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PR01900

Identifier
YIDCPROTEIN  [View Relations]  [View Alignment]  
Accession
PR01900
No. of Motifs
3
Creation Date
03-FEB-2003
Title
YidC translocation/secretion protein signature
Database References
Literature References
1. BIEKER, K.L., PHILLIPS, G.J. AND SILHAVY, T.J.
The sec and prl genes of Escherichia coli.
J.BIOENERG.BIOMEMBR. 22 291-310 (1990).
 
2. SCOTTI, P.A., URBANUS, M.L., BRUNNER, J., DE GIER, J-W.L., VON HEIJNE, G.,
VAN DER DOES, C., DRIESSEN, A.J., OUDEGA, B. AND LUIRINK, J.
YidC, the Escherichia coli homologue of mitochondrial Oxa1p, is a component
of the Sec translocase. 
EMBO J. 19 542-549 (2000).
 
3. VAN DER LAAN, M., HOUBEN, E.N., NOUWEN, N., LUIRINK, J. AND DRIESSEN, A.J.
Reconstitution of Sec-dependent membrane protein insertion: nascent FtsQ 
interacts with YidC in a SecYEG-dependent manner. 
EMBO REP. 2 519-523 (2001). 
 
4. NOUWEN, N. AND DRIESSEN, A.J.
SecDFyajC forms a heterotetrameric complex with YidC.
MOL.MICROBIOL. 44 1397-1405 (2002).

Documentation
Secretion across the inner membrane in some Gram-negative bacteria occurs 
via the preprotein translocase pathway. Proteins are produced in the 
cytoplasm as precursors, and require a chaperone subunit to direct them to 
the translocase component [1]. From there, the mature proteins are either
targeted to the outer membrane, or remain as periplasmic proteins [1]. The 
translocase protein subunits are encoded on the bacterial chromosome. 
 
The translocase itself comprises 7 proteins, including a chaperone (SecB), 
ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two 
additional membrane proteins that promote the release of the mature peptide 
into the periplasm (SecD and SecF) [1]. Other cytoplasmic/periplasmic 
proteins play a part in preprotein translocase activity, namely YidC and 
YajC [2]. The former is involved in the insertion of hydrophobic sequences 
into the lipid bilayer after recognition by the SecYEG membrane complex [2].
YidC itself is a homologue of the Saccharomyces cerevisiae Oxa1p, a 
mitochondrial inner membrane protein that facilitates export from the 
organelle [2]. Other similarities have been found between YidC, sporulation 
proteins from Bacillus spp., and Gram-negative bacterial 60kDa inner 
membrane moieties, suggesting a common ancestor for these translocation 
pathway proteins [3]. 
 
Recently, the precise interactions between the E.coli SecYEG complex, 
SecD, SecF, and the two essential membrane proteins YajC and YidC, have 
been researched [4]. Rather than acting individually, the four proteins form 
a heterotetrameric complex and associate with the SecYEG heterotrimeric 
complex [4]. 
 
YIDCPROTEIN is a 3-element fingerprint that provides a signature for the
YidC translocation/secretion protein family. The fingerprint was derived
from an initial alignment of 10 sequences: the motifs were drawn from
conserved regions spanning the C-terminal portion of the alignment. Two
iterations on SPTR40_20f were required to reach convergence, at which point
a true set comprimising 33 sequences was identified. Two partial matches
were also found, both of which are related Bacillus sporulation proteins. 
Summary Information
  33 codes involving  3 elements
2 codes involving 2 elements
Composite Feature Index
3333333
2022
123
True Positives
60IM_BUCAI    60IM_BUCAP    60IM_COXBU    60IM_ECOLI    
60IM_HAEIN 60IM_PSEPU O25989 O66561
O83915 O84253 Q8XB42 Q8Y3H6
Q8YDA3 Q8Z2N7 Q8Z9U3 Q8ZKY4
Q92JJ3 Q92SF5 Q98D88 Q9AA40
Q9CLQ2 Q9HT06 Q9JS24 Q9JW48
Q9JXS4 Q9KVY4 Q9P9U1 Q9PKE3
Q9PNX7 Q9RNL5 Q9Z8M8 Q9ZE97
Q9ZJG8
True Positive Partials
Codes involving 2 elements
Q9RCA5 SP3J_BACSU
Sequence Titles
60IM_BUCAI  60 kDa inner-membrane protein homolog - Buchnera aphidicola (subsp. Acyrthosiphon pisum) (Acyrthosiphon pisum symbiotic bacterium). 
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.
O25989 60 KDA INNER-MEMBRANE PROTEIN - Helicobacter pylori (Campylobacter pylori).
O66561 HYPOTHETICAL PROTEIN AQ_175 - Aquifex aeolicus.
O83915 MEMBRANE PROTEIN - Treponema pallidum.
O84253 60 KDA INNER MEMBRANE PROTEIN - Chlamydia trachomatis.
Q8XB42 60 KD INNER-MEMBRANE PROTEIN - Escherichia coli O157:H7.
Q8Y3H6 PROBABLE TRANSMEMBRANE PROTEIN - Ralstonia solanacearum (Pseudomonas solanacearum).
Q8YDA3 60 KDA INNER MEMBRANE PROTEIN YIDC - Brucella melitensis.
Q8Z2N7 PUTATIVE MEMBRANE PROTEIN - Salmonella typhi.
Q8Z9U3 PROBABLE MEMBRANE PROTEIN - Yersinia pestis.
Q8ZKY4 PUTATIVE PREPROTEIN TRANSLOCASE SUBUNIT YIDC - Salmonella typhimurium.
Q92JJ3 60 KDA INNER-MEMBRANE PROTEIN - Rickettsia conorii.
Q92SF5 PUTATIVE INNER-MEMBRANE TRANSMEMBRANE PROTEIN - Rhizobium meliloti (Sinorhizobium meliloti).
Q98D88 HYPOTHETICAL PROTEIN MLR4812 - Rhizobium loti (Mesorhizobium loti).
Q9AA40 60 KD INNER-MEMBRANE PROTEIN - Caulobacter crescentus.
Q9CLQ2 YIDC - Pasteurella multocida.
Q9HT06 HYPOTHETICAL PROTEIN PA5568 - Pseudomonas aeruginosa.
Q9JS24 60 KDA INNER MEMBRANE PROTEIN (INNER MEMBRANE PROTEIN, PUTATIVE) - Chlamydia pneumoniae (Chlamydophila pneumoniae).
Q9JW48 PUTATIVE INTEGRAL MEMBRANE PROTEIN - Neisseria meningitidis (serogroup A).
Q9JXS4 60 KDA INNER-MEMBRANE PROTEIN - Neisseria meningitidis (serogroup B).
Q9KVY4 INNER MEMBRANE PROTEIN, 60 KDA - Vibrio cholerae.
Q9P9U1 60KDA INNER-MEMBRANE PROTEIN - Xylella fastidiosa.
Q9PKE3 INNER MEMBRANE PROTEIN, PUTATIVE - Chlamydia muridarum.
Q9PNX7 PUTATIVE MEMBRANE PROTEIN - Campylobacter jejuni.
Q9RNL5 60KD INNER-MEMBRANE PROTEIN YIDC - Zymomonas mobilis.
Q9Z8M8 60 KDA INNER MEMBRANE PROTEIN - Chlamydia pneumoniae (Chlamydophila pneumoniae).
Q9ZE97 60 KDA INNER-MEMBRANE PROTEIN (YIDC) - Rickettsia prowazekii.
Q9ZJG8 PUTATIVE INNER MEMBRANE PROTEIN - Helicobacter pylori J99 (Campylobacter pylori J99).

Q9RCA5 SPOIIIJ PROTEIN (ESSENTIAL FOR SIGMA-G ACTIVITY AT STAGE III) - Bacillus halodurans.
SP3J_BACSU Stage III sporulation protein J precursor - Bacillus subtilis.
Scan History
SPTR40_20f 2  300  NSINGLE    
Initial Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
PLFKLLKWIHSFVGNWG 60IM_ECOLI 339 339 -
PLFKLLKWIHSFVGNWG Q8ZKY4 339 339 -
PLFKLLKWIHSFVGNWG Q8XB42 339 339 -
PLFWLLTFIQSIVQNWG Q9CLQ2 335 335 -
PLFWLLNQLHNIIGNWG Q9JXS4 339 339 -
PVFYAMNFFYGYVGNFG Q92JJ3 346 346 -
PMFYLIDWIYKFTGNFG Q8YDA3 351 351 -
PMFWLIDTLYKFLGNFG Q98D88 367 367 -
GLFWILSHLNSLLHNWG Q9P9U1 355 355 -
VFFYYLDWLFLHVGNYG Q9RNL5 345 345 -

Motif 2 width=16
Element Seqn Id St Int Rpt
PILMGVTMFFIQKMSP 60IM_ECOLI 468 112 -
PILMGVTMFFIQKMSP Q8ZKY4 468 112 -
PILMGVTMFFIQKMSP Q8XB42 468 112 -
PILMGASMFLLQKMSP Q9CLQ2 464 112 -
PIIMAATMFAQTYLNP Q9JXS4 468 112 -
PILMAITMFLQQKMSP Q92JJ3 494 131 -
PIIMGIIMFLQMRMNP Q8YDA3 499 131 -
PLIMGVTMFLQMRMNP Q98D88 515 131 -
PLLNIVIMWATQKLTP Q9P9U1 484 112 -
PIILGITMWLQFRASP Q9RNL5 493 131 -

Motif 3 width=25
Element Seqn Id St Int Rpt
DPMQQKIMTFMPVIFTVFFLWFPSG 60IM_ECOLI 488 4 -
DPMQQKIMTFMPVIFTVFFLWFPSG Q8ZKY4 488 4 -
DPMQQKIMTFMPVIFTVFFLWFPSG Q8XB42 488 4 -
DPTQQKIMNFMPLIFMVFFLWFPSG Q9CLQ2 484 4 -
DPMQAKMMKIMPLVFSVMFFFFPAG Q9JXS4 487 3 -
DPMQAQVMKFMPLIFLFMFSSFPVG Q92JJ3 513 3 -
DPTQAAIFTWMPIIFTFMLASFPAG Q8YDA3 518 3 -
DPTQAAIFTWMPVIFTFMMAGFPAG Q98D88 534 3 -
DPIAGKMMQVMPLIFGVMMAFVPSG Q9P9U1 505 5 -
EPAQQQIMSFLPLISVIFMAPLAAG Q9RNL5 512 3 -
Final Motifs
Motif 1  width=17
Element Seqn Id St Int Rpt
PLFKLLKWIHSFVGNWG 60IM_ECOLI 339 339 -
PLFKLLKWIHSFVGNWG Q8ZKY4 339 339 -
PLFKLLKWIHSFVGNWG Q8Z2N7 339 339 -
PLFKLLKWIHSFVGNWG Q8XB42 339 339 -
PLFKLLKFIHSFVGNWG Q8Z9U3 338 338 -
PLFWLLTFIQSIVQNWG Q9CLQ2 335 335 -
PIFWLLQHIHSLLGNWG 60IM_PSEPU 356 356 -
PLFWLLTFIQGIVSNWG 60IM_HAEIN 335 335 -
PLHWLLSVIQTFVGNWG Q9KVY4 337 337 -
PMFEFLNFLHQYIGNWG Q9PNX7 321 321 -
PLFKLLSTIHNFIGNWG 60IM_BUCAP 334 334 -
PIFWLLQHIHSLIGNWG Q9HT06 376 376 -
PLFKLLTILYSIIGNWG 60IM_BUCAI 331 331 -
PLFWLLNQLHNIIGNWG Q9JW48 339 339 -
PLFWLLNQLHNIIGNWG Q9JXS4 339 339 -
PVFYAMNFFYGYVGNFG Q92JJ3 346 346 -
PLFWLLEKIHKLLGNWG Q8Y3H6 348 348 -
PVFYAMNFFYGYVGNFG Q9ZE97 346 346 -
PMFYLIDWIYKFTGNFG Q8YDA3 351 351 -
PMFWLIDTLYKFLGNFG Q98D88 367 367 -
LLFWILSAVHAVVKNWG 60IM_COXBU 354 354 -
PMFKMMDFFFRLFGNFG Q92SF5 359 359 -
GVFVLLDYLYQFVGNWG O25989 337 337 -
GVFVLLDYLYQFVGNWG Q9ZJG8 340 340 -
LLFIIMKFFQFLTGSWG Q9PKE3 555 555 -
LLFVIMKFFKFLTGSWG O84253 555 555 -
PLFLFLYWIYEHTGSWV O66561 297 297 -
LLFIIMKFFKLVTGSWG Q9JS24 561 561 -
LLFIIMKFFKLVTGSWG Q9Z8M8 561 561 -
PIFNILEVFYKLVGNFG Q9AA40 373 373 -
GLFWILSHLNSLLHNWG Q9P9U1 355 355 -
VFFYYLDWLFLHVGNYG Q9RNL5 345 345 -
LLKWLLRLFYTLIPNWG O83915 445 445 -

Motif 2 width=16
Element Seqn Id St Int Rpt
PILMGVTMFFIQKMSP 60IM_ECOLI 468 112 -
PILMGVTMFFIQKMSP Q8ZKY4 468 112 -
PILMGVTMFFIQKMSP Q8Z2N7 468 112 -
PILMGVTMFFIQKMSP Q8XB42 468 112 -
PILMGITMYFIQKMSP Q8Z9U3 467 112 -
PILMGASMFLLQKMSP Q9CLQ2 464 112 -
PIIMGATMFIQQRLNP 60IM_PSEPU 485 112 -
PILMGISMFLLQKMSP 60IM_HAEIN 464 112 -
PLLMGASMFVIQKMSP Q9KVY4 466 112 -
PILMGATMFLQQLITP Q9PNX7 450 112 -
PIFMGLTMFFIQRTSS 60IM_BUCAP 463 112 -
PIVMGGTMLIQQMLNP Q9HT06 505 112 -
PVIMGLTMFFIQKISS 60IM_BUCAI 460 112 -
PIIMAATMFAQTYLNP Q9JW48 468 112 -
PIIMAATMFAQTYLNP Q9JXS4 468 112 -
PILMAITMFLQQKMSP Q92JJ3 494 131 -
PILMAVSMFVQTRLNP Q8Y3H6 477 112 -
PILMAITMFLHQKMSP Q9ZE97 494 131 -
PIIMGIIMFLQMRMNP Q8YDA3 499 131 -
PLIMGVTMFLQMRMNP Q98D88 515 131 -
PIIMGLSMLAQQWVSP 60IM_COXBU 483 112 -
PIIMGVTMFLQMRMNP Q92SF5 507 131 -
PLLMGASMYWHQSVTP O25989 466 112 -
PLLMGASMYWHQSVTP Q9ZJG8 469 112 -
PILLGIVMFAQQKISA Q9PKE3 699 127 -
PILLGVVMFAQQKISA O84253 699 127 -
PVIMGLTMILQQKMTP O66561 425 111 -
PILLGIVMFLQQKVTS Q9JS24 705 127 -
PILLGIVMFLQQKVTS Q9Z8M8 705 127 -
PLLYGFTMWLTTAMNP Q9AA40 528 138 -
PLLNIVIMWATQKLTP Q9P9U1 484 112 -
PIILGITMWLQFRASP Q9RNL5 493 131 -
PFALPVTQWTQMRMLP O83915 575 113 -

Motif 3 width=25
Element Seqn Id St Int Rpt
DPMQQKIMTFMPVIFTVFFLWFPSG 60IM_ECOLI 488 4 -
DPMQQKIMTFMPVIFTVFFLWFPSG Q8ZKY4 488 4 -
DPMQQKIMTFMPVIFTVFFLWFPSG Q8Z2N7 488 4 -
DPMQQKIMTFMPVIFTVFFLWFPSG Q8XB42 488 4 -
DPMQQKIMTFMPVIFTVFFLWFPAG Q8Z9U3 487 4 -
DPTQQKIMNFMPLIFMVFFLWFPSG Q9CLQ2 484 4 -
DPMQAKVMKMMPIIFTFFFLWFPAG 60IM_PSEPU 504 3 -
DPTQQKVMNFMPLVFMFFFLWFPSG 60IM_HAEIN 484 4 -
DPMQQKIMTFMPVMFTFFFLWFPSG Q9KVY4 486 4 -
DPMQAKIMKFLPVIFTFFFITFPAG Q9PNX7 470 4 -
DPFQQKIMHFMPFIFTVFFLWFPSG 60IM_BUCAP 483 4 -
DPMQAKVMKLMPIIFTFFFLWFPAG Q9HT06 524 3 -
DPLQKKIMNFMPVIFTAFFLWFPSG 60IM_BUCAI 481 5 -
DPMQAKMMKIMPLVFSVMFFFFPAG Q9JW48 487 3 -
DPMQAKMMKIMPLVFSVMFFFFPAG Q9JXS4 487 3 -
DPMQAQVMKFMPLIFLFMFSSFPVG Q92JJ3 513 3 -
DPVQAKMMMFMPIAFSVMFFFFPAG Q8Y3H6 496 3 -
DPIQAQVMKFMPLIFLFMFSSFPVG Q9ZE97 513 3 -
DPTQAAIFTWMPIIFTFMLASFPAG Q8YDA3 518 3 -
DPTQAAIFTWMPVIFTFMMAGFPAG Q98D88 534 3 -
DPTQQKMMWILPVIFTVFFINFPAG 60IM_COXBU 502 3 -
DPTQAMLFTWMPVVFTFMLASFPAG Q92SF5 526 3 -
DPMQAKIFKLLPLLFTIFLITFPAG O25989 486 4 -
DPMQAKIFKLLPLLFTIFLITFPAG Q9ZJG8 489 4 -
QRQQEAMGTMMALLFTFMFYNFPSG Q9PKE3 725 10 -
QRQQEAMGTMMALLFTFMFYNFPSG O84253 725 10 -
DPKQALVGYITSVAFTLLFINFPAG O66561 443 2 -
QKQQQVMGNMMAILFTAMFYNFPSG Q9JS24 731 10 -
QKQQQVMGNMMAILFTAMFYNFPSG Q9Z8M8 731 10 -
DPIQQKIFQWFPVIFTFTLSGFAVG Q9AA40 547 3 -
DPIAGKMMQVMPLIFGVMMAFVPSG Q9P9U1 505 5 -
EPAQQQIMSFLPLISVIFMAPLAAG Q9RNL5 512 3 -
KTSMTIMTYVMPLFFFFFFYDAPSG O83915 613 22 -