YRC Public Data Repository - Protein Structure Prediction

Protein:	RFC2
Organism:	Saccharomyces cerevisiae
Length:	353 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 RFC2.

Description	E-value	Query Range	Subject Range
RFC2_YEAST - Replication factor C subunit 2 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC2 PE=1... RFC2 - Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase t...	1.0E-84	[1..353]	[1..353]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	2.0E-79	[3..352]	[14..345]
RFC2_MOUSE - Replication factor C subunit 2 OS=Mus musculus GN=Rfc2 PE=1 SV=1	3.0E-79	[2..352]	[11..341]
RFC2_CHICK - Replication factor C subunit 2 OS=Gallus gallus GN=RFC2 PE=2 SV=1	5.0E-78	[15..352]	[31..351]
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 /...	2.0E-76	[27..353]	[7..316]
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-76	[18..350]	[21..337]
gi\|15988297, gi\|... - gi\|15988302\|pdb\|1IQP\|F Chain F, Crystal Structure Of The Clamp Loader Small Subunit From Pyrococcus ...	3.0E-76	[13..350]	[1..321]
RFC4_ARATH - Replication factor C subunit 4 OS=Arabidopsis thaliana GN=RFC4 PE=2 SV=1	1.0E-75	[22..343]	[6..321]
RFC2_ORYSJ - Replication factor C subunit 2 OS=Oryza sativa subsp. japonica GN=RFC2 PE=2 SV=1 gi\|125535960 - gi\|125535960\|gb\|EAY82448.1\| hypothetical protein OsI_37665 [Oryza sativa Indica Group]	1.0E-75	[23..343]	[7..319]

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Predicted Domain #1

Region A:
Residues: [1-30]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MFEGFGPNKK RKISKLAAEQ SLAQQPWVEK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [193-262]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DASNAIDRLR FISEQENVKC DDGVLERILD ISAGDLRRGI TLLQSASKGA QYLGDGKNIT  60
   61 STQVEELAGV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	679.315398
Match:	1iqpA_
Description:	Replication factor C
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
binding	2.64537357529343	bayes_pls_golite062009
mismatched DNA binding	2.51625633651862	bayes_pls_golite062009
DNA helicase activity	2.2817164193758	bayes_pls_golite062009
nucleic acid binding	2.21184938313192	bayes_pls_golite062009
pyrophosphatase activity	2.13284212711072	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
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
microtubule motor activity	1.35938517416356	bayes_pls_golite062009
structure-specific DNA binding	1.2539059700735	bayes_pls_golite062009
protein binding	1.22129154759482	bayes_pls_golite062009
purine ribonucleotide binding	1.21658213854831	bayes_pls_golite062009
ribonucleotide binding	1.21652144153182	bayes_pls_golite062009
purine nucleotide binding	1.21571071905795	bayes_pls_golite062009
nucleotide binding	1.20347573865566	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
motor activity	1.14667913749579	bayes_pls_golite062009
double-stranded DNA binding	1.117585097627	bayes_pls_golite062009
catalytic activity	1.00104173493322	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
GTPase activity	0.406399103964327	bayes_pls_golite062009
DNA strand annealing activity	0.283577486331079	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.147579541298736	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
structural constituent of ribosome	0.089234257580272	bayes_pls_golite062009
3'-5' DNA helicase activity	0.0769112340058804	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: [31-192]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YRPKNLDEVT AQDHAVTVLK KTLKSANLPH MLFYGPPGTG KTSTILALTK ELYGPDLMKS  60
   61 RILELNASDE RGISIVREKV KNFARLTVSK PSKHDLENYP CPPYKIIILD EADSMTADAQ 120
  121 SALRRTMETY SGVTRFCLIC NYVTRIIDPL ASRCSKFRFK AL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [263-353]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VPHDILIEIV EKVKSGDFDE IKKYVNTFMK SGWSAASVVN QLHEYYITND NFDTNFKNQI  60
   61 SWLLFTTDSR LNNGTNEHIQ LLNLLVKISQ L

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	679.315398
Match:	1iqpA_
Description:	Replication factor C
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

Predicted functions: