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View Structure Prediction Details

Protein: RFA1
Organism: Saccharomyces cerevisiae
Length: 621 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 RFA1.

Description E-value Query
Range		 Subject
Range
RPA1 - replication protein A1, 70kDa
 0.0 [2..620] [1..615]
gi|151941394 - gi|151941394|gb|EDN59765.1| RF-A [Saccharomyces cerevisiae YJM789]
RFA1 - Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded D...
RFA1_YEAST - Replication factor A protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFA1 PE=1...
 0.0 [1..621] [1..621]
RFA1_MOUSE - Replication protein A 70 kDa DNA-binding subunit OS=Mus musculus GN=Rpa1 PE=1 SV=1
 0.0 [2..617] [1..621]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
 0.0 [1..617] [1..602]
gi|28922877, gi|... - gi|32404590|ref|XP_322908.1| hypothetical protein [Neurospora crassa], gi|28922877|gb|EAA32097.1| re...
gi|85102469 - gi|85102469|ref|XP_961333.1| replication factor-A protein 1 [Neurospora crassa OR74A]
 0.0 [2..615] [1..602]
RFA1_XENLA - Replication protein A 70 kDa DNA-binding subunit OS=Xenopus laevis GN=rpa1 PE=1 SV=1
 0.0 [1..617] [1..603]
RFA1A_ARATH - Replication protein A 70 kDa DNA-binding subunit A OS=Arabidopsis thaliana GN=RPA1A PE=1 SV=1
 0.0 [2..615] [1..638]
gi|13536993 - gi|13536993|dbj|BAB40712.1| replication protein A 70kDa [Oryza sativa Japonica Group]
 0.0 [4..619] [2..651]
ssb1 - DNA replication factor A subunit Ssb1
RFA1_SCHPO - Replication factor A protein 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=ssb1 PE=1 S...
 0.0 [2..618] [1..608]

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Predicted Domain #1
Region A:
Residues: [1-116] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSSVQLSRGD FHSIFTNKQR YDNPTGGVYQ VYNTRKSDGA NSNRKNLIMI SDGIYHMKAL  60
   61 LRNQAASKFQ SMELQRGDII RVIIAEPAIV RERKKYVLLV DDFELVQSRA DMVNQT

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 32.39794
Match: 1ewiA_
Description: Replication protein A 70 KDa subunit (RPA70)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
telomeric DNA binding 7.07761964836826 bayes_pls_golite062009
single-stranded telomeric DNA binding 6.04637014849887 bayes_pls_golite062009
telomerase inhibitor activity 5.40477712257453 bayes_pls_golite062009
nucleic acid binding 4.02967008021862 bayes_pls_golite062009
DNA binding 3.62735703519187 bayes_pls_golite062009
single-stranded DNA binding 3.59212997362902 bayes_pls_golite062009
structure-specific DNA binding 3.53214384646348 bayes_pls_golite062009
binding 2.83465364476231 bayes_pls_golite062009
structural constituent of ribosome 2.25006883439646 bayes_pls_golite062009
transcription regulator activity 2.20239961025491 bayes_pls_golite062009
structural molecule activity 2.07809455998137 bayes_pls_golite062009
protein binding 1.20309946451799 bayes_pls_golite062009
ribonuclease activity 1.19236946227657 bayes_pls_golite062009
DNA helicase activity 1.12203697857261 bayes_pls_golite062009
transcription factor activity 1.05816813143865 bayes_pls_golite062009
sequence-specific DNA binding 0.86170694706755 bayes_pls_golite062009
DNA-directed RNA polymerase activity 0.79554655100991 bayes_pls_golite062009
RNA polymerase activity 0.79554655100991 bayes_pls_golite062009
hydrolase activity 0.724860465280978 bayes_pls_golite062009
DNA-dependent ATPase activity 0.638831894247026 bayes_pls_golite062009
nuclease activity 0.57381531077345 bayes_pls_golite062009
DEAD/H-box RNA helicase binding 0.440977654731901 bayes_pls_golite062009
translation regulator activity 0.41164963411369 bayes_pls_golite062009
double-stranded DNA binding 0.378383789953688 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.360862776629591 bayes_pls_golite062009
nucleotidyltransferase activity 0.325774164899685 bayes_pls_golite062009
four-way junction helicase activity 0.31769813397725 bayes_pls_golite062009
RNA binding 0.31028563542112 bayes_pls_golite062009
translation initiation factor activity 0.30211828233765 bayes_pls_golite062009
exonuclease activity 0.28313884527829 bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups 0.226916777208049 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 0.223941674251642 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 0.125256208482441 bayes_pls_golite062009
exoribonuclease activity 0.109774918833391 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 0.0954216620147701 bayes_pls_golite062009
ATP-dependent DNA helicase activity 0.0179535526984695 bayes_pls_golite062009
helicase activity 0.0121541775159524 bayes_pls_golite062009

Predicted Domain #2
Region A:
Residues: [117-176] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STFLDNYFSE HPNETLKDED ITDSGNVANQ TNASNAGVPD MLHSNSNLNA NERKFANENP  60
   61

[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 0.643 a.4.5 "Winged helix" DNA-binding domain
View Download 0.642 a.4.1 Homeodomain-like
View Download 0.636 a.144.1 PABC (PABP) domain
View Download 0.556 a.4.2 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
View Download 0.548 a.4.5 "Winged helix" DNA-binding domain
View Download 0.541 a.4.5 "Winged helix" DNA-binding domain
View Download 0.528 a.4.1 Homeodomain-like
View Download 0.450 a.35.1 lambda repressor-like DNA-binding domains
View Download 0.432 a.46.2 Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View Download 0.428 d.48.1 RecA protein, C-terminal domain
View Download 0.424 a.52.1 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View Download 0.360 a.60.1 SAM/Pointed domain
View Download 0.347 a.44.1 Disulphide-bond formation facilitator (DSBA), insertion domain
View Download 0.296 a.179.1 Replisome organizer (g39p helicase loader/inhibitor protein)
View Download 0.273 a.4.1 Homeodomain-like
View Download 0.237 a.46.2 Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View Download 0.233 a.60.3 C-terminal domain of RNA polymerase alpha subunit
View Download 0.227 a.64.1 Saposin
View Download 0.223 a.5.2 UBA-like
View Download 0.223 a.112.1 Description not found.
View Download 0.218 a.52.1 Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin

Predicted functions:

Term Confidence Notes
telomeric DNA binding 7.07761964836826 bayes_pls_golite062009
single-stranded telomeric DNA binding 6.04637014849887 bayes_pls_golite062009
telomerase inhibitor activity 5.40477712257453 bayes_pls_golite062009
nucleic acid binding 4.02967008021862 bayes_pls_golite062009
DNA binding 3.62735703519187 bayes_pls_golite062009
single-stranded DNA binding 3.59212997362902 bayes_pls_golite062009
structure-specific DNA binding 3.53214384646348 bayes_pls_golite062009
binding 2.83465364476231 bayes_pls_golite062009
structural constituent of ribosome 2.25006883439646 bayes_pls_golite062009
transcription regulator activity 2.20239961025491 bayes_pls_golite062009
structural molecule activity 2.07809455998137 bayes_pls_golite062009
protein binding 1.20309946451799 bayes_pls_golite062009
ribonuclease activity 1.19236946227657 bayes_pls_golite062009
DNA helicase activity 1.12203697857261 bayes_pls_golite062009
transcription factor activity 1.05816813143865 bayes_pls_golite062009
sequence-specific DNA binding 0.86170694706755 bayes_pls_golite062009
DNA-directed RNA polymerase activity 0.79554655100991 bayes_pls_golite062009
RNA polymerase activity 0.79554655100991 bayes_pls_golite062009
hydrolase activity 0.724860465280978 bayes_pls_golite062009
DNA-dependent ATPase activity 0.638831894247026 bayes_pls_golite062009
nuclease activity 0.57381531077345 bayes_pls_golite062009
DEAD/H-box RNA helicase binding 0.440977654731901 bayes_pls_golite062009
translation regulator activity 0.41164963411369 bayes_pls_golite062009
double-stranded DNA binding 0.378383789953688 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.360862776629591 bayes_pls_golite062009
nucleotidyltransferase activity 0.325774164899685 bayes_pls_golite062009
four-way junction helicase activity 0.31769813397725 bayes_pls_golite062009
RNA binding 0.31028563542112 bayes_pls_golite062009
translation initiation factor activity 0.30211828233765 bayes_pls_golite062009
exonuclease activity 0.28313884527829 bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups 0.226916777208049 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 0.223941674251642 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 0.125256208482441 bayes_pls_golite062009
exoribonuclease activity 0.109774918833391 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 0.0954216620147701 bayes_pls_golite062009
ATP-dependent DNA helicase activity 0.0179535526984695 bayes_pls_golite062009
helicase activity 0.0121541775159524 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [177-299] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSQKTRPIFA IEQLSPYQNV WTIKARVSYK GEIKTWHNQR GDGKLFNVNF LDTSGEIRAT  60
   61 AFNDFATKFN EILQEGKVYY VSKAKLQPAK PQFTNLTHPY ELNLDRDTVI EECFDESNVP 120
  121 KTH

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 604.927757
Match: 1fguA_
Description: Replication protein A 70 KDa subunit (RPA70)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
telomeric DNA binding 7.07761964836826 bayes_pls_golite062009
single-stranded telomeric DNA binding 6.04637014849887 bayes_pls_golite062009
telomerase inhibitor activity 5.40477712257453 bayes_pls_golite062009
nucleic acid binding 4.02967008021862 bayes_pls_golite062009
DNA binding 3.62735703519187 bayes_pls_golite062009
single-stranded DNA binding 3.59212997362902 bayes_pls_golite062009
structure-specific DNA binding 3.53214384646348 bayes_pls_golite062009
binding 2.83465364476231 bayes_pls_golite062009
structural constituent of ribosome 2.25006883439646 bayes_pls_golite062009
transcription regulator activity 2.20239961025491 bayes_pls_golite062009
structural molecule activity 2.07809455998137 bayes_pls_golite062009
protein binding 1.20309946451799 bayes_pls_golite062009
ribonuclease activity 1.19236946227657 bayes_pls_golite062009
DNA helicase activity 1.12203697857261 bayes_pls_golite062009
transcription factor activity 1.05816813143865 bayes_pls_golite062009
sequence-specific DNA binding 0.86170694706755 bayes_pls_golite062009
DNA-directed RNA polymerase activity 0.79554655100991 bayes_pls_golite062009
RNA polymerase activity 0.79554655100991 bayes_pls_golite062009
hydrolase activity 0.724860465280978 bayes_pls_golite062009
DNA-dependent ATPase activity 0.638831894247026 bayes_pls_golite062009
nuclease activity 0.57381531077345 bayes_pls_golite062009
DEAD/H-box RNA helicase binding 0.440977654731901 bayes_pls_golite062009
translation regulator activity 0.41164963411369 bayes_pls_golite062009
double-stranded DNA binding 0.378383789953688 bayes_pls_golite062009
translation factor activity, nucleic acid binding 0.360862776629591 bayes_pls_golite062009
nucleotidyltransferase activity 0.325774164899685 bayes_pls_golite062009
four-way junction helicase activity 0.31769813397725 bayes_pls_golite062009
RNA binding 0.31028563542112 bayes_pls_golite062009
translation initiation factor activity 0.30211828233765 bayes_pls_golite062009
exonuclease activity 0.28313884527829 bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups 0.226916777208049 bayes_pls_golite062009
hydrolase activity, acting on ester bonds 0.223941674251642 bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters 0.125256208482441 bayes_pls_golite062009
exoribonuclease activity 0.109774918833391 bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 0.0954216620147701 bayes_pls_golite062009
ATP-dependent DNA helicase activity 0.0179535526984695 bayes_pls_golite062009
helicase activity 0.0121541775159524 bayes_pls_golite062009

Predicted Domain #4
Region A:
Residues: [300-440] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FNFIKLDAIQ NQEVNSNVDV LGIIQTINPH FELTSRAGKK FDRRDITIVD DSGFSISVGL  60
   61 WNQQALDFNL PEGSVAAIKG VRVTDFGGKS LSMGFSSTLI PNPEIPEAYA LKGWYDSKGR 120
  121 NANFITLKQE PGMGGQSAAS L

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 604.927757
Match: 1fguA_
Description: Replication protein A 70 KDa subunit (RPA70)
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [441-621] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TKFIAQRITI ARAQAENLGR SEKGDFFSVK AAISFLKVDN FAYPACSNEN CNKKVLEQPD  60
   61 GTWRCEKCDT NNARPNWRYI LTISIIDETN QLWLTLFDDQ AKQLLGVDAN TLMSLKEEDP 120
  121 NEFTKITQSI QMNEYDFRIR AREDTYNDQS RIRYTVANLH SLNYRAEADY LADELSKALL 180
  181 A

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 355.39794
Match: 1l1oC_
Description: Replication protein A 70 KDa subunit (RPA70)
Matching Structure (courtesy of the PDB):
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle