Identifier | LPSBIOSNTHSS  [View Relations]  [View Alignment]  
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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
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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).
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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.
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Summary Information | 12 codes involving 5 elements 1 codes involving 4 elements 0 codes involving 3 elements 0 codes involving 2 elements
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Composite Feature Index | 5 | 12 | 12 | 12 | 12 | 12 | 4 | 1 | 1 | 0 | 1 | 1 | 3 | 0 | 0 | 0 | 0 | 0 | 2 | 0 | 0 | 0 | 0 | 0 | | 1 | 2 | 3 | 4 | 5 |
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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 |
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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).
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Scan History | OWL30_2 2 200 NSINGLE SPTR37_9f 2 34 NSINGLE
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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 -
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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 -
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