YRC Public Data Repository - Protein Structure Prediction

Protein:	PBP2
Organism:	Saccharomyces cerevisiae
Length:	413 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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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 PBP2.

Description	E-value	Query Range	Subject Range
gi\|73987248 - gi\|73987248\|ref\|XP_542140.2\| PREDICTED: similar to KH-type splicing regulatory protein (FUSE binding...	262.0	[0..15]	[399..129]
gi\|114674909 - gi\|114674909\|ref\|XP_512315.2\| PREDICTED: KH-type splicing regulatory protein (FUSE binding protein 2...	259.0	[0..15]	[399..243]
PCBP1_MOUSE - Poly(rC)-binding protein 1 OS=Mus musculus GN=Pcbp1 PE=1 SV=1 ENSCJAT00000043255 - null PCBP1 - poly(rC) binding protein 1 gi\|53734604 - gb\|AAH84040.1\| Unknown (protein for MGC:98389) [Xenopus laevis] PCBP1_RABIT - Poly(rC)-binding protein 1 OS=Oryctolagus cuniculus GN=PCBP1 PE=2 SV=1 CCDS1898.1_1 - null gi\|114577924 - gi\|114577924\|ref\|XP_515530.2\| PREDICTED: poly(rC) binding protein 1 isoform 3 [Pan troglodytes] tr\|G3HXL1\|G3HXL1... - Poly(RC)-binding protein 1 OS=Cricetulus griseus GN=I79_015737 PE=4 SV=1 PCBP1_BOVIN - Poly(rC)-binding protein 1 OS=Bos taurus GN=PCBP1 PE=2 SV=1 gi\|62647735 - gi\|62647735\|ref\|XP_575592.1\| PREDICTED: similar to Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP-E1)... gi\|149727502 - gi\|149727502\|ref\|XP_001490425.1\| PREDICTED: similar to Poly(rC)-binding protein 1 (Alpha-CP1) (hnRNP... gi\|208968661 - gi\|208968661\|dbj\|BAG74169.1\| poly(rC) binding protein 1 [synthetic construct]	257.0	[0..66]	[402..13]
gi\|5453854, gi\|4... - gi\|5453854\|ref\|NP_006187.1\| poly(rC) binding protein 1 [Homo sapiens], gi\|460771\|emb\|CAA55016.1\| hnR...	256.0	[0..66]	[402..13]
gi\|76622127 - gi\|76622127\|ref\|XP_581869.2\| PREDICTED: similar to KH-type splicing regulatory protein (FUSE binding...	255.0	[0..15]	[399..41]
FUBP2_RAT - Far upstream element-binding protein 2 OS=Rattus norvegicus GN=Khsrp PE=1 SV=1	254.0	[0..15]	[399..93]

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Predicted Domain #1

Region A:
Residues: [1-143]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTETTKPSI TTTPTTVLVS PNTLKRKKGE DTSEEQLEAE IKRVALKDAD SHSDNDHDSP  60
   61 DNVPSDVHLR MLCLVKHASL IVGHKGATIS RIKSETSARI NISNNIRGVP ERIVYVRGTC 120
  121 DDVAKAYGMI VRALLEEHGN EDN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	41.37734
Match:	1j4wA
Description:	Far upstream binding element, FBP, KH3 and KH4 domains
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [144-243]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GEDIEISINL LIPHHLMGCI IGKRGSRLRE IEDLSAAKLF ASPNQLLLSN DRILTINGVP  60
   61 DAIHIATFYI SQTLLNFQME SPQKNVKRSI YYQPTQFNSV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	41.37734
Match:	1j4wA
Description:	Far upstream binding element, FBP, KH3 and KH4 domains
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [244-322]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LIDHSQPNTI FHQRNHQYHP SDKLLSYKPN KNLPISSTLL SMATPQYTTA SVANATAFQP  60
   61 NFVIPNVTVL DGPVISPAP

[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 #4

Region A:
Residues: [323-413]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GNHLLMNFVQ QEIFIDEKFV GNVIGKDGKH INSVKESTGC SIIIQDPVEG SSERRLTIRG  60
   61 TFMASQAAIM LISNKIEIDR SNAERKRRSP L

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.69897
Match:	1j5kA
Description:	HnRNP K, KH3
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