YRC Public Data Repository - Protein Structure Prediction

Protein:	RFC3
Organism:	Saccharomyces cerevisiae
Length:	340 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 RFC3.

Description	E-value	Query Range	Subject Range
RFC3_YEAST - Replication factor C subunit 3 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC3 PE=1... RFC3 - Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase t...	8.0E-86	[1..340]	[1..340]
gi\|15988297, gi\|... - gi\|15988302\|pdb\|1IQP\|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From Pyrococcus ...	1.0E-85	[1..333]	[1..327]
gi\|14601459, gi\|... - gi\|5105207\|dbj\|BAA80521.1\| 346aa long hypothetical replication factor C subunit [Aeropyrum pernix K1... RFCS_AERPE - (Q9YBS7) Replication factor C small subunit (RFC small subunit) (Clamp loader small subunit)	2.0E-85	[6..335]	[21..346]
RFCS_ARCFU - Replication factor C small subunit OS=Archaeoglobus fulgidus GN=rfcS PE=1 SV=1 RFCS_ARCFU - Replication factor C small subunit OS=Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 /...	8.0E-85	[15..327]	[7..313]
RFC2_MOUSE - Replication factor C subunit 2 OS=Mus musculus GN=Rfc2 PE=1 SV=1	9.0E-85	[5..329]	[23..341]
RFC2_CHICK - Replication factor C subunit 2 OS=Gallus gallus GN=RFC2 PE=2 SV=1	7.0E-84	[1..329]	[29..351]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	2.0E-82	[2..329]	[25..345]
RFCS_SULTO - Replication factor C small subunit OS=Sulfolobus tokodaii (strain DSM 16993 / JCM 10545 / NBRC 10014... RFCS_SULTO - Replication factor C small subunit OS=Sulfolobus tokodaii GN=rfcS PE=3 SV=1	7.0E-81	[10..335]	[4..324]
gi\|15991286 - gi\|15991286\|dbj\|BAB69675.1\| replication factor C 40kDa subunit [Oryza sativa Japonica Group] gi\|218195393, gi... - gi\|218195393\|gb\|EEC77820.1\| hypothetical protein OsI_17026 [Oryza sativa Indica Group], gi\|116310007...	3.0E-80	[2..339]	[5..335]

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Predicted Domain #1

Region A:
Residues: [1-20]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSTSTEKRSK ENLPWVEKYR

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [171-239]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QEAIERRIAN VLVHEKLKLS PNAEKALIEL SNGDMRRVLN VLQSCKATLD NPDEDEISDD  60
   61 VIYECCGAP

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.917458
Match:	1lfsA_
Description:	No description for 1lfsA_ was found.

Predicted functions:

Term	Confidence	Notes
DNA clamp loader activity	6.51495346697904	bayes_pls_golite062009
protein-DNA loading ATPase activity	6.40748863504898	bayes_pls_golite062009
mismatched DNA binding	2.51625633651862	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
pyrophosphatase activity	2.23646936731119	bayes_pls_golite062009
nucleic acid binding	2.21184938313192	bayes_pls_golite062009
DNA binding	1.94055378599526	bayes_pls_golite062009
ATP-dependent DNA helicase activity	1.88455339138556	bayes_pls_golite062009
	1.85506769032946	bayes_pls_golite062009
transcription regulator activity	1.83584389083042	bayes_pls_golite062009
binding	1.82708462182661	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
guanine/thymine mispair binding	1.69026972999845	bayes_pls_golite062009
DNA insertion or deletion binding	1.68890613599528	bayes_pls_golite062009
RNA helicase activity	1.63960194106079	bayes_pls_golite062009
DNA replication origin binding	1.62491387774159	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.61735400124552	bayes_pls_golite062009
RNA-dependent ATPase activity	1.60404584546501	bayes_pls_golite062009
catalytic activity	1.32370671504792	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2537888487362	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
motor activity	1.14667913749579	bayes_pls_golite062009
microtubule motor activity	1.1277447806079	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
DNA-directed DNA polymerase activity	0.971476020912368	bayes_pls_golite062009
DNA polymerase activity	0.928091843881235	bayes_pls_golite062009
transcription factor activity	0.697256579145077	bayes_pls_golite062009
transcription repressor activity	0.677612020025357	bayes_pls_golite062009
guanyl nucleotide binding	0.656009904481476	bayes_pls_golite062009
guanyl ribonucleotide binding	0.64416740142962	bayes_pls_golite062009
GTP binding	0.643084645864898	bayes_pls_golite062009
single base insertion or deletion binding	0.629563765934841	bayes_pls_golite062009
single-stranded DNA binding	0.568457189190858	bayes_pls_golite062009
cytoskeletal protein binding	0.500462538667228	bayes_pls_golite062009
protein binding	0.424505363166733	bayes_pls_golite062009
GTPase activity	0.406399103964327	bayes_pls_golite062009
DNA strand annealing activity	0.283577486331079	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.248432446853676	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.217252531553173	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.215962398124297	bayes_pls_golite062009
structural constituent of ribosome	0.089234257580272	bayes_pls_golite062009
3'-5' DNA helicase activity	0.0769112340058804	bayes_pls_golite062009
ATPase activity	0.0740243885501273	bayes_pls_golite062009
lysine N-acetyltransferase activity	0.0320943071400439	bayes_pls_golite062009
histone acetyltransferase activity	0.0320943071400439	bayes_pls_golite062009
double-strand/single-strand DNA junction binding	0.0136229525922795	bayes_pls_golite062009
actin binding	0.00482938540552702	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [21-170]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PETLDEVYGQ NEVITTVRKF VDEGKLPHLL FYGPPGTGKT STIVALAREI YGKNYSNMVL  60
   61 ELNASDDRGI DVVRNQIKDF ASTRQIFSKG FKLIILDEAD AMTNAAQNAL RRVIERYTKN 120
  121 TRFCVLANYA HKLTPALLSR CTRFRFQPLP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [240-340]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPSDLKAVLK SILEDDWGTA HYTLNKVRSA KGLALIDLIE GIVKILEDYE LQNEETRVHL  60
   61 LTKLADIEYS ISKGGNDQIQ GSAVIGAIKA SFENETVKAN V

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1000.917458
Match:	1lfsA_
Description:	No description for 1lfsA_ was found.

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: