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 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	0.689	a.118.1	ARM repeat
View	Download	0.521	a.28.1	ACP-like
View	Download	0.434	a.4.1	Homeodomain-like
View	Download	0.434	a.4.1	Homeodomain-like
View	Download	0.429	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.424	a.39.1	EF-hand
View	Download	0.416	a.156.1	S13-like H2TH domain
View	Download	0.380	a.2.3	Chaperone J-domain
View	Download	0.378	a.77.1	DEATH domain
View	Download	0.369	a.4.5	"Winged helix" DNA-binding 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