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PR01743

Identifier
SSDNABINDING  [View Relations]  [View Alignment]  
Accession
PR01743
No. of Motifs
5
Creation Date
01-JUL-2002
Title
Single-strand DNA-binding protein signature
Database References
Literature References
1. BAYARSAIHAN, D., SOTO, R.J. AND LUKENS, L.N.
Cloning and characterisation of a novel sequence-specific single-stranded
DNA binding protein.
BIOCHEM.J. 331 447-452 (1998).
 
2. CASTRO, P., LIANG, H., LIANG, J.C. AND NAGARAJAN, L.
A novel, evolutionary conserved gene family with putative
sequence-specific single-stranded DNA-binding activity.
GENOMICS 80(1) 78-85 (2002).

Documentation
The sequence-specific single-strand DNA-binding protein (SSDP) family is
thought to be involved in transciption regulation. SSDP specifically binds
single-stranded pyrimidine-rich mirror repeat elements commonly found in
promoter regions, and is believed to regulate alpha-2(I) collagen [1]. It
has been identified as a target for unbalanced translocations and deletions
in acute myelogenous leukemia cells, implying a role as a tumour suppressor
gene [2]. It is expressed in spleen, lymph node, peripheral blood, bone
marrow, thymus and foetal liver [2]. Family members have been identified in
chicken, human, rat, mouse and Drosophila. The highest sequence identity is
observed in the first 100 N-terminal residues, which contains a tryptophan-
rich region in its centre. The C-terminus is more viariable, with glycine/
proline-rich low complexity regions.
 
SSDNABINDING is a 5-element fingerprint that provides a signature for the
single-strand DNA-binding proteins. The fingerprint was derived from an
initial alignment of 6 sequences: the motifs were drawn from the conserved
N-terminal region. Two iterations on SPTR40_20f were required to reach 
convergence, at which point a true set comprising 18 sequences was
identified. A single partial match was also found, Q9P038, a human protein
that lacks the N-terminal residues characteristic of other family members.
Summary Information
  18 codes involving  5 elements
0 codes involving 4 elements
0 codes involving 3 elements
1 codes involving 2 elements
Composite Feature Index
51818181818
400000
300000
200011
12345
True Positives
P81877        Q99LC6        Q99LX9        Q99LZ8        
Q9BTM0 Q9BWG4 Q9BWW3 Q9BWW4
Q9BWW5 Q9BWW6 Q9CYZ8 Q9D032
Q9D6L4 Q9DB78 Q9EQP3 Q9R050
Q9VEB9 Q9Y4T7
True Positive Partials
Codes involving 2 elements
Q9P038
Sequence Titles
P81877      SINGLE-STRAND DNA-BINDING PROTEIN (SSDP) (CSDP) - Homo sapiens (Human). 
Q99LC6 SIMILAR TO RIKEN CDNA 2610200M23 GENE - Mus musculus (Mouse).
Q99LX9 SIMILAR TO SINGLE-STRANDED-DNA-BINDING PROTEIN - Mus musculus (Mouse).
Q99LZ8 SIMILAR TO SINGLE-STRANDED-DNA-BINDING PROTEIN - Mus musculus (Mouse).
Q9BTM0 SIMILAR TO RIKEN CDNA 2610200M23 GENE - Homo sapiens (Human).
Q9BWG4 SIMILAR TO SINGLE-STRANDED-DNA-BINDING PROTEIN - Homo sapiens (Human).
Q9BWW3 SINGLE STRANDED DNA BINDING PROTEIN-1 - Homo sapiens (Human).
Q9BWW4 SINGLE STRANDED DNA BINDING PROTEIN-1 - Homo sapiens (Human).
Q9BWW5 SINGLE STRANDED DNA BINDING PROTEIN-3 - Homo sapiens (Human).
Q9BWW6 SINGLE-STRANDED DNA-BINDING PROTEIN 2 (HYPOTHETICAL 37.8 KDA PROTEIN) - Homo sapiens (Human).
Q9CYZ8 2310079I02RIK PROTEIN (SEQUENCE SPECIFIC SINGLE-STRANDED DNA-BINDING PROTEIN 2) - Mus musculus (Mouse).
Q9D032 2610200M23RIK PROTEIN - Mus musculus (Mouse).
Q9D6L4 2310079I02RIK PROTEIN - Mus musculus (Mouse).
Q9DB78 1500004K09RIK PROTEIN - Mus musculus (Mouse).
Q9EQP3 LCK-ASSOCIATED SIGNAL TRANSDUCER LAST - Mus musculus (Mouse).
Q9R050 SEQUENCE-SPECIFIC SINGLE-STRANDED-DNA-BINDING PROTEIN - Rattus norvegicus (Rat).
Q9VEB9 CG7187 PROTEIN - Drosophila melanogaster (Fruit fly).
Q9Y4T7 HYPOTHETICAL 37.9 KDA PROTEIN - Homo sapiens (Human).

Q9P038 HSPC116 - Homo sapiens (Human).
Scan History
SPTR40_20f 2  150  NSINGLE    
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
SAVPSDSQAREKLALYVYEY Q9CYZ8 10 10 -
SAVPSDSQAREKLALYVYEY Q9BWW6 10 10 -
SAVPSDSQAREKLALYVYEY Q99LX9 10 10 -
SAVPSDGQAREKLALYVYEY Q9R050 8 8 -
SAVPSDGQAREKLALYVYEY Q9BTM0 8 8 -
SAVPSDAQAREKLALYVYEY Q9VEB9 8 8 -

Motif 2 width=16
Element Seqn Id St Int Rpt
LHVGAQKSAQTFLSEI Q9CYZ8 31 1 -
LHVGAQKSAQTFLSEI Q9BWW6 31 1 -
LHVGAQKSAQTFLSEI Q99LX9 31 1 -
LHVGAQKSAQTFLSEI Q9R050 29 1 -
LHVGAQKSAQTFLSEI Q9BTM0 29 1 -
LHVGAQKAAQTFLSEI Q9VEB9 29 1 -

Motif 3 width=18
Element Seqn Id St Int Rpt
RWEKNITLGEPPGFLHSW Q9CYZ8 47 0 -
RWEKNITLGEPPGFLHSW Q9BWW6 47 0 -
RWEKNITLGEPPGFLHSW Q99LX9 47 0 -
RWEKNITLGEPPGFLHSW Q9R050 45 0 -
RWEKNITLGEPPGFLHSW Q9BTM0 45 0 -
RWEKNITLGEPPGFLHTW Q9VEB9 45 0 -

Motif 4 width=14
Element Seqn Id St Int Rpt
WCVFWDLYCAAPER Q9CYZ8 65 0 -
WCVFWDLYCAAPER Q9BWW6 65 0 -
WCVFWDLYCAAPER Q99LX9 65 0 -
WCVFWDLYCAAPER Q9R050 63 0 -
WCVFWDLYCAAPER Q9BTM0 63 0 -
WCVFWDLYCAAPER Q9VEB9 63 0 -

Motif 5 width=16
Element Seqn Id St Int Rpt
RETCEHSSEAKAFHDY Q9CYZ8 79 0 -
RETCEHSSEAKAFHDY Q9BWW6 79 0 -
RETCEHSSEAKAFHDY Q99LX9 79 0 -
RDTCEHSSEAKAFHDY Q9R050 77 0 -
RDTCEHSSEAKAFHDY Q9BTM0 77 0 -
RDQCDHSSEAKAFHDY Q9VEB9 77 0 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
SAVPSDSQAREKLALYVYEY P81877 10 10 -
SAVPSDSQAREKLALYVYEY Q9Y4T7 10 10 -
SAVPSDSQAREKLALYVYEY Q9DB78 10 10 -
SAVPSDSQAREKLALYVYEY Q9D6L4 10 10 -
SAVPSDSQAREKLALYVYEY Q9CYZ8 10 10 -
SAVPSDSQAREKLALYVYEY Q9BWW6 10 10 -
SAVPSDSQAREKLALYVYEY Q99LX9 10 10 -
SAVPSDGQAREKLALYVYEY Q99LC6 8 8 -
SAVPSDGQAREKLALYVYEY Q9R050 8 8 -
SAVPSDGQAREKLALYVYEY Q9EQP3 8 8 -
SAVPSDGQAREKLALYVYEY Q9D032 8 8 -
SAVPSDGQAREKLALYVYEY Q9BWW4 8 8 -
SAVPSDGQAREKLALYVYEY Q9BWW3 8 8 -
SAVPSDGQAREKLALYVYEY Q9BTM0 8 8 -
SAVPSDSQAREKLALYVYEY Q9BWG4 9 9 -
SAVPSDSQAREKLALYVYEY Q9BWW5 9 9 -
SAVPSDAQAREKLALYVYEY Q9VEB9 8 8 -
GCAPSDGQAREKLALYVYEY Q99LZ8 8 8 -

Motif 2 width=16
Element Seqn Id St Int Rpt
LHVGAQKSAQTFLSEI P81877 31 1 -
LHVGAQKSAQTFLSEI Q9Y4T7 31 1 -
LHVGAQKSAQTFLSEI Q9DB78 31 1 -
LHVGAQKSAQTFLSEI Q9D6L4 31 1 -
LHVGAQKSAQTFLSEI Q9CYZ8 31 1 -
LHVGAQKSAQTFLSEI Q9BWW6 31 1 -
LHVGAQKSAQTFLSEI Q99LX9 31 1 -
LHVGAQKSAQTFLSEI Q99LC6 29 1 -
LHVGAQKSAQTFLSEI Q9R050 29 1 -
LHVGAQKSAQTFLSEI Q9EQP3 29 1 -
LHVGAQKSAQTFLSEI Q9D032 29 1 -
LHVGAQKSAQTFLSEI Q9BWW4 29 1 -
LHVGAQKSAQTFLSEI Q9BWW3 29 1 -
LHVGAQKSAQTFLSEI Q9BTM0 29 1 -
LHIGAQKSAQTFLSEI Q9BWG4 30 1 -
LHIGAQKSAQTFLSEI Q9BWW5 30 1 -
LHVGAQKAAQTFLSEI Q9VEB9 29 1 -
LHVGAQKSAQTFLSEI Q99LZ8 29 1 -

Motif 3 width=18
Element Seqn Id St Int Rpt
RWEKNITLGEPPGFLHSW P81877 47 0 -
RWEKNITLGEPPGFLHSW Q9Y4T7 47 0 -
RWEKNITLGEPPGFLHSW Q9DB78 47 0 -
RWEKNITLGEPPGFLHSW Q9D6L4 47 0 -
RWEKNITLGEPPGFLHSW Q9CYZ8 47 0 -
RWEKNITLGEPPGFLHSW Q9BWW6 47 0 -
RWEKNITLGEPPGFLHSW Q99LX9 47 0 -
RWEKNITLGEPPGFLHSW Q99LC6 45 0 -
RWEKNITLGEPPGFLHSW Q9R050 45 0 -
RWEKNITLGEPPGFLHSW Q9EQP3 45 0 -
RWEKNITLGEPPGFLHSW Q9D032 45 0 -
RWEKNITLGEPPGFLHSW Q9BWW4 45 0 -
RWEKNITLGEPPGFLHSW Q9BWW3 45 0 -
RWEKNITLGEPPGFLHSW Q9BTM0 45 0 -
RWEKNITLGEPPGFLHSW Q9BWG4 46 0 -
RWEKNITLGEPPGFLHSW Q9BWW5 46 0 -
RWEKNITLGEPPGFLHTW Q9VEB9 45 0 -
RWEKNITLGEPPGFLHSW Q99LZ8 45 0 -

Motif 4 width=14
Element Seqn Id St Int Rpt
WCVFWDLYCAAPER P81877 65 0 -
WCVFWDLYCAAPER Q9Y4T7 65 0 -
WCVFWDLYCAAPER Q9DB78 65 0 -
WCVFWDLYCAAPER Q9D6L4 65 0 -
WCVFWDLYCAAPER Q9CYZ8 65 0 -
WCVFWDLYCAAPER Q9BWW6 65 0 -
WCVFWDLYCAAPER Q99LX9 65 0 -
WCVFWDLYCAAPER Q99LC6 63 0 -
WCVFWDLYCAAPER Q9R050 63 0 -
WCVFWDLYCAAPER Q9EQP3 63 0 -
WCVFWDLYCAAPER Q9D032 63 0 -
WCVFWDLYCAAPER Q9BWW4 63 0 -
WCVFWDLYCAAPER Q9BWW3 63 0 -
WCVFWDLYCAAPER Q9BTM0 63 0 -
WCVFWDLYCAAPDR Q9BWG4 64 0 -
WCVFWDLYCAAPDR Q9BWW5 64 0 -
WCVFWDLYCAAPER Q9VEB9 63 0 -
WCVFWDLYCAAPDR Q99LZ8 63 0 -

Motif 5 width=16
Element Seqn Id St Int Rpt
RETCEHSSEAKAFHDY P81877 79 0 -
RETCEHSSEAKAFHDY Q9Y4T7 79 0 -
RETCEHSSEAKAFHDY Q9DB78 79 0 -
RETCEHSSEAKAFHDY Q9D6L4 79 0 -
RETCEHSSEAKAFHDY Q9CYZ8 79 0 -
RETCEHSSEAKAFHDY Q9BWW6 79 0 -
RETCEHSSEAKAFHDY Q99LX9 79 0 -
RDTCEHSSEAKAFHDY Q99LC6 77 0 -
RDTCEHSSEAKAFHDY Q9R050 77 0 -
RDTCEHSSEAKAFHDY Q9EQP3 77 0 -
RDTCEHSSEAKAFHDY Q9D032 77 0 -
RDTCEHSSEAKAFHDY Q9BWW4 77 0 -
RDTCEHSSEAKAFHDY Q9BWW3 77 0 -
RDTCEHSSEAKAFHDY Q9BTM0 77 0 -
REACEHSGEAKAFQDY Q9BWG4 78 0 -
REACEHSGEAKAFQDY Q9BWW5 78 0 -
RDQCDHSSEAKAFHDY Q9VEB9 77 0 -
REACEHSSEAKVFQDY Q99LZ8 77 0 -