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PR01020

Identifier
LPSBIOSNTHSS  [View Relations]  [View Alignment]  
Accession
PR01020
No. of Motifs
5
Creation Date
25-NOV-1998  (UPDATE 10-JUN-1999)
Title
Lipopolysaccharide core biosynthesis protein signature
Database References

INTERPRO; IPR001980
Literature References
1. CLEMENTZ T., RAETZ C.R.
A gene coding for 3-deoxy-D-manno-octulosonic-acid transferase in 
Escherichia coli. Identification, mapping, cloning, and sequencing.
J.BIOL.CHEM. 266 9687-9696 (1991). 
 
2. RONCERO, C. AND CASADABAN, M.J.
Genetic analysis of the genes involved in synthesis of the lipopoly-
saccharide core in Escherichia coli K-12: three operons in the rfa locus.
J.BACTERIOL. 174 3250-3260 (1992). 

Documentation
Temperature-sensitive mutants of Escherichia coli, defective in the transfer
of 3-deoxy-D-manno-octulosonic acid (KDO) from CMP-KDO to a tetraacyldi-
saccharide 1,4'-bisphosphate precursor of lipid A, have been used to map
KDO transferase activity on the E.coli chromosome [1]. The KDO transferase
gene, designated kdtA, was shown to code for a 43kDa polypeptide [1]. 
Overexpression of this single gene product greatly stimulates incorporation 
of two stereochemically distinct KDO residues during lipopolysaccharide
biosynthesis in extracts of E.coli [1]. 
 
The role of some genes in the synthesis of the lipopolysaccharide (LPS) core
of Escherichia coli has been defined by complementation analysis with known
Salmonella typhimurium LPS mutants [2]. The genetic organisation of this 
locus seems to be identical in E.coli K-12 and S.typhimurium [2]. 
 
LPSBIOSNTHSS is a 5-element fingerprint that provides a signature for
lipopolysaccharide core biosynthesis protein kdtB. The fingerprint was
derived from an initial alignment of 6 sequences: the motifs were drawn
from short conserved regions spanning virtually the full alignment length.
Two iterations on OWL30.2 were required to reach convergence, at which
point a true set comprising 12 sequences was identified. Several partial
matches were also found: E70187 is a kdtB homologue that fails to make
a significant match with motif 3; B64447 and S75359 are hypothetical
proteins from Methanococcus jannaschii and Synechocystis sp. respectively,
and TAGD_BACSU is a glycerol-3-phosphate cytidylyltransferase, all of 
which match motifs 1 and 2 (the kdtA and cytidylyltransferase sequences
share a high degree of similarity in this N-terminal region). 
 
An update on SPTR37_9f identified a true set of 12 sequences, and 1
partial match.
Summary Information
  12 codes involving  5 elements
1 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
51212121212
411011
300000
200000
12345
True Positives
KDTB_ECOLI    KDTB_HAEIN    KDTB_MYCCA    O26010        
O34797 O66614 O69466 O83307
P71154 Q50452 Q55235 Q55435
True Positive Partials
Codes involving 4 elements
O51645
Sequence Titles
KDTB_ECOLI  LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN KDTB - ESCHERICHIA COLI. 
KDTB_HAEIN LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN KDTB - HAEMOPHILUS INFLUENZAE.
KDTB_MYCCA LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN KDTB HOMOLOG - MYCOPLASMA CAPRICOLUM.
O26010 LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN (KDTB) - HELICOBACTER PYLORI (CAMPYLOBACTER PYLORI).
O34797 YLBI PROTEIN - BACILLUS SUBTILIS.
O66614 LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN - AQUIFEX AEOLICUS.
O69466 LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN - MYCOBACTERIUM LEPRAE.
O83307 LIPOPOLYSACCHARIDE CORE BIOSYNTHESIS PROTEIN (KDTB) - TREPONEMA PALLIDUM.
P71154 PROTEIN THOUGHT TO PARTICIPATE IN THE SYNTHESIS OF THE LIPOPOLYSACCHARIDE CORE - CHROMATIUM VINOSUM.
Q50452 U0002E - MYCOBACTERIUM TUBERCULOSIS.
Q55235 FOUR ORFS, THREE COMPLETE, AND ONE 3' END - SYNECHOCOCCUS SP.
Q55435 KDTB - SYNECHOCYSTIS SP. (STRAIN PCC 6803).

O51645 LIPOPOLYSACCHARIDE BIOSYNTHESIS-RELATED PROTEIN (KDTB) - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
Scan History
OWL30_2    2  200  NSINGLE    
SPTR37_9f 2 34 NSINGLE
Initial Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
KIGIYPGTFDPVTNGHIDI C64704 3 3 -
RTVVYPGTFDPITNGHVDL S72166 2 2 -
MKAIFAGSFDPPTFGHLDL AE00120910 1 1 -
TSVIYPGTFDPITNGHLDI KDTB_HAEIN 2 2 -
KRAIYPGTFDPITNGHIDI KDTB_ECOLI 3 3 -
KIAIYPGSFNPFHKGHLNI KDTB_MYCCA 2 2 -

Motif 2 width=22
Element Seqn Id St Int Rpt
LVLRARSLFAEVHVLVAVNVQK AE00120910 19 -1 -
IIERSAVIFPRVLVAVANSPSK KDTB_HAEIN 20 -1 -
IVTRATQMFDHVILAIAASPSK KDTB_ECOLI 21 -1 -
ILKKAILLFDKVYVVVSKNVNK KDTB_MYCCA 20 -1 -
IIHRSSELFEKLIVAVAHSSAK C64704 21 -1 -
LIHRAARLFDRVVVAVAADTGK S72166 20 -1 -

Motif 3 width=25
Element Seqn Id St Int Rpt
ERVDLMRQVLGDRPGVYVFPWRSLV AE00120910 48 7 -
ERVELVRGSVAGDPNVEILPFEGLL S72166 49 7 -
ERLKMIQLATKSFKNVECVAFEGLL C64704 50 7 -
SRVENIKNLIKDFSNVEIIINENKL KDTB_MYCCA 49 7 -
ERVALAQQATAHLGNVEVVGFSDLM KDTB_ECOLI 50 7 -
ERVELVRQSVVHLSNVEVFGFSDLL KDTB_HAEIN 49 7 -

Motif 4 width=17
Element Seqn Id St Int Rpt
LVRGVRNATDFCQEFDL AE00120910 84 11 -
LIRGLRAVADFEYEMQL KDTB_ECOLI 86 11 -
IIRGLRSQADFEYEIKY KDTB_MYCCA 86 12 -
IIRGVRTTTDFEYELQL KDTB_HAEIN 85 11 -
LVRGLRVVSDFEYELQM C64704 86 11 -
IMRGLRAVSDFEYEFQL S72166 85 11 -

Motif 5 width=23
Element Seqn Id St Int Rpt
VDSLFFPPAEKWAFVSSTIVREI KDTB_HAEIN 112 10 -
LETVFLAAKPCYAALRSSMVREV AE00120910 111 10 -
IETLFLTPAEQYAYISSSLVREI S72166 112 10 -
IEVVYFISDYDKRSLSSTILREI KDTB_MYCCA 113 10 -
LETLYFMPTLQNAFISSSIVRSI C64704 113 10 -
LESVFLMPSKEWSFISSSLVKEV KDTB_ECOLI 113 10 -
Final Motifs
Motif 1  width=19
Element Seqn Id St Int Rpt
LNAIYPGSFDPITFGHLDI Q55235 2 2 -
SIAVCPGSFDPVTYGHLDI O34797 3 3 -
TSVIYPGTFDPITNGHLDI KDTB_HAEIN 2 2 -
RTVVYPGTFDPITNGHVDL P71154 2 2 -
TGAVCPGSFDPVTLGHVDI Q50452 2 2 -
KRAIYPGTFDPITNGHIDI KDTB_ECOLI 3 3 -
MIAIYPGSFDPITLGHLDI Q55435 1 1 -
SSVVCPGSFDPVTLGHIDV O69466 2 2 -
KRVVYPGTFDPPHYGHLDI O66614 3 3 -
KIGIYPGTFDPVTNGHIDI O26010 3 3 -
MKAIFAGSFDPPTFGHLDL O83307 1 1 -
KIAIYPGSFNPFHKGHLNI KDTB_MYCCA 2 2 -

Motif 2 width=22
Element Seqn Id St Int Rpt
IIERGCRLFDQVYVAVLRNPNK Q55235 20 -1 -
IIERGSGLFEQIIVAVLCNPSK Q55435 19 -1 -
IIKRGAHIFEQVYVCVLNNSSK O34797 21 -1 -
IIERSAVIFPRVLVAVANSPSK KDTB_HAEIN 20 -1 -
LIHRAARLFDRVVVAVAADTGK P71154 20 -1 -
IFERAAAQFDEVVVAILVNPAK Q50452 20 -1 -
IVTRATQMFDHVILAIAASPSK KDTB_ECOLI 21 -1 -
VFERAAAQFDEVVVAILINPVK O69466 20 -1 -
IVKRSARIFDEVVVAVAKKPRK O66614 21 -1 -
IIHRSSELFEKLIVAVAHSSAK O26010 21 -1 -
LVLRARSLFAEVHVLVAVNVQK O83307 19 -1 -
ILKKAILLFDKVYVVVSKNVNK KDTB_MYCCA 20 -1 -

Motif 3 width=25
Element Seqn Id St Int Rpt
ERVDLMRQVLGDRPGVYVFPWRSLV O83307 48 7 -
ERLEQIAKAIAHLPNAQVDSFEGLT Q55235 49 7 -
KRLEQIRHCTQHLTNVTVDSFNGLT Q55435 48 7 -
ERCELLREVTKDIPNITVETSQGLL O34797 50 7 -
ERVELVRQSVVHLSNVEVFGFSDLL KDTB_HAEIN 49 7 -
ERVELVRGSVAGDPNVEILPFEGLL P71154 49 7 -
ERIAMVKESTTHLPNLRVQVGHGLV Q50452 49 7 -
ERVALAQQATAHLGNVEVVGFSDLM KDTB_ECOLI 50 7 -
ERIAMINESTMHLPNLRVEAGEGLV O69466 49 7 -
ERVKMFEKMVEDIPNVEVKMFDCLL O66614 50 7 -
ERLKMIQLATKSFKNVECVAFEGLL O26010 50 7 -
SRVENIKNLIKDFSNVEIIINENKL KDTB_MYCCA 49 7 -

Motif 4 width=17
Element Seqn Id St Int Rpt
ILRGLRVLSDFELELQM Q55235 85 11 -
IIRGVRTTTDFEYELQL KDTB_HAEIN 85 11 -
LLRGLRVLSDFEKELQM Q55435 84 11 -
ILRGLRAVSDFEYEMQG O34797 86 11 -
IMRGLRAVSDFEYEFQL P71154 85 11 -
IVKGLRTGTDFEYELQM Q50452 85 11 -
LIRGLRAVADFEYEMQL KDTB_ECOLI 86 11 -
IVKGLRTGVDFEYELQM O69466 85 11 -
IVRGVRLFTDFEYELQI O66614 86 11 -
LVRGLRVVSDFEYELQM O26010 86 11 -
LVRGVRNATDFCQEFDL O83307 84 11 -
IIRGLRSQADFEYEIKY KDTB_MYCCA 86 12 -

Motif 5 width=23
Element Seqn Id St Int Rpt
LETVFLTTSTEYSFLSSSLVKEV Q55235 112 10 -
VETVFLATAKEYSFLSSSIVKEI Q55435 111 10 -
IETFFMMTNNQYSFLSSSIVKEV O34797 113 10 -
VDSLFFPPAEKWAFVSSTIVREI KDTB_HAEIN 112 10 -
IETLFLTPAEQYAYISSSLVREI P71154 112 10 -
VDTFFVATAPRYSFVSSSLAKEV Q50452 111 9 -
LESVFLMPSKEWSFISSSLVKEV KDTB_ECOLI 113 10 -
VDTFFVATAPRYSFVSSSLVKEV O69466 111 9 -
VETVFMMPSQEYIHISSTIVRDV O66614 112 9 -
LETLYFMPTLQNAFISSSIVRSI O26010 113 10 -
LETVFLAAKPCYAALRSSMVREV O83307 111 10 -
IEVVYFISDYDKRSLSSTILREI KDTB_MYCCA 113 10 -