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PR00337

Identifier
LEUILEVALBP  [View Relations]  [View Alignment]  
Accession
PR00337
No. of Motifs
7
Creation Date
09-NOV-1994  (UPDATE 07-JUN-1999)
Title
Leu/Ile/Val-binding protein family signature
Database References

INTERPRO; IPR000709
PDB; 2LBP
SCOP; 2LBP
Literature References
1. LANDICK, R. AND OXENDER, D.L.
The complete nucleotide sequences of the Escherichia coli LIV-BP and
LS-BP genes. Implications for the mechanism of high-affinity branched-
chain amino acid transport.
J.BIOL.CHEM. 260 8257-8261 (1985).
 
2. SACK, J.S., SAPER, M.A. AND QUIOCHO, F.A.
Periplasmic binding protein structure and function. Refined X-ray
structures of the leucine/isoleucine/valine-binding protein and its
complex with leucine.
J.MOL.BIOL. 206 171-191 (1989).
 
3. WILSON, S.A., WACHIRA, S.J., DREW, R.E., JONES, D. AND PEARL, L.H.
Antitermination of amidase expression in Pseudomonas aeruginosa is
controlled by a novel cytoplasmic amide-binding protein.
EMBO J. 12 3637-3542 (1993).

Documentation
Leu/Ile/Val/Thr- and Leu-binding proteins, which share a high degree of
sequence similarity, are components of the leucine-specific transport
system: this is one of two periplasmic binding protein-dependent systems
in the high-affinity transport of branched-chain amino acids in bacteria
[1,2]. A much weaker sequence relationship has been reported between the
periplasmic binding proteins and the aliphatic amidase expression-
regulating protein, AmiC [3]. On this basis, it has been suggested that
AmiC may be capable of adopting a similar 3D fold [3]. 
 
LEUILEVALBP is a 7-element fingerprint that provides a signature for
Leu/Ile/Val/Thr- and Leu-binding proteins. The fingerprint was derived
from an initial alignment of 5 sequences: the motifs were drawn from
conserved regions along the full alignment length, 1-2 and 4-6 encompassing
alpha helical domains, and 3 and 7 spanning beta strand regions. Two
iterations on OWL24.0 were required to reach convergence, at which point
a true set comprising 9 sequences was identified. A single partial match
was also found: this is AmiC, which matches motifs 2, 4 and 6.
 
An update on SPTR37_9f identified a true set of 6 sequences.
Summary Information
6 codes involving  7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
76666666
60000000
50000000
40000000
30000000
20000000
1234567
True Positives
BRAC_PSEAE    LIVJ_CITFR    LIVJ_ECOLI    LIVJ_SALTY    
LIVK_ECOLI LIVK_SALTY
Sequence Titles
BRAC_PSEAE  LEUCINE-, ISOLEUCINE-, VALINE-, THREONINE-, AND ALANINE-BINDING PROTEIN PRECURSOR (LIVAT-BP) (LEU/ILE/VAL/THR/ALA-BINDING PROTEIN) - PSEUDOMONAS AERUGINOSA. 
LIVJ_CITFR LEU/ILE/VAL-BINDING PROTEIN PRECURSOR (LIV-BP) - CITROBACTER FREUNDII.
LIVJ_ECOLI LEU/ILE/VAL-BINDING PROTEIN PRECURSOR (LIV-BP) - ESCHERICHIA COLI.
LIVJ_SALTY LEU/ILE/VAL/THR-BINDING PROTEIN PRECURSOR (LIVT-BP) - SALMONELLA TYPHIMURIUM.
LIVK_ECOLI LEUCINE-SPECIFIC BINDING PROTEIN PRECURSOR (LS-BP) (L-BP) - ESCHERICHIA COLI.
LIVK_SALTY LEUCINE-SPECIFIC BINDING PROTEIN PRECURSOR (LS-BP) (L-BP) - SALMONELLA TYPHIMURIUM.
Scan History
OWL24_0    2  50   NSINGLE    
SPTR37_9f 2 7 NSINGLE
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
IKIALAGPVTGPVAQYG BRAC_PSEAE 30 30 -
IKVAVVGAMSGPIAQWG LIVK_ECOLI 26 26 -
IKVAVVGAMSGPVAQYG LIVB_SALTY 24 24 -
IKVAIVGAMSGPVAQWG LIVC_SALTY 26 26 -
IKVAVVGAMSGPIAQWG NRL_2LBP 3 3 -

Motif 2 width=17
Element Seqn Id St Int Rpt
GARQAIKDINAKGGIKG LIVC_SALTY 48 5 -
GALMAIEQINKAGGVNG BRAC_PSEAE 52 5 -
GAEQAIADINAKGGIKG LIVB_SALTY 46 5 -
GAEQAIKDINAKGGIKG NRL_2LBP 25 5 -
GAEQAIKDINAKGGIKG LIVK_ECOLI 48 5 -

Motif 3 width=19
Element Seqn Id St Int Rpt
LVGVEYDDACDPKQAVAVA LIVK_ECOLI 67 2 -
LEGVIYDDACDPKQAVAVA BRAC_PSEAE 71 2 -
LVAVKYDDACDPKQAVAVA LIVB_SALTY 65 2 -
LVGVEYDDACDPKQAVAVA NRL_2LBP 44 2 -
LVGVEYDDACDPKQAVAVA LIVC_SALTY 67 2 -

Motif 4 width=11
Element Seqn Id St Int Rpt
IVNDGIKYVIG LIVK_ECOLI 88 2 -
VVNDGVKFVVG BRAC_PSEAE 92 2 -
IVNDGIQYVIG LIVC_SALTY 88 2 -
IVNDGIKYVIG NRL_2LBP 65 2 -
VVNDGIKYVIG LIVB_SALTY 86 2 -

Motif 5 width=19
Element Seqn Id St Int Rpt
ASLSNIAGGAAEGMLVTMP LIVC_SALTY 254 155 -
ASLSNIAGDAAEGMLVTMP NRL_2LBP 231 155 -
VSLSNIAGESAEGLLVTKP LIVB_SALTY 252 155 -
SEITAIAGDASEGMLATLP BRAC_PSEAE 258 155 -
ASLSNIAGDAAEGMLVTMP LIVK_ECOLI 254 155 -

Motif 6 width=14
Element Seqn Id St Int Rpt
QDPANKAIVEALKA LIVC_SALTY 277 4 -
QVPANKPIVDAIKA LIVB_SALTY 275 4 -
QDPANQGIVDALKA NRL_2LBP 254 4 -
QDPANQGIVDALKA LIVK_ECOLI 277 4 -
QDPKNKALIDAFKA BRAC_PSEAE 281 4 -

Motif 7 width=16
Element Seqn Id St Int Rpt
LKGATVDTVMGPLSWD LIVB_SALTY 325 36 -
LKANGANTVIGPLNWD LIVK_ECOLI 329 38 -
LRANTFETPTGNLGFD BRAC_PSEAE 333 38 -
LKANGADTVIGPLKWD LIVC_SALTY 329 38 -
LKANGANTVIGPLNWD NRL_2LBP 306 38 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
IKVAVVGAMSGPVAQYG LIVJ_CITFR 26 26 -
IKVAVVGAMSGPVAQYG LIVJ_SALTY 24 24 -
IKVAVVGAMSGPVAQYG LIVJ_ECOLI 26 26 -
IKVAVVGAMSGPIAQWG LIVK_ECOLI 26 26 -
IKVAIVGAMSGPVAQWG LIVK_SALTY 26 26 -
IKIALAGPVTGPVAQYG BRAC_PSEAE 30 30 -

Motif 2 width=17
Element Seqn Id St Int Rpt
GAEQAIADINAKGGVKG LIVJ_CITFR 48 5 -
GAEQAIADINAKGGIKG LIVJ_SALTY 46 5 -
GAEQAVADINAKGGIKG LIVJ_ECOLI 48 5 -
GAEQAIKDINAKGGIKG LIVK_ECOLI 48 5 -
GARQAIKDINAKGGIKG LIVK_SALTY 48 5 -
GALMAIEQINKAGGVNG BRAC_PSEAE 52 5 -

Motif 3 width=19
Element Seqn Id St Int Rpt
LVMVKYDDACDPKQAVAVA LIVJ_CITFR 67 2 -
LVAVKYDDACDPKQAVAVA LIVJ_SALTY 65 2 -
LQIAKYDDACDPKQAVAVA LIVJ_ECOLI 67 2 -
LVGVEYDDACDPKQAVAVA LIVK_ECOLI 67 2 -
LVGVEYDDACDPKQAVAVA LIVK_SALTY 67 2 -
LEGVIYDDACDPKQAVAVA BRAC_PSEAE 71 2 -

Motif 4 width=11
Element Seqn Id St Int Rpt
VVNDGIKYVIG LIVJ_CITFR 88 2 -
VVNDGIKYVIG LIVJ_SALTY 86 2 -
VVNDGIKYVIG LIVJ_ECOLI 88 2 -
IVNDGIKYVIG LIVK_ECOLI 88 2 -
IVNDGIQYVIG LIVK_SALTY 88 2 -
VVNDGVKFVVG BRAC_PSEAE 92 2 -

Motif 5 width=19
Element Seqn Id St Int Rpt
VSLSNIAGESAEGLLVTKP LIVJ_CITFR 254 155 -
VSLSNIAGESAEGLLVTKP LIVJ_SALTY 252 155 -
VSLSNIAGESAEGLLVTKP LIVJ_ECOLI 254 155 -
ASLSNIAGDAAEGMLVTMP LIVK_ECOLI 254 155 -
ASLSNIAGGAAEGMLVTMP LIVK_SALTY 254 155 -
SEITAIAGDASEGMLATLP BRAC_PSEAE 258 155 -

Motif 6 width=14
Element Seqn Id St Int Rpt
QVPANKPIVDAIKA LIVJ_CITFR 277 4 -
QVPANKPIVDAIKA LIVJ_SALTY 275 4 -
QVPANKPIVDAIKA LIVJ_ECOLI 277 4 -
QDPANQGIVDALKA LIVK_ECOLI 277 4 -
QDPANKAIVEALKA LIVK_SALTY 277 4 -
QDPKNKALIDAFKA BRAC_PSEAE 281 4 -

Motif 7 width=16
Element Seqn Id St Int Rpt
LKANSVETVMGPLSWD LIVJ_CITFR 327 36 -
LKGATVDTVMGPLSWD LIVJ_SALTY 325 36 -
LKANSVDTVMGPLTWD LIVJ_ECOLI 327 36 -
LKANGANTVIGPLNWD LIVK_ECOLI 329 38 -
LKANGADTVIGPLKWD LIVK_SALTY 329 38 -
LRANTFETPTGNLGFD BRAC_PSEAE 333 38 -