\| tRNA pseudouridine 55 synthase [Vibrio cholerae 2740-80], gi\|1215479... gi\|124118436, gi... - gi\|153223100\|ref\|ZP_01953655.1\| tRNA pseudouridine 55 synthase [Vibrio cholerae MAK 757], gi\|1241184... gi\|153818688, gi... - gi\|153818688\|ref\|ZP_01971355.1\| tRNA pseudouridine 55 synthase [Vibrio cholerae NCTC 8457], gi\|12651... gi\|229608844, gi... - gi\|229608844\|ref\|YP_002879492.1\| tRNA pseudouridine synthase B [Vibrio cholerae MJ-1236], gi\|2293714... gi\|229509234, gi... - gi\|229509234\|ref\|ZP_04398719.1\| tRNA pseudouridine synthase B [Vibrio cholerae B33], gi\|229353806\|gb... gi\|229344247, gi... - gi\|229519558\|ref\|ZP_04409001.1\| tRNA pseudouridine synthase B [Vibrio cholerae RC9], gi\|229344247\|gb... gi\|229357956, gi... - gi\|229505733\|ref\|ZP_04395243.1\| tRNA pseudouridine synthase B [Vibrio cholerae BX 330286], gi\|229357... TRUB_VIBCM - tRNA pseudouridine synthase B OS=Vibrio cholerae serotype O1 (strain M66-2) GN=truB PE=3 SV=1 TRUB_VIBCH - tRNA pseudouridine synthase B OS=Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N1696... gi\|254846584, gi... - gi\|75831565\|ref\|ZP_00760827.1\| COG0130: Pseudouridine synthase [Vibrio cholerae MO10], gi\|254850879\|... gi\|75815894, gi\|... - gi\|75815894\|ref\|ZP_00746382.1\| COG0130: Pseudouridine synthase [Vibrio cholerae V52], gi\|121728409\|r...	304.0	[0..312]	[539..2]
TRUB_SHIBS - tRNA pseudouridine synthase B OS=Shigella boydii serotype 4 (strain Sb227) GN=truB PE=3 SV=1	304.0	[0..312]	[537..3]
gi\|225354812, gi... - gi\|254226548\|ref\|ZP_04920131.1\| tRNA pseudouridine 55 synthase [Vibrio cholerae V51], gi\|225354812\|r... gi\|149739687, gi... - gi\|153826507\|ref\|ZP_01979174.1\| tRNA pseudouridine 55 synthase [Vibrio cholerae MZO-2], gi\|149739687... gi\|229512907, gi... - gi\|229512907\|ref\|ZP_04402374.1\| tRNA pseudouridine synthase B [Vibrio cholerae TMA 21], gi\|229350156... gi\|229332223, gi... - gi\|229530450\|ref\|ZP_04419838.1\| tRNA pseudouridine synthase B [Vibrio cholerae 12129(1)], gi\|2293322...	304.0	[0..312]	[539..2]
TRUB_VIBC3 - tRNA pseudouridine synthase B OS=Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 39...	304.0	[0..313]	[539..3]

Back

Predicted Domain #1

Region A:
Residues: [1-217]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MAKSLHFTRL MSSSARMSMT SPLFFSSVKP WRNIHKPYLA SLFLSTTSTR YPLQYDMIIN  60
   61 RPTQSSLSQN RRRPPKAIES GAPDSAEPEF DSWVDNKLAM EREQGRPGSG DPEMDKAKRK 120
  121 YYSKRRKRLY GSDSEDETSS RKSDEGFVEL KPEVVEFDRL HQREEELYFY DTFAYPWEKD 180
  181 KHYKMVYQLE KKYYPDQCLD KAFLQPGEVL KKSDDSG

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [218-320]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KVRGKKKVVA ALGGKRSEVK RIGMENCDED DDKLVFFDEV KEKEEKKKSE DDVVVVTEKK  60
   61 VEQFFKGLTK SPNEKGMASG GGDGEPFLVT RNGELPPRWD GPN

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [321-540]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GTVLLVNKPK GWTSFTVCGK LRRLVKVKKV GHAGTLDPMA TGLLIVCVGK ATKVVDRYQG  60
   61 MIKGYSGVFR LGEATSTLDA DSPVIQRESW EHIKDDDIKK ALTSFLGEIW QVPPMFSAIK 120
  121 VGGEKMYEKA RRGETVELSP RRISIFQFDI ERSLDDRQNL IFRVICSKGT YIRSLCADLA 180
  181 KALGSCAHLT ALRRDSIGEY SANDAWEFNE LEAAITKNYF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	82.221849
Match:	1r3fA
Description:	Crystal Structure of tRNA Pseudouridine Synthase TruB and Its RNA Complex: RNA-protein Recognition Through a Combination of Rigid Docking and Induced Fit
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