YRC Public Data Repository - Protein Structure Prediction

Protein:	RFC1
Organism:	Saccharomyces cerevisiae
Length:	861 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 RFC1.

Description	E-value	Query Range	Subject Range
RFC1_YEAST - Replication factor C subunit 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC1 PE=1... RFC1 - Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase t...	0.0	[1..861]	[1..861]
gi\|460932 - gi\|460932\|gb\|AAC52140.1\| ISRE-binding protein	0.0	[5..856]	[258..1131]
gi\|1399917 - gi\|1399917\|gb\|AAC60361.1\| replication factor C large subunit [Anas platyrhynchos]	0.0	[3..860]	[256..1144]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[5..856]	[244..1117]
RFC1 - replication factor C (activator 1) 1, 145kDa	0.0	[9..829]	[248..1119]
gi\|4103934 - gi\|4103934\|gb\|AAD01890.1\| replication factor C [Rattus norvegicus]	0.0	[7..830]	[248..1104]
RFC1_SCHPO - Replication factor C subunit 1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rfc1 PE=1 S... rfc1 - DNA replication factor C complex subunit Rfc1	0.0	[6..836]	[96..904]

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Predicted Domain #1

Region A:
Residues: [1-196]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVNISDFFGK NKKSVRSSTS RPTRQVGSSK PEVIDLDTES DQESTNKTPK KMPVSNVIDV  60
   61 SETPEGEKKL PLPAKRKASS PTVKPASSKK TKPSSKSSDS ASNITAQDVL DKIPSLDLSN 120
  121 VHVKENAKFD FKSANSNADP DEIVSEIGSF PEGKPNCLLG LTIVFTGVLP TLERGASEAL 180
  181 AKRYGARVTK SISSKT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	70.0
Match:	1e32A_
Description:	Membrane fusion atpase p97 N-terminal domain , P97-Nn; Membrane fusion atpase p97, D1 domain; Membrane fusion atpase p97 domain 2, P97-Nc
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [197-280]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SVVVLGDEAG PKKLEKIKQL KIKAIDEEGF KQLIAGMPAE GGDGEAAEKA RRKLEEQHNI  60
   61 ATKEAELLVK KEEERSKKLA ATRV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	70.0
Match:	1e32A_
Description:	Membrane fusion atpase p97 N-terminal domain , P97-Nn; Membrane fusion atpase p97, D1 domain; Membrane fusion atpase p97 domain 2, P97-Nc
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA clamp loader activity	6.51495346697904	bayes_pls_golite062009
protein-DNA loading ATPase activity	6.40748863504898	bayes_pls_golite062009
DNA-dependent ATPase activity	2.72462789867829	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.88455339138556	bayes_pls_golite062009
structure-specific DNA binding	1.88004981070099	bayes_pls_golite062009
mismatched DNA binding	1.75879616923546	bayes_pls_golite062009
binding	1.62320027057768	bayes_pls_golite062009
microtubule motor activity	1.30090199952739	bayes_pls_golite062009
	1.27220313435557	bayes_pls_golite062009
guanine/thymine mispair binding	1.10234539735776	bayes_pls_golite062009
motor activity	1.03253378953548	bayes_pls_golite062009
helicase activity	1.0321619822241	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
DNA-directed DNA polymerase activity	0.971476020912368	bayes_pls_golite062009
DNA insertion or deletion binding	0.94261959567056	bayes_pls_golite062009
DNA polymerase activity	0.928091843881235	bayes_pls_golite062009
nucleic acid binding	0.833704518618903	bayes_pls_golite062009
ATP-dependent helicase activity	0.5607032154839	bayes_pls_golite062009
purine NTP-dependent helicase activity	0.5607032154839	bayes_pls_golite062009
double-stranded DNA binding	0.35687254758087	bayes_pls_golite062009
DNA binding	0.277415156373835	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.147579541298736	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.113504049290503	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.111293884322157	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	bayes_pls_golite062009
structural constituent of ribosome	0.089234257580272	bayes_pls_golite062009
transcription regulator activity	0.0109066016297058	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [281-301]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGGHLERDNV VREEDKLWTV K

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [479-542]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DANSIKSRLM TIAIREKFKL DPNVIDRLIQ TTRGDIRQVI NLLSTISTTT KTINHENINE  60
   61 ISKA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	207.06601
Match:	1iqpA_
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [302-478]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YAPTNLQQVC GNKGSVMKLK NWLANWENSK KNSFKHAGKD GSGVFRAAML YGPPGIGKTT  60
   61 AAHLVAQELG YDILEQNASD VRSKTLLNAG VKNALDNMSV VGYFKHNEEA QNLNGKHFVI 120
  121 IMDEVDGMSG GDRGGVGQLA QFCRKTSTPL ILICNERNLP KMRPFDRVCL DIQFRRP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [543-663]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WEKNIALKPF DIAHKMLDGQ IYSDIGSRNF TLNDKIALYF DDFDFTPLMI QENYLSTRPS  60
   61 VLKPGQSHLE AVAEAANCIS LGDIVEKKIR SSEQLWSLLP LHAVLSSVYP ASKVAGHMAG 120
  121 R

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	207.06601
Match:	1iqpA_
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [664-861]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 INFTAWLGQN SKSAKYYRLL QEIHYHTRLG TSTDKIGLRL DYLPTFRKRL LDPFLKQGAD  60
   61 AISSVIEVMD DYYLTKEDWD SIMEFFVGPD VTTAIIKKIP ATVKSGFTRK YNSMTHPVAI 120
  121 YRTGSTIGGG GVGTSTSTPD FEDVVDADDN PVPADDEETQ DSSTDLKKDK LIKQKAKPTK 180
  181 RKTATSKPGG SKKRKTKA

[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.

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: