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PR00701

Identifier
60KDINNERMP  [View Relations]  [View Alignment]  
Accession
PR00701
No. of Motifs
9
Creation Date
28-MAY-1997  (UPDATE 07-JUN-1999)
Title
60Kd inner membrane protein signature
Database References

INTERPRO; IPR001708
Literature References
1. ERRINGTON, J., APPLEBY, L., DANIEL, R.A., GOODFELLOW, H.,
PARTRIDGE, S.R. AND YUDKIN, M.D.
Structure and function of the spoIIIJ gene of Bacillus subtilis: a
vegetatively expressed gene that is essential for sigma G activity at an
intermediate stage of sporulation. 
J.GEN.MICROBIOL. 138(12) 2609-2618 (1992). 
 
2. BURLAND, V., PLUNKETT, G. III, DANIELS, D.L. AND BLATTNER, F.R.
DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: 
organizational symmetry around the origin of replication. 
GENOMICS 16(3) 551-561 (1993).
 
3. FLEISCHMANN, R.D., ADAMS, M.D., WHITE, O., CLAYTON, R.A., KIRKNESS, E.F.,
KERLAVAGE, A.R., BULT, C.J., TOMB, J.F., DOUGHERTY, B.A., MERRICK, J.M.,
MCKENNEY, K., SUTTON, G., FITZHUGH, W., FIELDS, C.A., GOCAYNE, J.D.,
SCOTT, J.D., SHIRLEY, R., LIU, L.-I., GLODEK, A., KELLEY, J.M.,
WEIDMAN, J.F., PHILLIPS, C.A., SPRIGGS, T., HEDBLOM, E., COTTON, M.D.,
UTTERBACK, T.R., HANNA, M.C., NGUYEN, D.T., SAUDEK, D.M., BRANDON, R.C.,
FINE, L.D., FRITCHMAN, J.L., FUHRMANN, J.L., GEOGHAGEN, N.S.M., GNEHM, C.L.,
MCDONALD, L.A., SMALL, K.V., FRASER, C.M., SMITH, H.O. AND VENTER J.C.
Whole-genome random sequencing and assembly of Haemophilus influenzae RD. 
SCIENCE 269 496-512 (1995).
 
4.OGASAWARA N., YOSHIKAWA H.
Genes and their organization in the replication origin region of the
bacterial chromosome.
MOL.MICROBIOL. 6(5) 629-634 (1992).
 
5. SUHAN, M., CHEN, S.Y., THOMPSON, H.A., HOOVER, T.A., HILL, A. AND
WILLIAMS, J.C.
Cloning and characterization of an autonomous replication sequence from
Coxiella burnetii.
J.BACTERIOL. 176(17) 5233-5243 (1994). 

Documentation
Stage III sporulation protein J (SP3J) is a probable lipoprotein, rich in
basic and hydrophobic amino acids. Mutations in the protein abolish the
transcription of prespore-specific genes transcribed by the sigma G form of
RNA polymerase [1]. SP3J could be involved in a signal transduction pathway
coupling gene expression in the prespore to events in the mother cell, or it
may be necessary for essential metabolic interactions between the two cells
[1]. The protein shows a high degree of similarity to B.subtilis YQJG, to
yeast OXA1 and also to bacterial 60Kd inner-membrane proteins [2-5]. These
are integral membrane proteins of uncharacterised function that contain 
several potential transmembrane domains - one of these is located at the
N-terminus, the rest residing within the C-terminal portion of the protein. 
 
60KDINNERMP is a 9-element fingerprint that provides a signature for
bacterial 60Kd inner membrane proteins. The fingerprint was derived from
an initial alignment of 5 sequences: the motifs were drawn from conserved
regions spanning the full alignment length - motif 1 spans the N-terminal
hydrophobic domain, and motifs 5-9 encode other strongly hydrophobic 
regions. A single iteration on OWL29.3 was required to reach convergence,
no further sequences being identified beyond the starting set. Several
partial matches were found, all of which are either N-terminal fragments,
or homologues that fail to make significant matches with one or more motifs
- these include B.subtillis SP3J and YQJG, and the human homologue of OXA1. 
 
An update on SPTR37_9f identified a true set of 5 sequences, and 12
partial matches.
Summary Information
   5 codes involving  9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
1 codes involving 4 elements
4 codes involving 3 elements
7 codes involving 2 elements
Composite Feature Index
9555555555
8000000000
7000000000
6000000000
5000000000
4000001111
3000000444
2000000707
123456789
True Positives
60IM_BUCAP    60IM_COXBU    60IM_ECOLI    60IM_HAEIN    
60IM_PSEPU
True Positive Partials
Codes involving 4 elements
O66561
Codes involving 3 elements
O25989 O32298 O84253 SP3J_BACSU
Codes involving 2 elements
O04451 O04665 O04699 O51398
O54569 O83915 P97041
Sequence Titles
60IM_BUCAP  60 kDa inner-membrane protein homolog - Buchnera aphidicola (subsp. Schizaphis graminum). 
60IM_COXBU 60 kDa inner-membrane protein homolog - Coxiella burnetii.
60IM_ECOLI 60 kDa inner-membrane protein - Escherichia coli.
60IM_HAEIN 60 kDa inner-membrane protein homolog - Haemophilus influenzae.
60IM_PSEPU 60 kDa inner-membrane protein homolog - Pseudomonas putida.

O66561 HYPOTHETICAL PROTEIN AQ_175 - Aquifex aeolicus.

O25989 60 KDA INNER-MEMBRANE PROTEIN - Helicobacter pylori (Campylobacter pylori).
O32298 SPOIIIJ PROTEIN - BACILLUS SUBTILIS.
O84253 60 KDA INNER MEMBRANE PROTEIN - Chlamydia trachomatis.
SP3J_BACSU Stage III sporulation protein J precursor - Bacillus subtilis.

O04451 F21J9.13 - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O04665 CHLOROPLAST MEMBRANE PROTEIN ALBINO3 - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O04699 POST-FLORAL-SPECIFIC PROTEIN (PPF-1 PROTEIN) - PISUM SATIVUM (GARDEN PEA).
O51398 INNER MEMBRANE PROTEIN - BORRELIA BURGDORFERI (LYME DISEASE SPIROCHETE).
O54569 INNER MEMBRANE PROTEIN - STREPTOMYCES COELICOLOR.
O83915 MEMBRANE PROTEIN - Treponema pallidum.
P97041 DNA FOR 5S RRNA - LEPTOSPIRA INTERROGANS.
Scan History
OWL29_3    1  100  NSINGLE    
SPTR37_9f 2 20 NSINGLE
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
DIKRTILIAALAVVSYVMVLKW 60IM_PSEPU 2 2 -
DSRRSLLVLALIFISFLVYQQW 60IM_HAEIN 2 2 -
DSQRNLLVIALLFVSFMIWQAW 60IM_ECOLI 2 2 -
DIKRIILYVIVALLAIALFNAW 60IM_COXBU 2 2 -
ELQRNFFIFAFLFVSFLLWQAW BUH60K 2 2 -

Motif 2 width=22
Element Seqn Id St Int Rpt
DVLELAIDPVGGDIVQLNLPKY 60IM_PSEPU 88 64 -
DVLDVEIDTQGGNIVSAKLPKY 60IM_COXBU 86 62 -
DVLRLVINMYGGDIEEASLLDY BUH60K 58 34 -
DVLDLTINTRGGDVEQALLPAY 60IM_ECOLI 66 42 -
DVFRLKIDTLGGDVISSELLKY 60IM_HAEIN 71 47 -

Motif 3 width=21
Element Seqn Id St Int Rpt
GVNYIKRFSFKRGEYDLNVSY 60IM_PSEPU 179 69 -
GLLVTKTYTFHRDDYAIHLAY 60IM_COXBU 174 66 -
GITYIKNFILKPGKYNVEVEY BUH60K 150 70 -
GNTFTKTFVLKRGDYAVNVNY 60IM_ECOLI 158 70 -
GVTYQKIFVLKRGSYDLGVDY 60IM_HAEIN 160 67 -

Motif 4 width=19
Element Seqn Id St Int Rpt
TYTGGAYSSSETNYKKYSF 60IM_HAEIN 213 32 -
TFRGAAYSSSDAKYEKYKF BUH60K 209 38 -
TFRGAAYSTPDEKYEKYKF 60IM_ECOLI 217 38 -
TYLGAALWTASEPYKKVSM 60IM_PSEPU 235 35 -
SYNGASMGSPQTPYEKLSY 60IM_COXBU 228 33 -

Motif 5 width=16
Element Seqn Id St Int Rpt
GWVAMLQQYFATAWIP 60IM_ECOLI 251 15 -
GWIAMQQHYFLSAWVP 60IM_COXBU 261 14 -
GWIAMLQQYFVVAWVP BUH60K 243 15 -
GWVAWLQHYFVTAWIP 60IM_PSEPU 268 14 -
GWVAVLQHYFVSAWIP 60IM_HAEIN 246 14 -

Motif 6 width=21
Element Seqn Id St Int Rpt
LDLTVDYGFLWFLSQPLFKLL BUH60K 319 60 -
LDLTVDYGWLWFISQPLFKLL 60IM_ECOLI 324 57 -
LDLTVDYGWAWFIAKPLFWLL 60IM_HAEIN 320 58 -
LELTVDYGFLWFIAQPIFWLL 60IM_PSEPU 341 57 -
LERTIDYGWLWPISMLLFWIL 60IM_COXBU 339 62 -

Motif 7 width=24
Element Seqn Id St Int Rpt
EKINPLGGCLPILVQMPVFLALYW 60IM_PSEPU 432 70 -
EKINPLGGCLPMLIQVPVFIAFYY 60IM_COXBU 430 70 -
EKINPLGGCLPVFIQMPIFLSLYY BUH60K 410 70 -
EKVNPLGGCFPLLIQMPIFLALYY 60IM_ECOLI 415 70 -
EKVNPLGGCLPILLQMPIFIALYW 60IM_HAEIN 411 70 -

Motif 8 width=23
Element Seqn Id St Int Rpt
DPFFILPIIMGATMFIQQRLNPT 60IM_PSEPU 479 23 -
DPYYVLPIFMGLTMFFIQRTSSN BUH60K 457 23 -
DPYYILPILMGVTMFFIQKMSPT 60IM_ECOLI 462 23 -
DPYYILPILMGISMFLLQKMSPT 60IM_HAEIN 458 23 -
DPYYILPIIMGLSMLAQQWVSPT 60IM_COXBU 477 23 -

Motif 9 width=24
Element Seqn Id St Int Rpt
PVIFTVFFLWFPSGLVLYYIVSNL 60IM_ECOLI 499 14 -
PVIFTVFFINFPAGLVLYWITNNV 60IM_COXBU 513 13 -
PIIFTFFFLWFPAGLVLYWVVNNC 60IM_PSEPU 515 13 -
PLVFMFFFLWFPSGLVLYWLVSNL 60IM_HAEIN 495 14 -
PFIFTVFFLWFPSGLVLYYIVSNL BUH60K 494 14 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
DSQRNLLVIALLFVSFMIWQAW 60IM_ECOLI 2 2 -
DSRRSLLVLALIFISFLVYQQW 60IM_HAEIN 2 2 -
ELQRNFFIFAFLFVSFLLWQAW 60IM_BUCAP 2 2 -
DIKRTILIAALAVVSYVMVLKW 60IM_PSEPU 2 2 -
DIKRIILYVIVALLAIALFNAW 60IM_COXBU 2 2 -

Motif 2 width=22
Element Seqn Id St Int Rpt
DVLDLTINTRGGDVEQALLPAY 60IM_ECOLI 66 42 -
DVFRLKIDTLGGDVISSELLKY 60IM_HAEIN 71 47 -
DVLRLVINMYGGDIEEASLLDY 60IM_BUCAP 58 34 -
DVLELAIDPVGGDIVQLNLPKY 60IM_PSEPU 88 64 -
DVLDVEIDTQGGNIVSAKLPKY 60IM_COXBU 86 62 -

Motif 3 width=21
Element Seqn Id St Int Rpt
GNTFTKTFVLKRGDYAVNVNY 60IM_ECOLI 158 70 -
GVTYQKIFVLKRGSYDLGVDY 60IM_HAEIN 160 67 -
GITYIKNFILKPGKYNVEVEY 60IM_BUCAP 150 70 -
GVNYIKRFSFKRGEYDLNVSY 60IM_PSEPU 179 69 -
GLLVTKTYTFHRDDYAIHLAY 60IM_COXBU 174 66 -

Motif 4 width=19
Element Seqn Id St Int Rpt
TFRGAAYSTPDEKYEKYKF 60IM_ECOLI 217 38 -
TYTGGAYSSSETNYKKYSF 60IM_HAEIN 213 32 -
TFRGAAYSSSDAKYEKYKF 60IM_BUCAP 209 38 -
TYLGAALWTASEPYKKVSM 60IM_PSEPU 235 35 -
SYNGASMGSPQTPYEKLSY 60IM_COXBU 228 33 -

Motif 5 width=16
Element Seqn Id St Int Rpt
GWVAMLQQYFATAWIP 60IM_ECOLI 251 15 -
GWVAVLQHYFVSAWIP 60IM_HAEIN 246 14 -
GWIAMLQQYFVVAWVP 60IM_BUCAP 243 15 -
GWVAWLQHYFVTAWIP 60IM_PSEPU 268 14 -
GWIAMQQHYFLSAWVP 60IM_COXBU 261 14 -

Motif 6 width=21
Element Seqn Id St Int Rpt
LDLTVDYGWLWFISQPLFKLL 60IM_ECOLI 324 57 -
LDLTVDYGWAWFIAKPLFWLL 60IM_HAEIN 320 58 -
LDLTVDYGFLWFLSQPLFKLL 60IM_BUCAP 319 60 -
LELTVDYGFLWFIAQPIFWLL 60IM_PSEPU 341 57 -
LERTIDYGWLWPISMLLFWIL 60IM_COXBU 339 62 -

Motif 7 width=24
Element Seqn Id St Int Rpt
EKVNPLGGCFPLLIQMPIFLALYY 60IM_ECOLI 415 70 -
EKVNPLGGCLPILLQMPIFIALYW 60IM_HAEIN 411 70 -
EKINPLGGCLPVFIQMPIFLSLYY 60IM_BUCAP 410 70 -
EKINPLGGCLPILVQMPVFLALYW 60IM_PSEPU 432 70 -
EKINPLGGCLPMLIQVPVFIAFYY 60IM_COXBU 430 70 -

Motif 8 width=23
Element Seqn Id St Int Rpt
DPYYILPILMGVTMFFIQKMSPT 60IM_ECOLI 462 23 -
DPYYILPILMGISMFLLQKMSPT 60IM_HAEIN 458 23 -
DPYYVLPIFMGLTMFFIQRTSSN 60IM_BUCAP 457 23 -
DPFFILPIIMGATMFIQQRLNPT 60IM_PSEPU 479 23 -
DPYYILPIIMGLSMLAQQWVSPT 60IM_COXBU 477 23 -

Motif 9 width=24
Element Seqn Id St Int Rpt
PVIFTVFFLWFPSGLVLYYIVSNL 60IM_ECOLI 499 14 -
PLVFMFFFLWFPSGLVLYWLVSNL 60IM_HAEIN 495 14 -
PFIFTVFFLWFPSGLVLYYIVSNL 60IM_BUCAP 494 14 -
PIIFTFFFLWFPAGLVLYWVVNNC 60IM_PSEPU 515 13 -
PVIFTVFFINFPAGLVLYWITNNV 60IM_COXBU 513 13 -