Identifier | CYTCHROMECIC  [View Relations]  [View Alignment]  
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Accession | PR00605 |
No. of Motifs | 2 |
Creation Date | 09-JUL-1996  (UPDATE 14-JUN-1999) |
Title | Class IC cytochrome C signature |
Database References | PROSITE; PS00190 CYTOCHROME_C BLOCKS; BL00190 INTERPRO; IPR002329 PDB; 1C53; 1CYI SCOP; 1C53; 1CYI CATH; 1C53; 1CYI
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Literature References | 1. PETTIGREW, G.W. AND MOORE, G.R.
Cytochromes c. Biological Aspects.
SPRINGER-VERLAG, BERLIN-HEIDELBERG-NEW YORK (1987).
2. AMBLER, R.P.
Sequence variability in bacterial cytochromes c.
BIOCHIM.BIOPHYS.ACTA 1058 42-47 (1991).
3. KERFELD, C.A., ANWAR, H.P., INTERRANTE, R., MERCHANT, S. AND YEATES, T.O.
The structure of chloroplast cytochrome c6 at 1.9 A resolution: evidence
for functional oligomerization.
J.MOL.BIOL. 250 627-647 (1995).
4. NAKAGAWA, A., HIGUCHI, Y., YASUOKA, N., KATSUBE, Y. AND YAGI, T.
S-class cytochromes c have a variety of folding patterns: structure of
cytochrome c-553 from Desulfovibrio vulgaris determined by the
multi-wavelength anomalous dispersion method.
J.BIOCHEMISTRY 108 701-703 (1990).
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Documentation | Cytochromes c (cyt c) can be defined as electron-transfer proteins having
one or several haem c groups, bound to the protein by one or, more
generally, two thioether bonds involving sulphydryl groups of cysteine
residues. The fifth haem iron ligand is always provided by a histidine
residue. Cyt c possess a wide range of properties and function in a large
number of different redox processes [1].
Ambler [2] recognised four classes of cyt c. Class I includes the low-spin
soluble cyt c of mitochondria and bacteria, with the haem-attachment site
towards the N-terminus, and the sixth ligand provided by a methionine
residue about 40 residues further on towards the C-terminus. On the basis
of sequence similarity, class I cyt c were further subdivided into five
classes, IA to IE. Class IC, "split-alpha-band" cyt c, possess a widened
or split alpha-band of lowered absorptivity. This class includes dihaem
cyt c4 and monohaem cyt c6 (cyt c-553) and cyt c-554.
The 3D structures of Chlamydomonas reinhardtii cyt c6 [3] and Desulfovibrio
vulgaris cyt c-553 [4] have been determined. The proteins consist of 4
alpha-helices; three "core" helices form a "basket" around the haem group,
with one haem edge exposed to the solvent.
CYTCHROMECIC is a 2-element fingerprint that provides a signature for the
class IC cyt c. The fingerprint was derived from an initial alignment of 17
sequences: motif 1 is situated in the loop between helices 1 and 2, and
includes two invariant Cys residues, which covalently bind the haem group,
and a His residue, which provides the fifth haem iron ligand (cf. PROSITE
pattern CYTOCHROME_C); and motif 2 includes both an invariant Met, which
provides the sixth haem iron ligand, and the N-terminal part of helix 4,
which contains a conserved aromatic residue. Two iterations on OWL28.0 were
required to reach convergence, at which point a true set comprising 41
sequences was identified.
An update on SPTR37_9f identified a true set of 50 sequences.
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Summary Information | 50 codes involving 2 elements
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Composite Feature Index | |
True Positives | C553_DESDN C553_DESVH C553_DESVM C554_PARSP C554_THINE COX2_BACSU CYC4_AZOVI CYC4_PSEAE CYC4_PSEST CYC6_ALAES CYC6_ANANI CYC6_ANASP CYC6_ANASQ CYC6_ANAVA CYC6_APHFL CYC6_BRYMA CYC6_BUMFI CYC6_CHLRE CYC6_EUGGR CYC6_EUGVI CYC6_MICAE CYC6_MONBR CYC6_MONLU CYC6_PETFA CYC6_PLEBO CYC6_PORPU CYC6_PORTE CYC6_SPIMA CYC6_SYNEN CYC6_SYNLI CYC6_SYNP2 CYC6_SYNP7 CYC6_SYNSP CYC6_SYNY3 CYCA_ACEPO CYCA_GLUSU CYSD_CHLLT O30730 O34215 O34404 O69780 P72287 Q03075 Q05577 Q43945 Q46444 Q51682 Q52689 Q53114 Q57536 |
Sequence Titles | C553_DESDN CYTOCHROME C-553 (C553) - DESULFOVIBRIO DESULFURICANS (STRAIN NORWAY 4). C553_DESVH CYTOCHROME C-553 PRECURSOR (C553) (LOW POTENTIAL CYTOCHROME C) - DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH). C553_DESVM CYTOCHROME C-553 PRECURSOR (C553) - DESULFOVIBRIO VULGARIS (STRAIN MIYAZAKI). C554_PARSP CYTOCHROME C-554(548) (C554) - PARACOCCUS SP. (STRAIN ATCC 12084). C554_THINE CYTOCHROME C-554(547) (C554) - THIOBACILLUS NEAPOLITANUS. COX2_BACSU CYTOCHROME C OXIDASE POLYPEPTIDE II PRECURSOR (EC 1.9.3.1) (CYTOCHROME AA3 SUBUN CYC4_AZOVI CYTOCHROME C4 PRECURSOR - AZOTOBACTER VINELANDII. CYC4_PSEAE CYTOCHROME C4 - PSEUDOMONAS AERUGINOSA. CYC4_PSEST CYTOCHROME C4 PRECURSOR - PSEUDOMONAS STUTZERI (PSEUDOMONAS PERFECTOMARINA). CYC6_ALAES CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ALARIA ESCULENTA (ATLANTIC WAKAME) (BADDERLOCKS). CYC6_ANANI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANACYSTIS NIDULANS. CYC6_ANASP CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA SP. (STRAIN PCC 7120). CYC6_ANASQ CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA SP. (STRAIN PCC 7937). CYC6_ANAVA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANABAENA VARIABILIS. CYC6_APHFL CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - APHANIZOMENON FLOS-AQUAE. CYC6_BRYMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BRYOPSIS MAXIMA. CYC6_BUMFI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BUMILLERIOPSIS FILIFORMIS. CYC6_CHLRE CYTOCHROME C6 PRECURSOR (CYTOCHROME C552) - CHLAMYDOMONAS REINHARDTII. CYC6_EUGGR CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUGLENA GRACILIS. CYC6_EUGVI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUGLENA VIRIDIS. CYC6_MICAE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - MICROCYSTIS AERUGINOSA. CYC6_MONBR CYTOCHROME C6 (CYTOCHROME C552) - MONORAPHIDIUM BRAUNII. CYC6_MONLU CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PAVLOVA LUTHERII (MONOCHRYSIS LUTHERI). CYC6_PETFA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PETALONIA FASCIA (KELP). CYC6_PLEBO CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PLECTONEMA BORYANUM. CYC6_PORPU CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PORPHYRA PURPUREA. CYC6_PORTE CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PORPHYRA TENERA. CYC6_SPIMA CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SPIRULINA MAXIMA. CYC6_SYNEN CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS ELONGATUS NAEGELI. CYC6_SYNLI CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS LIVIDUS. CYC6_SYNP2 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. (STRAIN PCC 7002) (AGMENELLUM QUADRUPLICATUM). CYC6_SYNP7 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2). CYC6_SYNSP CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCOCCUS SP. CYC6_SYNY3 CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYNECHOCYSTIS SP. (STRAIN PCC 6803). CYCA_ACEPO ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR - ACETOBACTER POLYOXOGENES, AND ACETOBACTER EUROPAEUS. CYCA_GLUSU ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR (CYTOCHROME C- 553) (C553) (G3-ADH SUBUNIT II) - GLUCONOBACTER SUBOXYDANS. CYSD_CHLLT CYTOCHROME SUBUNIT OF SULFIDE DEHYDROGENASE (FC) (FCSD) (FLAVOCYTOCHROME C CYTOCHROME SUBUNIT) - CHLOROBIUM LIMICOLA F.SP. THIOSULFATOPHILUM. O30730 DI-HEME CYTOCHROME CP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA). O34215 CYTOCHROME C PRECURSOR - ERWINIA CYPRIPEDII. O34404 CYTOCHROME C OXIDASE POLYPEPTIDE II (EC 1.9.3.1) - BACILLUS SUBTILIS. O69780 DI-HEME CYTOCHROME C - RHIZOBIUM ETLI. P72287 FIXPC - RHIZOBIUM LEGUMINOSARUM. Q03075 CYTOCHROME C - BRADYRHIZOBIUM JAPONICUM. Q05577 FIXP PROTEIN - RHIZOBIUM MELILOTI. Q43945 GENES FIXN, FIXO, FIXQ, FIXP AND FIXG - AZORHIZOBIUM CAULINODANS. Q46444 QUINOHAEMOPROTEIN ETHANOL DEHYDROGENASE TYPE I PRECURSOR (EC 1.1.99.-) (QH-EDH1) - COMAMONAS TESTOSTERONI (PSEUDOMONAS TESTOSTERONI). Q51682 CCOP - PARACOCCUS DENITRIFICANS. Q52689 CCOP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA). Q53114 CBB3-TYPE CYTOCHROME C OXIDASE CCOP SUBUNIT - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES). Q57536 CYTOCHROME C SUBUNIT OF ALCOHOL DEHYDROGENASE - ACETOBACTER PASTEURIANUS.
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Scan History | OWL28_0 2 160 NSINGLE SPTR37_9f 2 100 NSINGLE
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Initial Motifs | Motif 1 width=12 Element Seqn Id St Int Rpt AVCGACHGVDGN PSU05988 32 32 - ANCAACHAGGNN CYC6_PORTE 12 12 - ANCASCHAGGKN CYC6_ANASP 37 37 - ANCASCHMGGKN CYC6_MICAE 8 8 - ANCAACHASGGG CYC6_PLEBO 12 12 - ANCAQCHVGGGN CYC6_APHFL 12 12 - GNCAACHMGGRN CYC6_CHLRE 70 70 - GNCAACHAGGAN CYC6_BRYMA 13 13 - ANCSACHAGGNN CYC6_ALAES 12 12 - GNCAACHNGGLN CYC6_SYNY3 47 47 - NNCSSCHVNGGN CYC6_EUGVI 8 8 - AVCGACHGADGN CYC4_PSEAE 12 12 - GTCVACHGTDGQ C554_PARSP 12 12 - AVCGACHGPDGN CYC4_AZOVI 12 12 - KSCVGCHGADGS C553_DESVM 8 8 - KMCKSCHGADGS C553_DESDN 11 11 - ASCASCHGMQAQ C554_THINE 13 13 - Motif 2 width=23 Element Seqn Id St Int Rpt SAIMAPNAAGLSEQDMDNLSAYI C554_THINE 65 40 - VLEMTGMLDPLSDQDLEDIAAYF PSU05988 83 39 - KNAMPAFGGRLVDEDIEDAANYV CYC6_PORTE 55 31 - KNAMPAFKGRLKPEQIEDVAAYV CYC6_ANASP 80 31 - MGAMPAFGGRLSAEDIEAVANYV CYC6_MICAE 51 31 - KGAMPAFKGRLSDDQIQSVALYV CYC6_PLEBO 55 31 - KGAMPAFGIRLKAEQIENVAAYV CYC6_APHFL 55 31 - KGAMPAWADRLSEEEIQAVAEYV CYC6_CHLRE 115 33 - KGAMPAWSDRLDDEEIDGVVAYV CYC6_BRYMA 58 33 - KNAMPAFGSRLAETDIEDVANFV CYC6_ALAES 55 31 - NGAMPGFKGRISDSDMEDVAAYV CYC6_SYNY3 90 31 - KGPMPAWEGVLDESEIKEVTDYV CYC6_EUGVI 53 33 - VLEMTGLLTNLSNEDLADIAAYF CYC4_PSEAE 54 30 - AALMTPMAQGLSDEDIADIAAYY C554_PARSP 57 33 - VLEMTGMLDNFSDQDLADLAAYF CYC4_AZOVI 63 39 - KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 54 34 - KGMMERVVKSLTDEDIEVLATHI C553_DESDN 55 32 -
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Final Motifs | Motif 1 width=12 Element Seqn Id St Int Rpt ANCAACHAGGNN CYC6_BUMFI 12 12 - ANCAACHMGGGN CYC6_SYNSP 12 12 - GNCAACHMGGGN CYC6_SYNEN 12 12 - GNCAACHMGGGN CYC6_SYNLI 12 12 - ANCAACHAGGNN CYC6_PORPU 37 37 - ANCAACHAGGNN CYC6_PORTE 12 12 - ANCAACHAGGNN CYC6_SYNP2 36 36 - ANCASCHAGGKN CYC6_ANASP 37 37 - GNCAACHAGGGN CYC6_MONBR 13 13 - ANCAACHMGGRN CYC6_SPIMA 12 12 - ANCASCHAGGKN CYC6_ANASQ 37 37 - ANCASCHMGGKN CYC6_MICAE 8 8 - ANCAACHASGGG CYC6_PLEBO 12 12 - ANCSACHAGGNN CYC6_PETFA 12 12 - ANCAQCHVGGGN CYC6_APHFL 12 12 - ANCAACHLGGRN CYC6_SYNP7 36 36 - ANCASCHAGGKN CYC6_ANAVA 12 12 - GNCAACHMGGRN CYC6_CHLRE 70 70 - GNCAACHAGGAN CYC6_BRYMA 13 13 - ANCSACHAGGNN CYC6_ALAES 12 12 - ANCASCHLGGRN CYC6_ANANI 12 12 - GNCAACHNGGLN CYC6_SYNY3 47 47 - GNCAACHSVZZZ CYC6_MONLU 12 12 - DNCAPCHGAGGG Q43945 125 125 - TWCAQCHGSGAG Q51682 178 178 - DNCAACHGEDGT Q53114 217 217 - ENCVACHGDGGK Q03075 217 217 - DNCSTCHVNGGN CYC6_EUGGR 8 8 - NNCSSCHVNGGN CYC6_EUGVI 8 8 - DNCASCHGADAK Q05577 216 216 - DNCAACHGDDAK P72287 214 214 - ENCASCHGEDAK Q52689 217 217 - VNCAPCHGSGAS O69780 119 119 - AVCGACHGVDGN CYC4_PSEST 32 32 - TWCAQCHGAGAG O30730 119 119 - HNCAICHMNDGT CYCA_GLUSU 338 338 - DSCAACHKTDGS O34215 323 323 - AVCGACHGADGN CYC4_PSEAE 12 12 - GTCVACHGTDGQ C554_PARSP 12 12 - AVCGACHGPDGN CYC4_AZOVI 12 12 - KECAICHRNDGG CYCA_ACEPO 328 328 - ANCVFCHGVPGV Q46444 633 633 - EQCAICHRNDGG Q57536 329 329 - KSCVGCHGADGS C553_DESVM 8 8 - KMCKSCHGADGS C553_DESDN 11 11 - KNCLSCHAVEPN O34404 269 269 - KNCLSCHAVEPN COX2_BACSU 269 269 - LSCAGCHGTDGK CYSD_CHLLT 16 16 - KSCIGCHGADGS C553_DESVH 32 32 - ASCASCHGMQAQ C554_THINE 13 13 - Motif 2 width=23 Element Seqn Id St Int Rpt KNAMPAFGGRLSDSDIEDVANYV CYC6_BUMFI 55 31 - KNAMPAFGGRLSEAQIENVAAYV CYC6_SYNSP 55 31 - KNAMPAFAGRLTDEQIQDVAAYV CYC6_SYNEN 55 31 - KNAMPAFAGRLTDEQIQDVAAYV CYC6_SYNLI 55 31 - KNAMPAFGGRLVDEDIEDAANYV CYC6_PORPU 80 31 - KNAMPAFGGRLVDEDIEDAANYV CYC6_PORTE 55 31 - QGAMPAFGGRLSDADIANVAAYI CYC6_SYNP2 86 38 - KNAMPAFKGRLKPEQIEDVAAYV CYC6_ANASP 80 31 - KGAMPAWDGRLDEDEIAGVAAYV CYC6_MONBR 58 33 - KNAMPGFNGRLSPKQIEDVAAYV CYC6_SPIMA 59 35 - KNAMPAFKGRLKPDQIEDVAAYV CYC6_ANASQ 80 31 - MGAMPAFGGRLSAEDIEAVANYV CYC6_MICAE 51 31 - KGAMPAFKGRLSDDQIQSVALYV CYC6_PLEBO 55 31 - KNAMPAFGGRLSETDIEDVANFV CYC6_PETFA 55 31 - KGAMPAFGIRLKAEQIENVAAYV CYC6_APHFL 55 31 - KGAMPAFGSKLSADDIADVASYV CYC6_SYNP7 79 31 - KNAMPAFKGRLKPEEIZBVAAYV CYC6_ANAVA 55 31 - KGAMPAWADRLSEEEIQAVAEYV CYC6_CHLRE 115 33 - KGAMPAWSDRLDDEEIDGVVAYV CYC6_BRYMA 58 33 - KNAMPAFGSRLAETDIEDVANFV CYC6_ALAES 55 31 - KGAMPAFGAKLSADDIEGVASYA CYC6_ANANI 55 31 - NGAMPGFKGRISDSDMEDVAAYV CYC6_SYNY3 90 31 - KNAMPAFGGRLEDDEIANVASYV CYC6_MONLU 56 32 - GGVMPAWGPRLSPTTIKALTVYV Q43945 264 127 - FGVMPAWTGRLSEADIVAVAAYV Q51682 319 129 - FGVMPNWNARLTEADIRSVAVYV Q53114 261 32 - AGVMPAWEGRLDPSTIKAMAVYV Q03075 261 32 - KGPMPAWEGVLSEDEIVAVTDYV CYC6_EUGGR 53 33 - KGPMPAWEGVLDESEIKEVTDYV CYC6_EUGVI 53 33 - HGVMPAWLPRLGDDTVKQLAVFV Q05577 260 32 - HGVMPAWAGRLGDTTVKELTIFV P72287 258 32 - SWAADGAKPRLSEAQIRAVASYV Q52689 268 39 - HGVMPAWAARLGDTTVNELTNFV O69780 258 127 - VLEMTGMLDPLSDQDLEDIAAYF CYC4_PSEST 83 39 - SWAADGAKPRLSEAQIRAVASYV O30730 268 137 - AVAMPGFKNHLSDQEMADVVNFM CYCA_GLUSU 391 41 - AITMPAFGWRLNDQQVADVVNFI O34215 377 42 - VLEMTGLLTNLSNEDLADIAAYF CYC4_PSEAE 54 30 - AALMTPMAQGLSDEDIADIAAYY C554_PARSP 57 33 - VLEMTGMLDNFSDQDLADLAAYF CYC4_AZOVI 63 39 - AVAMPGYSKSLSAQQIADVVNFI CYCA_ACEPO 381 41 - VRGMPDFTGKLSGDDVESLKAFI Q46444 675 30 - AVAMPDYKNILSDQQIADVVNFI Q57536 382 41 - KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 54 34 - KGMMERVVKSLTDEDIEVLATHI C553_DESDN 55 32 - GNKMTGTYPKLSDSETNALYEYL O34404 326 45 - GNKMTGTYPKLSDSETNALYEYL COX2_BACSU 326 45 - STVMGRHAKGYSDEEIHQIAEYF CYSD_CHLLT 57 29 - KAMMTNAVKKYSDEELKALADYM C553_DESVH 78 34 - SAIMAPNAAGLSEQDMDNLSAYI C554_THINE 65 40 -
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