YRC Public Data Repository - Protein Structure Prediction

Protein:	RAD55
Organism:	Saccharomyces cerevisiae
Length:	406 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 RAD55.

Description	E-value	Query Range	Subject Range
RAD55 - Protein that stimulates strand exchange by stabilizing the binding of Rad51p to single-stranded DNA;... RAD55_YEAST - DNA repair protein RAD55 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RAD55 PE=1 SV=1	0.0	[1..406]	[1..406]
gi\|976445\|gb\|AAA... - RecA RECA_SPIPL - (P48293) RecA protein (Recombinase A) RECA_ARTPT - Protein RecA OS=Arthrospira platensis GN=recA PE=3 SV=1	5.0E-75	[2..303]	[32..315]
gi\|2119989 - pir\|\|I39509 recombination protein recA - Acinetobacter calcoaceticus RECA_ACIAD - Protein RecA OS=Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1) GN=recA PE=3 SV=1	2.0E-70	[1..303]	[26..311]
gi\|25300509 - pir\|\|AI2214 recombination protein [imported] - Nostoc sp. (strain PCC 7120) RECA_NOSS1 - Protein RecA OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=recA PE=3 SV=1	5.0E-69	[1..305]	[31..317]
RECA_BIFBR - Protein RecA OS=Bifidobacterium breve GN=recA PE=3 SV=1	7.0E-69	[1..303]	[44..329]
RECA_ANAVA - (P14167) Protein recA (Recombinase A)	1.0E-68	[1..305]	[31..317]
RECA_SALTI - Protein recA OS=Salmonella typhi GN=recA PE=3 SV=2 RECA_SALTY - Protein RecA OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) GN=recA PE=1 SV=2 gi\|29143089, gi\|... - gi\|29143089\|ref\|NP_806431.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str. T... RECA_SALCH - Protein RecA OS=Salmonella choleraesuis (strain SC-B67) GN=recA PE=3 SV=3 RECA_SALTY - Protein recA OS=Salmonella typhimurium GN=recA PE=3 SV=2 RECA_SALCH - Protein recA OS=Salmonella choleraesuis GN=recA PE=3 SV=3 RECA_SALTI - Protein RecA OS=Salmonella typhi GN=recA PE=3 SV=2 gi\|16761605 - gi\|16761605\|ref\|NP_457222.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str. C... gi\|168464049, gi... - gi\|195633723\|gb\|EDX52137.1\| protein RecA [Salmonella enterica subsp. enterica serovar Newport str. S... gi\|168820488, gi... - gi\|205342838\|gb\|EDZ29602.1\| protein RecA [Salmonella enterica subsp. enterica serovar Weltevreden st... RECA_SALNS - Protein RecA OS=Salmonella newport (strain SL254) GN=recA PE=3 SV=1 RECA_SALHS - Protein RecA OS=Salmonella heidelberg (strain SL476) GN=recA PE=3 SV=1 gi\|238909595 - gi\|238909595\|ref\|ZP_04653432.1\| recombinase A [Salmonella enterica subsp. enterica serovar Tennessee... gi\|205327960, gi... - gi\|205327960\|gb\|EDZ14724.1\| protein RecA [Salmonella enterica subsp. enterica serovar 4,[5],12:i:- s... gi\|168235857, gi... - gi\|197290652\|gb\|EDY30006.1\| protein RecA [Salmonella enterica subsp. enterica serovar Schwarzengrund... gi\|205335992, gi... - gi\|205335992\|gb\|EDZ22756.1\| protein RecA [Salmonella enterica subsp. enterica serovar Heidelberg str... gi\|168262060, gi... - gi\|205349184\|gb\|EDZ35815.1\| protein RecA [Salmonella enterica subsp. enterica serovar Hadar str. RI_... lcl\|NC_016856.1_... - [gene=recA] [protein=recombinase A] [protein_id=YP_005238927.1] [location=complement(2995089..299615... gi\|213648097 - gi\|213648097\|ref\|ZP_03378150.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... gi\|214000004 - gi\|214000004\|ref\|ZP_03410739.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... RECA_SALPC - Protein RecA OS=Salmonella paratyphi C (strain RKS4594) GN=recA PE=3 SV=1 gi\|213028317 - gi\|213028317\|ref\|ZP_03342764.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... gi\|109453384, gi... - gi\|109453400\|gb\|ABG34180.1\| RecA [Salmonella enterica subsp. enterica], gi\|109453398\|gb\|ABG34179.1\| ... gi\|213051937 - gi\|213051937\|ref\|ZP_03344815.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... gi\|213426123 - gi\|213426123\|ref\|ZP_03358873.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... RECA_SALPB - Protein RecA OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=recA PE=3 SV=1 gi\|213579899 - gi\|213579899\|ref\|ZP_03361725.1\| recombinase A [Salmonella enterica subsp. enterica serovar Typhi str... RECA_SALTY - Protein RecA OS=Salmonella typhimurium GN=recA PE=3 SV=2 RECA_SALPB - Protein recA OS=Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7) GN=recA PE=3 SV=1 gi\|199603797, gi... - gi\|200386699\|ref\|ZP_03213311.1\| protein RecA [Salmonella enterica subsp. enterica serovar Virchow st... RECA_SALCH - Protein RecA OS=Salmonella choleraesuis GN=recA PE=3 SV=3 gi\|204928070, gi... - gi\|204928070\|ref\|ZP_03219270.1\| protein RecA [Salmonella enterica subsp. enterica serovar Javiana st... RECA_SALG2 - Protein RecA OS=Salmonella gallinarum (strain 287/91 / NCTC 13346) GN=recA PE=3 SV=1 RECA_SALEP - Protein RecA OS=Salmonella enteritidis PT4 (strain P125109) GN=recA PE=3 SV=1 RECA_SALSV - Protein RecA OS=Salmonella schwarzengrund (strain CVM19633) GN=recA PE=3 SV=1 RECA_SALA4 - Protein RecA OS=Salmonella agona (strain SL483) GN=recA PE=3 SV=1 gi\|197241862, gi... - gi\|197263607\|ref\|ZP_03163681.1\| protein RecA [Salmonella enterica subsp. enterica serovar Saintpaul ... RECA_SALDC - Protein RecA OS=Salmonella dublin (strain CT_02021853) GN=recA PE=3 SV=1	2.0E-68	[1..303]	[28..313]
gi\|25300508 - gi\|25300508\|pir\|\|AE3350 recA protein [imported] - Brucella melitensis (strain 16M) gi\|17982728, gi\|... - gi\|17987070\|ref\|NP_539704.1\| recombinase A [Brucella melitensis 16M], gi\|17982728\|gb\|AAL51968.1\| rec...	2.0E-68	[1..308]	[54..345]
RECA_PECCA - Protein RecA OS=Pectobacterium carotovorum GN=recA PE=3 SV=1	3.0E-68	[1..305]	[28..315]

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Predicted Domain #1

Region A:
Residues: [1-262]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLGIPLSQL IVESPKPLSS GITGLDEILN LGFQARSIYE IFGPPGIGKT NFGIQLVCNS  60
   61 LEGIQQSEIN DDKILWIETF QEMPINILRE RFQKFKIVEE NVKRVRITKF GQLLYFFQNL 120
  121 FKLSQSVRYK LVIIDGFSQL VCDHLCTLSK RGGGMIDKTI HELKCRHLIL IFTVMTKYTH 180
  181 STGSTIIVLN DCMNTAFQSN EFESLEEYYE ILDDGSNFFV NSNNERRKNN VHILKSALVA 240
  241 NIAMGSKDST WEVFLRDRIG LF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	68.30103
Match:	2recA_
Description:	RecA
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [263-336]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RDWNEQVDET VFVKSKRVKA SSSQSNEGCT TIKEMRINKR NFENLRIAIV FNLHGEDRKR  60
   61 EGRNLKRSRS SDDR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	68.30103
Match:	2recA_
Description:	RecA
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [337-406]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NYIVKFDFDK ATGQLRDIID LKPDTANIAS FPTLSTSSSS CSQVFNNIDS NDNPLPNAEG  60
   61 KEEIIYDSEG

[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	0.416	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.396	b.40.4	Nucleic acid-binding proteins
View	Download	0.561	a.144.1	PABC (PABP) domain
View	Download	0.394	d.79.3	L30e-like
View	Download	0.409	a.28.3	Retrovirus capsid protein C-terminal domain
View	Download	0.388	a.60.11	Hypothetical protein YjbJ
View	Download	0.382	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.369	a.44.1	Disulphide-bond formation facilitator (DSBA), insertion domain
View	Download	0.365	d.68.3	SirA-like
View	Download	0.300	d.10.1	DNA-binding domain
View	Download	0.290	a.57.1	Protein HNS-dependent expression A; HdeA
View	Download	0.285	a.163.1	Crustacean CHH/MIH/GIH neurohormone
View	Download	0.270	a.28.1	ACP-like
View	Download	0.263	d.68.6	DNA-binding protein Sso10b (AlbA)
View	Download	0.244	b.1.1	Immunoglobulin
View	Download	0.233	a.61.1	Retroviral matrix proteins
View	Download	0.219	d.93.1	SH2 domain
View	Download	0.217	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.205	b.1.2	Fibronectin type III

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