WORKLIST ENTRIES (1):
CCBSBIOGNSIS View alignment Cytochrome c-type biogenesis protein CcbS signature
Type of fingerprint: COMPOUND with 10 elements
Links:
PRINTS; PR01410 CCBIOGENESIS; PR01411 CCMFBIOGNSIS; PR01413 NRFEBIOGNSIS
PRINTS; PR01414 CCMBBIOGNSIS; PR01386 CCMCBIOGNSIS
Creation date 30-APR-2000
1. DELGADO, M.J., YEOMAN, K.H., WU, G., VARGAS, C., DAVIES, A., POOLE, R.K.,
JOHNSTON, A.W.B. AND DOWNIE, J.A.
Characterization of the cycHJKL genes involved in cytochrome c
biogenesis and symbiotic nitrogen fixation in Rhizobium leguminosarum.
J.BACTERIOL. 177 4927-4934 (1995).
2.THOENY-MEYER, L., FISCHER, F., KUNZLER, P., RITZ, D. AND HENNECKE, H.
Escherichia coli genes required for cytochrome c maturation.
J.BACTERIOL. 177 4321-4326 (1995).
3. PAGE D., PEARCE D.A., NORRIS H.A. AND FERGUSON S.J.
The Paracoccus denitrificans ccmA, B and C genes: cloning and
sequencing, and analysis of the potential of their products to form a haem
or apo-c-type cytochrome transporter.
MICROBIOLOGY 143 563-576 (1997).
4. HUSSAIN, H., GROVE, J., GRIFFITHS, L., BUSBY, S. AND COLE, J.
A seven-gene operon essential for formate-dependent nitrite reduction to
ammonia by enteric bacteria.
MOL.MICROBIOL. 12 153-163 (1994).
5. SCHUSTER, W., COMBETTES, B., FLIEGER, K. AND BRENNICKE, A.
A plant mitochondrial gene encodes a protein involved in cytochrome c
biogenesis.
MOL.GEN.GENET. 239 49-57 (1993).
Within mitochondria and bacteria, a family of related proteins is involved
in the assembly of periplasmic c-type cytochromes: these include CycK [1],
CcmF [2,3], NrfE [4] and CcbS [5]. These proteins may play a role in
guidance of apocytochromes and haem groups for their covalent linkage
by the cytochrome-c-haem lyase. Members of the family are probably integral
membrane proteins, with up to 16 predicted transmembrane (TM) helices.
Analysis of a transcribed region in the mitochondrial genome of Oenothera
revealed an open reading frame (ORF) that is also conserved in carrot [5].
Extensive RNA editing (46 C to U transitions) alters the Oenothera mRNA
sequence, yielding a sequence with high similarity to the homologous gene
product in Marchantia [5]. The deduced polypeptides share significant
similarity with the ccl1-encoded protein involved in cytochrome c biogenesis
in the photosynthetic bacterium Rhodobacter capsulatus [5]. A highly
conserved domain is also found in plastid ORFs, suggesting that these
bacterial, chloroplast and mitochondrial genes encode polypeptides with
analogous functions in assembly and maturation of cytochromes c [5].
CCBSBIOGNSIS is a 10-element fingerprint that provides a signature for
plant cytochrome c-type biogenesis proteins. The fingerprint was derived
from an initial alignment of 3 sequences: the motifs were drawn from
conserved regions spanning virtually the full alignment length, focusing on
those sections that characterise the plant proteins but distinguish them
from the rest of the cytochrome c-type biogenesis protein family. Two
iterations on SPTR37_10f were required to reach convergence, at which point
a true set comprising 4 sequences was identified. Two partial matches were
also found, both of which are related plant proteins that fail to match the
C-terminal motifs.
SUMMARY INFORMATION
4 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
2 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 FINGERPRINT INDEX
10| 4 4 4 4 4 4 4 4 4 4
9| 0 0 0 0 0 0 0 0 0 0
8| 0 0 0 0 0 0 0 0 0 0
7| 2 2 2 2 2 2 2 0 0 0
6| 0 0 0 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0 0 0 0
--+---------------------------------------------------
| 1 2 3 4 5 6 7 8 9 10
True positives..
CCBS_DAUCA CCBS_OENBE Q35984 CCBS_MARPO
Subfamily: Codes involving 7 elements
Subfamily True positives..
P92585 Q31706
PROTEIN TITLES
CCBS_DAUCA PROBABLE CYTOCHROME C BIOSYNTHESIS PROTEIN - DAUCUS CAROTA (
CCBS_OENBE PROBABLE CYTOCHROME C BIOSYNTHESIS PROTEIN - OENOTHERA BERTI
Q35984 MITOCHONDRIAL RPS1A GENE AND ORF589 - TRITICUM AESTIVUM (WHE
CCBS_MARPO PROBABLE CYTOCHROME C BIOSYNTHESIS PROTEIN - MARCHANTIA POLY
P92585 CCL1 - BRASSICA NAPUS (RAPE).
Q31706 CCL1-LIKE PROTEIN - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
SCAN HISTORY
SPTR37_10f 1 30 NSINGLE
INITIAL MOTIF SETS
CCBSBIOGNSIS1 Length of motif = 16 Motif number = 1
Cytochrome c-type biogenesis protein CcbS motif I - 1
PCODE ST INT
ELGHYFLVLSIFVALT CCBS_MARPO 33 33
ELFHYPLFPGLFVAFT CCBS_OENBE 5 5
ELFHYSLFLGLFVAFT CCBS_DAUCA 5 5
CCBSBIOGNSIS2 Length of motif = 13 Motif number = 2
Cytochrome c-type biogenesis protein CcbS motif II - 1
PCODE ST INT
FFLFTMSFFGILF CCBS_MARPO 60 11
FWCILLSFLGLSF CCBS_OENBE 35 14
FWCILLSFLGLSF CCBS_DAUCA 35 14
CCBSBIOGNSIS3 Length of motif = 15 Motif number = 3
Cytochrome c-type biogenesis protein CcbS motif III - 1
PCODE ST INT
FCYISSDFSNYNVFT CCBS_MARPO 72 -1
FRHIPNNNSNYNVLT CCBS_OENBE 47 -1
FRHIPNNLSNYNVLT CCBS_DAUCA 47 -1
CCBSBIOGNSIS4 Length of motif = 17 Motif number = 4
Cytochrome c-type biogenesis protein CcbS motif IV - 1
PCODE ST INT
CWILSFYGFLFCYLARP CCBS_MARPO 113 26
CWIPSFYGFLLCYRGRP CCBS_OENBE 85 23
CRILSFYGFLLCYRGRP CCBS_DAUCA 85 23
CCBSBIOGNSIS5 Length of motif = 13 Motif number = 5
Cytochrome c-type biogenesis protein CcbS motif V - 1
PCODE ST INT
GIALFFSIFLLAS CCBS_MARPO 171 41
GIALFFSPFLSAS CCBS_OENBE 229 127
GIALFFSPFLSAS CCBS_DAUCA 231 129
CCBSBIOGNSIS6 Length of motif = 16 Motif number = 6
Cytochrome c-type biogenesis protein CcbS motif VI - 1
PCODE ST INT
FVRISFVCTKSLAELN CCBS_MARPO 187 3
FVRNFFVRTEPLAESN CCBS_OENBE 245 3
FVRNFFVRTEPLAESN CCBS_DAUCA 247 3
CCBSBIOGNSIS7 Length of motif = 22 Motif number = 7
Cytochrome c-type biogenesis protein CcbS motif VII - 1
PCODE ST INT
CIYAGYVASAIGFCLCLSKIIN CCBS_MARPO 216 13
CIYAGDVASAMGFCLCRSKMMN CCBS_OENBE 274 13
CIYAGDVASAMGFGLCRSKMMN CCBS_DAUCA 276 13
CCBSBIOGNSIS8 Length of motif = 14 Motif number = 8
Cytochrome c-type biogenesis protein CcbS motif VIII - 1
PCODE ST INT
WTCSANTVVWKQIQ CCBS_MARPO 305 67
WTAGANTVVSDQDQ CCBS_OENBE 400 104
WTAGANTVVSDQDQ CCBS_DAUCA 402 104
CCBSBIOGNSIS9 Length of motif = 22 Motif number = 9
Cytochrome c-type biogenesis protein CcbS motif IX - 1
PCODE ST INT
SVILPKLNDWTLFLNMVTFLCC CCBS_MARPO 371 52
SVILPLLHSCTSLINIVTLLCC CCBS_OENBE 470 56
SVILPLLHSWTSFLNIVTLPCC CCBS_DAUCA 472 56
CCBSBIOGNSIS10 Length of motif = 21 Motif number = 10
Cytochrome c-type biogenesis protein CcbS motif X - 1
PCODE ST INT
WCFFLLITSISFLFFFKMKQQ CCBS_MARPO 421 28
WRFFLLMTGISMILFSQMKQQ CCBS_OENBE 520 28
WRFFLLMTGISMILFSQMKQQ CCBS_DAUCA 522 28
FINAL MOTIF SETS
CCBSBIOGNSIS1 Length of motif = 16 Motif number = 1
Cytochrome c-type biogenesis protein CcbS motif I - 2
PCODE ST INT
ELFHYSLFLGLFVAFT CCBS_DAUCA 5 5
ELFHYPLFPGLFVAFT CCBS_OENBE 5 5
EFSHYSLFPGLFVAFT Q35984 19 19
ELGHYFLVLSIFVALT CCBS_MARPO 33 33
CCBSBIOGNSIS2 Length of motif = 13 Motif number = 2
Cytochrome c-type biogenesis protein CcbS motif II - 2
PCODE ST INT
FWCILLSFLGLSF CCBS_DAUCA 35 14
FWCILLSFLGLSF CCBS_OENBE 35 14
FWCILLPFLGLSF Q35984 49 14
FFLFTMSFFGILF CCBS_MARPO 60 11
CCBSBIOGNSIS3 Length of motif = 15 Motif number = 3
Cytochrome c-type biogenesis protein CcbS motif III - 2
PCODE ST INT
FRHIPNNLSNYNVLT CCBS_DAUCA 47 -1
FRHIPNNNSNYNVLT CCBS_OENBE 47 -1
FRHIPNNLSNYNVLT Q35984 61 -1
FCYISSDFSNYNVFT CCBS_MARPO 72 -1
CCBSBIOGNSIS4 Length of motif = 17 Motif number = 4
Cytochrome c-type biogenesis protein CcbS motif IV - 2
PCODE ST INT
CRILSFYGFLLCYRGRP CCBS_DAUCA 85 23
CWIPSFYGFLLCYRGRP CCBS_OENBE 85 23
CWIPSFYGFLFCYRGRP Q35984 99 23
CWILSFYGFLFCYLARP CCBS_MARPO 113 26
CCBSBIOGNSIS5 Length of motif = 13 Motif number = 5
Cytochrome c-type biogenesis protein CcbS motif V - 2
PCODE ST INT
GIALFFSPFLSAS CCBS_DAUCA 231 129
GIALFFSPFLSAS CCBS_OENBE 229 127
GIALFFSPFLSAS Q35984 240 124
GIALFFSIFLLAS CCBS_MARPO 171 41
CCBSBIOGNSIS6 Length of motif = 16 Motif number = 6
Cytochrome c-type biogenesis protein CcbS motif VI - 2
PCODE ST INT
FVRNFFVRTEPLAESN CCBS_DAUCA 247 3
FVRNFFVRTEPLAESN CCBS_OENBE 245 3
FVRNFFVRTEPLAESN Q35984 256 3
FVRISFVCTKSLAELN CCBS_MARPO 187 3
CCBSBIOGNSIS7 Length of motif = 22 Motif number = 7
Cytochrome c-type biogenesis protein CcbS motif VII - 2
PCODE ST INT
CIYAGDVASAMGFGLCRSKMMN CCBS_DAUCA 276 13
CIYAGDVASAMGFCLCRSKMMN CCBS_OENBE 274 13
CIYAGDVASAMGFGLCRSKMMN Q35984 285 13
CIYAGYVASAIGFCLCLSKIIN CCBS_MARPO 216 13
CCBSBIOGNSIS8 Length of motif = 14 Motif number = 8
Cytochrome c-type biogenesis protein CcbS motif VIII - 2
PCODE ST INT
WTAGANTVVSDQDQ CCBS_DAUCA 402 104
WTAGANTVVSDQDQ CCBS_OENBE 400 104
WTAGANTVVSDQDQ Q35984 410 103
WTCSANTVVWKQIQ CCBS_MARPO 305 67
CCBSBIOGNSIS9 Length of motif = 22 Motif number = 9
Cytochrome c-type biogenesis protein CcbS motif IX - 2
PCODE ST INT
SVILPLLHSWTSFLNIVTLPCC CCBS_DAUCA 472 56
SVILPLLHSCTSLINIVTLLCC CCBS_OENBE 470 56
SVILPLLHSWTSLLNILTLPCC Q35984 480 56
SVILPKLNDWTLFLNMVTFLCC CCBS_MARPO 371 52
CCBSBIOGNSIS10 Length of motif = 21 Motif number = 10
Cytochrome c-type biogenesis protein CcbS motif X - 2
PCODE ST INT
WRFFLLMTGISMILFSQMKQQ CCBS_DAUCA 522 28
WRFFLLMTGISMILFSQMKQQ CCBS_OENBE 520 28
WRFFLLITGISMTLFYQMKQE Q35984 530 28
WCFFLLITSISFLFFFKMKQQ CCBS_MARPO 421 28
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