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

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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|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]

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

Found no 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 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	0.404	a.24.21	Description not found.
View	Download	0.404	a.29.4	RecG, N-terminal domain
View	Download	0.388	a.24.7	FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View	Download	0.388	a.24.7	FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View	Download	0.379	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.367	a.24.18	Description not found.
View	Download	0.318	a.29.16	Description not found.
View	Download	0.296	a.23.1	HSC20 (HSCB), C-terminal oligomerisation domain
View	Download	0.288	a.24.3	Cytochromes
View	Download	0.267	b.40.2	Bacterial enterotoxins

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