YRC Public Data Repository - Protein Structure Prediction

Protein:	PRP5
Organism:	Saccharomyces cerevisiae
Length:	849 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 PRP5.

Description	E-value	Query Range	Subject Range
PRP5_YEAST - Pre-mRNA-processing ATP-dependent RNA helicase PRP5 OS=Saccharomyces cerevisiae (strain ATCC 204508 ... PRP5 - RNA helicase in the DEAD-box family, necessary for prespliceosome formation, bridges U1 and U2 snRNP...	0.0	[1..849]	[1..849]
PRP11_SCHPO - Pre-mRNA-processing ATP-dependent RNA helicase prp11 OS=Schizosaccharomyces pombe (strain 972 / ATCC... prp11 - ATP-dependent RNA helicase Prp11	0.0	[13..836]	[192..995]
CE27427 - helicase status:Partially_confirmed UniProt:Q965K2 protein_id:AAK68386.1	0.0	[3..845]	[44..961]
gi\|13514813, gi\|... - gi\|2580552\|gb\|AAC51830.1\| dead box, X isoform [Homo sapiens], gi\|2580550\|gb\|AAC51829.1\| dead box, X ...	0.0	[106..663]	[24..579]
DDX3X_MOUSE - ATP-dependent RNA helicase DDX3X OS=Mus musculus GN=Ddx3x PE=1 SV=3	0.0	[106..663]	[24..579]
gi\|5270 - gi\|5270\|emb\|CAA36873.1\| p68 protein [Schizosaccharomyces pombe]	0.0	[146..660]	[14..504]

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Predicted Domain #1

Region A:
Residues: [1-218]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 METIDSKQNI NRESLLEERR KKLAKWKQKK AQFDAQKEHQ TSRNDIVTNS LEGKQTTEKF  60
   61 TERQERVKEE LRKRKNEFRK SDEPVSVKPS KKKSKRSKVK KKISFDFSDD DDSEIGVSFR 120
  121 SKEHIQKAPE HDNEKDPLDE FMTSLKEEKM SNSKGMYDRG DILDVEDQLF ELGGTDDEDV 180
  181 EDNTDNSNIA KIAKLKAKKR VKQIYYSPEE LEPFQKNF

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [219-278]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YIESETVSSM SEMEVEELRL SLDNIKIKGT GCPKPVTKWS QLGLSTDTMV LITEKLHFGS  60
   61

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	461.0
Match:	1fuuA_
Description:	Initiation factor 4a
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [279-473]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LTPIQSQALP AIMSGRDVIG ISKTGSGKTI SYLLPLLRQV KAQRPLSKHE TGPMGLILAP  60
   61 TRELALQIHE EVTKFTEADT SIRSVCCTGG SEMKKQITDL KRGTEIVVAT PGRFIDILTL 120
  121 NDGKLLSTKR ITFVVMDEAD RLFDLGFEPQ ITQIMKTVRP DKQCVLFSAT FPNKLRSFAV 180
  181 RVLHSPISIT INSKG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [671-746]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKKGKFRLSK GFGGKGLENI KSKREEAQNK DLELKKNDKR SDDLEKKISN PREGHDSVSE  60
   61 SSALIPRLNY ELFKES

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.30103
Match:	1gm5A_
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [474-670]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVNENVKQKF RICHSEDEKF DNLVQLIHER SEFFDEVQSE NDGQSSDVEE VDAKAIIFVS  60
   61 SQNICDFISK KLLNAGIVTC AIHAGKPYQE RLMNLEKFKR EKNSILLCTE VLSRGLNVPE 120
  121 VSLVIIYNAV KTFAQYVHTT GRTARGSRSG TAITLLLHDE LSGAYILSKA MRDEEIKALD 180
  181 PLQAKELQEM SAKFESG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	13.30103
Match:	1gm5A_
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [747-849]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TDGSIIFYAK VYINDLPQIV RWEATKNTTL LFIKHETGCS ITNKGKFYPE GKEPKNENDE  60
   61 PKLYLLIEGQ DEKDIQLSIE LLEQKVKEGV VKAASLSLKS TKY

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	8.62
Match:	1k1gA
Description:	RNA splicing factor 1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
RNA binding	6.35205331138538	bayes_pls_golite062009
	4.77327442333813	bayes_pls_golite062009
mRNA binding	4.67566555881601	bayes_pls_golite062009
nucleic acid binding	4.53130750638836	bayes_pls_golite062009
translation factor activity, nucleic acid binding	3.73042056823822	bayes_pls_golite062009
translation regulator activity	3.73023228922019	bayes_pls_golite062009
binding	3.31439627344982	bayes_pls_golite062009
transcription regulator activity	2.27014249542806	bayes_pls_golite062009
DNA binding	2.0152088603757	bayes_pls_golite062009
poly-pyrimidine tract binding	1.75736205236351	bayes_pls_golite062009
transcription repressor activity	1.72867277839034	bayes_pls_golite062009
structure-specific DNA binding	1.40423326576059	bayes_pls_golite062009
transcription factor activity	1.30878011063724	bayes_pls_golite062009
single-stranded DNA binding	1.27324890490526	bayes_pls_golite062009
protein binding	1.09698608157472	bayes_pls_golite062009
ribonuclease activity	0.925909354724523	bayes_pls_golite062009
single-stranded RNA binding	0.795008427109843	bayes_pls_golite062009
hydrolase activity	0.715182212485288	bayes_pls_golite062009
mRNA 3'-UTR binding	0.370287528838428	bayes_pls_golite062009
transcription activator activity	0.281896115904289	bayes_pls_golite062009
transcription factor binding	0.207514957974522	bayes_pls_golite062009
exoribonuclease activity	0.150228013820667	bayes_pls_golite062009
catalytic activity	0.1435046019283	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	0.110425673333101	bayes_pls_golite062009
sequence-specific DNA binding	0.0108102459345405	bayes_pls_golite062009

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

Predicted functions: