YRC Public Data Repository - Protein Structure Prediction

Protein:	RFC5
Organism:	Saccharomyces cerevisiae
Length:	354 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 RFC5.

Description	E-value	Query Range	Subject Range
RFC4_ARATH - Replication factor C subunit 4 OS=Arabidopsis thaliana GN=RFC4 PE=2 SV=1	5.0E-69	[2..353]	[9..332]
gi\|2984127, gi\|1... - gi\|2984127\|gb\|AAC07663.1\| DNA polymerase III gamma subunit [Aquifex aeolicus VF5], gi\|15606894\|ref\|N... gi\|7514776 - pir\|\|A70460 DNA polymerase III gamma subunit - Aquifex aeolicus	9.0E-69	[3..314]	[5..296]
RFC3 - replication factor C (activator 1) 3, 38kDa gi\|123994885, gi... - gi\|60812373\|gb\|AAX36209.1\| replication factor C 3 [synthetic construct], gi\|123994885\|gb\|ABM85044.1\|...	2.0E-68	[1..350]	[1..340]
gi\|255028847 - gi\|255028847\|ref\|ZP_05300798.1\| hypothetical protein LmonL_06056 [Listeria monocytogenes LO28] gi\|224502886 - gi\|224502886\|ref\|ZP_03671193.1\| hypothetical protein LmonFR_10254 [Listeria monocytogenes FSL R2-561... gi\|224499379 - gi\|224499379\|ref\|ZP_03667728.1\| hypothetical protein LmonF1_06652 [Listeria monocytogenes Finland 19... gi\|16804741 - gi\|16804741\|ref\|NP_466226.1\| hypothetical protein lmo2704 [Listeria monocytogenes EGD-e] gi\|133728725, gi... - gi\|254827269\|ref\|ZP_05231956.1\| hypothetical protein LmonocytogeFSL_02341 [Listeria monocytogenes FS... gi\|25288580, gi\|... - pir\|\|AG1412 DNA polymerase III (gamma and tau chains) homolog dnaX [imported] - Listeria monocytogen...	3.0E-68	[2..338]	[4..320]
gi\|16415387, gi\|... - pir\|\|AF1788 DNA polymerase III (gamma and tau chains) homolog dnaX [imported] - Listeria innocua (st... gi\|16801912 - gi\|16801912\|ref\|NP_472180.1\| hypothetical protein lin2852 [Listeria innocua Clip11262]	5.0E-68	[2..338]	[4..320]
gi\|151946482 - gi\|151946482\|gb\|EDN64704.1\| replication factor C subunit 5 [Saccharomyces cerevisiae YJM789] RFC5_YEAST - Replication factor C subunit 5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RFC5 PE=1... RFC5 - Subunit of heteropentameric Replication factor C (RF-C), which is a DNA binding protein and ATPase t... gi\|190408751 - gi\|190408751\|gb\|EDV12016.1\| replication factor C subunit 5 [Saccharomyces cerevisiae RM11-1a] gi\|207347704 - gi\|207347704\|gb\|EDZ73792.1\| YBR087Wp-like protein [Saccharomyces cerevisiae AWRI1631]	6.0E-68	[1..354]	[1..354]
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 /...	7.0E-68	[2..347]	[5..311]
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)	1.0E-67	[3..347]	[29..335]
gi\|90584244, gi\|... - gi\|90584244\|ref\|ZP_01239984.1\| AAA ATPase, central region [Staphylococcus aureus subsp. aureus JH1],... gi\|15926155, gi\|... - gi\|15926155\|ref\|NP_373688.1\| DNA polymerase III gamma and tau subunits [Staphylococcus aureus subsp.... gi\|156720941, gi... - gi\|156978806\|ref\|YP_001441065.1\| DNA polymerase III gamma and tau subunits [Staphylococcus aureus su... gi\|25288574 - pir\|\|G89813 DNA polymerase III gamma and tau subunits [imported] - Staphylococcus aureus (strain N31... gi\|14246246, gi\|... - gi\|15923468\|ref\|NP_371002.1\| DNA polymerase III gamma and tau subunits [Staphylococcus aureus subsp.... gi\|253315726 - gi\|253315726\|ref\|ZP_04838939.1\| DNA polymerase III gamma and tau subunits [Staphylococcus aureus sub... gi\|90429477, gi\|... - gi\|90586946\|ref\|ZP_01242630.1\| AAA ATPase, central region [Staphylococcus aureus subsp. aureus JH9],... gi\|255005271 - gi\|255005271\|ref\|ZP_05143872.2\| DNA polymerase III gamma and tau subunits [Staphylococcus aureus sub...	1.0E-67	[2..346]	[4..322]
gi\|17232424, gi\|... - gi\|17232424\|ref\|NP_488972.1\| DNA polymerase III gamma and tau subunits [Nostoc sp. PCC 7120], gi\|171... gi\|25531836 - pir\|\|AD2422 DNA polymerase III gamma and tau chains [imported] - Nostoc sp. (strain PCC 7120)	2.0E-67	[3..339]	[5..323]

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Predicted Domain #1

Region A:
Residues: [1-7]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLWVDK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [194-261]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SDSEISTILS DVVTNERIQL ETKDILKRIA QASNGNLRVS LLMLESMALN NELALKSSSP  60
   61 IIKPDWII

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	313.274545
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
structure-specific DNA binding	1.2539059700735	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
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
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
DNA strand annealing activity	0.283577486331079	bayes_pls_golite062009
protein binding	0.170837278876362	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
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: [8-193]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YRPKSLNALS HNEELTNFLK SLSDQPRDLP HLLLYGPNGT GKKTRCMALL ESIFGPGVYR  60
   61 LKIDVRQFVT ASNRKLELNV VSSPYHLEIT PSDMGNNDRI VIQELLKEVA QMEQVDFQDS 120
  121 KDGLAHRYKC VIINEANSLT KDAQAALRRT MEKYSKNIRL IMVCDSMSPI IAPIKSRCLL 180
  181 IRCPAP

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [262-354]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VIHKLTRKIV KERSVNSLIE CRAVLYDLLA HCIPANIILK ELTFSLLDVE TLNTTNKSSI  60
   61 IEYSSVFDER LSLGNKAIFH LEGFIAKVMC CLD

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	313.274545
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: