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PR01245

Identifier
RAD1REC1  [View Relations]  [View Alignment]  
Accession
PR01245
No. of Motifs
8
Creation Date
01-NOV-1999
Title
Repair protein Rad1/Rec1 family signature
Database References
PRINTS; PR01246 RAD1REPAIR; PR01247 RECEXONCLASE
INTERPRO; IPR003021
Literature References
1. THELEN, M.P., ONEL, K. AND HOLLOMAN, W.K. 
The REC1 gene of Ustilago maydis involved in the cellular response to DNA
damage encodes an exonuclease.
J.BIOL.CHEM. 269 747-754 (1994).
 
2. LONG, K.E., SUNNERHAGEN, P. AND SUBRAMANI, S.
The Schizosaccharomyces pombe rad1 gene consists of three exons and the
cDNA sequence is partially homologous to the Ustilago maydis REC1 cDNA.
GENE 148 155-159 (1994). 

Documentation
REC1 of Ustilago maydis plays a key role in regulating the genetic system
of the fungus. REC1 mutants are very sensitive to UV light - mutation
leads to a complex phenotype with alterations in DNA repair, recombination,
mutagenesis, meiosis and cell division [1]. The predicted product of the
REC1 gene is a polypeptide of 522 amino acid residues with molecular mass 
57 kDa. The protein shows 3'-->5' exonuclease activity, but only in cells
over-expressing REC1 [1]. While it is distinguishable from the major
bacterial nucleases, the protein has certain enzymatic features in common
with epsilon, the proof-reading exonuclease subunit of E.coli DNA polymerase
III holoenzyme [1].
 
The rad1 gene of Schizosaccharomyces pombe comprises three exons and encodes
a 37kDa protein that exhibits partial similarity to the REC1 gene of 
Ustilago maydis [2]. The two genes share putative functional similarities
in their respective organisms. 
 
RAD1REC1 is an 8-element fingerprint that provides a signature for Rad1
repair and related Rec1 proteins. The fingerprint was derived from an
initial alignment of 3 sequences: the motifs were drawn from short conserved
regions spanning virtually the full alignment length. Two iterations on
SPTR37_10f were required to reach convergence, at which point a true set 
comprising 7 sequences was identified. Two partial matches were also found,
both of which are related Rad-like proteins that match 2 motifs.
Summary Information
   7 codes involving  8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
2 codes involving 2 elements
Composite Feature Index
877777777
700000000
600000000
500000000
400000000
300000000
211010010
12345678
True Positives
O60671        O70452        O75572        O88391        
Q99110 RAD1_SCHPO REC1_USTMA
True Positive Partials
Codes involving 2 elements
O95304 RA17_YEAST
Sequence Titles
O60671      CELL CYCLE CHECKPOINT PROTEIN HRAD1 (DNA REPAIR EXONUCLEASE) - HOMO SAPIENS (HUM 
O70452 CELL CYCLE CHECKPOINT PROTEIN MRAD1 - MUS MUSCULUS (MOUSE).
O75572 RAD1 - HOMO SAPIENS (HUMAN).
O88391 RAD1P - MUS MUSCULUS (MOUSE).
Q99110 EXODEOXYRIBONUCLEASE - USTILAGO MAYDIS (SMUT FUNGUS).
RAD1_SCHPO DNA REPAIR PROTEIN RAD1 - SCHIZOSACCHAROMYCES POMBE (FISSION YEAST).
REC1_USTMA REC1 PROTEIN - USTILAGO MAYDIS (SMUT FUNGUS).

O95304 RAD1-LIKE PROTEIN - HOMO SAPIENS (HUMAN).
RA17_YEAST DNA DAMAGE CHECKPOINT CONTROL PROTEIN RAD17 - SACCHAROMYCES CEREVISIAE (BAKER'S
Scan History
SPTR37_10f 2  70   NSINGLE    
Initial Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
ATLSDVTGLANLLKSVAI Q99110 17 17 -
ATLSDVTGLANLLKSVAI REC1_USTMA 17 17 -
AETVCLKQIQSTLRCIDF RAD1_SCHPO 4 4 -

Motif 2 width=18
Element Seqn Id St Int Rpt
ASSSGLEIITELNRTLQA Q99110 42 7 -
ASSSGLEIITELNRTLQA REC1_USTMA 42 7 -
ITSRGLRFAVEESQSLQA RAD1_SCHPO 29 7 -

Motif 3 width=17
Element Seqn Id St Int Rpt
AHAYLYSHMFDSYRFEN Q99110 59 -1 -
AHAYLYSHMFDSYRFEN REC1_USTMA 59 -1 -
AHAFLDKSLFQTFNFQG RAD1_SCHPO 46 -1 -

Motif 4 width=18
Element Seqn Id St Int Rpt
MKLSYQGHGNPLVLELEQ Q99110 238 162 -
MKLSYQGHGNPLVLELEQ REC1_USTMA 238 162 -
CKVQYNGPGCPFIWEVEE RAD1_SCHPO 112 49 -

Motif 5 width=21
Element Seqn Id St Int Rpt
NVLTRVSMSTYEPSFLTDMVF Q99110 258 2 -
NVLTRVSMSTYEPSFLTDMVF REC1_USTMA 258 2 -
GYATACELLTMECEDDVDINR RAD1_SCHPO 132 2 -

Motif 6 width=18
Element Seqn Id St Int Rpt
YDFTLLSRTMSVLRSSIK Q99110 384 105 -
YDFTLLSRTMSVLRSSIK REC1_USTMA 384 105 -
YRFSLIRHALKALQVGSK RAD1_SCHPO 229 76 -

Motif 7 width=18
Element Seqn Id St Int Rpt
KTSLRMDEAGLISFQFMM Q99110 401 -1 -
KTSLRMDEAGLISFQFMM REC1_USTMA 401 -1 -
KVNLRIDENGTLSIQIML RAD1_SCHPO 246 -1 -

Motif 8 width=16
Element Seqn Id St Int Rpt
DEQDAFCEFLCCPLDT Q99110 443 24 -
DEQDAFCEFLVSTFTC REC1_USTMA 443 24 -
EGLCTFVDFCIVPLDL RAD1_SCHPO 267 3 -
Final Motifs
Motif 1  width=18
Element Seqn Id St Int Rpt
ASLDNVRNLSTVLKAIHF O88391 19 19 -
ASLDNVRNLSTILKAIHF O75572 19 19 -
ASLDNVRNLSTILKAIHF O60671 19 19 -
ASLDNVRNLFTVLKAIHF O70452 19 19 -
ATLSDVTGLANLLKSVAI Q99110 17 17 -
ATLSDVTGLANLLKSVAI REC1_USTMA 17 17 -
AETVCLKQIQSTLRCIDF RAD1_SCHPO 4 4 -

Motif 2 width=18
Element Seqn Id St Int Rpt
ATKNGIKVTVENAKCVQA O88391 44 7 -
ATKNGIKVTVENAKCVQA O75572 44 7 -
ATKNGIKVTVENAKCVQA O60671 44 7 -
ATKNGIKVTVENAKCVQA O70452 44 7 -
ASSSGLEIITELNRTLQA Q99110 42 7 -
ASSSGLEIITELNRTLQA REC1_USTMA 42 7 -
ITSRGLRFAVEESQSLQA RAD1_SCHPO 29 7 -

Motif 3 width=17
Element Seqn Id St Int Rpt
ANAFIQADVFQEFVIQE O88391 61 -1 -
ANAFIQAGIFQEFKVQE O75572 61 -1 -
ANAFIQAGIFQEFKVQE O60671 61 -1 -
ANAFIQADVFQEFVIQE O70452 61 -1 -
AHAYLYSHMFDSYRFEN Q99110 59 -1 -
AHAYLYSHMFDSYRFEN REC1_USTMA 59 -1 -
AHAFLDKSLFQTFNFQG RAD1_SCHPO 46 -1 -

Motif 4 width=18
Element Seqn Id St Int Rpt
LRMCYQGYGHPLMLFLEE O88391 108 30 -
LRMCYQGYGYPLMLFLEE O75572 108 30 -
LRMCYQGYGYPLMLFLEE O60671 108 30 -
LRMCYQGYGHPLMLFLEE O70452 108 30 -
MKLSYQGHGNPLVLELEQ Q99110 238 162 -
MKLSYQGHGNPLVLELEQ REC1_USTMA 238 162 -
CKVQYNGPGCPFIWEVEE RAD1_SCHPO 112 49 -

Motif 5 width=21
Element Seqn Id St Int Rpt
GVVTVCKITTQEPEETLDFDF O88391 127 1 -
GVVTVCKITTQEPEETLDFDF O75572 127 1 -
GVVTVCKINTQEPEETLDFDF O60671 127 1 -
GVVTVCKITTQEPEETLDFDF O70452 127 1 -
NVLTRVSMSTYEPSFLTDMVF Q99110 258 2 -
NVLTRVSMSTYEPSFLTDMVF REC1_USTMA 258 2 -
GYATACELLTMECEDDVDINR RAD1_SCHPO 132 2 -

Motif 6 width=18
Element Seqn Id St Int Rpt
YKLSLLKPSTKALALSCK O88391 223 75 -
YKISLLKPSTKALVLSCK O75572 223 75 -
YKISLLKPSTKALVLSCK O60671 223 75 -
YKLSLLKPSTKALALSCK O70452 223 75 -
YDFTLLSRTMSVLRSSIK Q99110 384 105 -
YDFTLLSRTMSVLRSSIK REC1_USTMA 384 105 -
YRFSLIRHALKALQVGSK RAD1_SCHPO 229 76 -

Motif 7 width=18
Element Seqn Id St Int Rpt
KVSIRTDNRGFLSLQYMI O88391 240 -1 -
KVSIRTDNRGFLSLQYMI O75572 240 -1 -
KVSIRTDNRGFLSLQYMI O60671 240 -1 -
KVSIRTDNRGFLSLQYMI O70452 240 -1 -
KTSLRMDEAGLISFQFMM Q99110 401 -1 -
KTSLRMDEAGLISFQFMM REC1_USTMA 401 -1 -
KVNLRIDENGTLSIQIML RAD1_SCHPO 246 -1 -

Motif 8 width=16
Element Seqn Id St Int Rpt
DGQICFVEYYCCPDEE O88391 261 3 -
DGQICFVEYYCCPDEE O75572 261 3 -
DGQICFVEYYCCPDEE O60671 261 3 -
DGQICFVEYYCCPDEE O70452 261 3 -
DEQDAFCEFLCCPLDT Q99110 443 24 -
DEQDAFCEFLVSTFTC REC1_USTMA 443 24 -
EGLCTFVDFCIVPLDL RAD1_SCHPO 267 3 -