WORKLIST ENTRIES (1):

CYTCHROMECIC View alignment View Structure    Class IC cytochrome C signature
 Type of fingerprint: COMPOUND with 2  elements
Links:
   PRINTS; PR00603 CYTOCHROMEC1; PR00604 CYTCHRMECIAB; PR00606 CYTCHROMECID
   PRINTS; PR00607 CYTCHROMECIE; PR00608 CYTCHROMECII; PR00609 CYTOCHROMEC3
   PRINTS; PR00610 CYTOCHROMEF
   INTERPRO; IPR002329
   PROSITE; PS00190 CYTOCHROME_C
   PDB; 1C53 3Dinfo; 1CYI 3Dinfo 
   SCOP; 1C53; 1CYI
   CATH; 1C53; 1CYI

 Creation date 09-JUL-1996; UPDATE 14-JUN-1999

   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 1.9A 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.BIOCHEM. 108 701-703 (1990).

   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.

  SUMMARY INFORMATION
     50 codes involving  2 elements

   COMPOSITE FINGERPRINT INDEX
  
    2|  50   50  
   --+-----------
     |   1    2  

True positives..
 CYC6_BUMFI     CYC6_SYNSP     CYC6_SYNEN     CYC6_SYNLI     
 CYC6_PORPU     CYC6_PORTE     CYC6_SYNP2     CYC6_ANASP     
 CYC6_MONBR     CYC6_SPIMA     CYC6_ANASQ     CYC6_MICAE     
 CYC6_PLEBO     CYC6_PETFA     CYC6_APHFL     CYC6_SYNP7     
 CYC6_ANAVA     CYC6_CHLRE     CYC6_BRYMA     CYC6_ALAES     
 CYC6_ANANI     CYC6_SYNY3     CYC6_MONLU     Q43945         
 Q51682         Q53114         Q03075         CYC6_EUGGR     
 CYC6_EUGVI     Q05577         P72287         Q52689         
 O69780         CYC4_PSEST     O30730         CYCA_GLUSU     
 O34215         CYC4_PSEAE     C554_PARSP     CYC4_AZOVI     
 CYCA_ACEPO     Q46444         Q57536         C553_DESVM     
 C553_DESDN     O34404         COX2_BACSU     CYSD_CHLLT     
 C553_DESVH     C554_THINE     


  PROTEIN TITLES
   CYC6_BUMFI       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BUM
   CYC6_SYNSP       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYN
   CYC6_SYNEN       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYN
   CYC6_SYNLI       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SYN
   CYC6_PORPU       CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
   CYC6_PORTE       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - POR
   CYC6_SYNP2       CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
   CYC6_ANASP       CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
   CYC6_MONBR       CYTOCHROME C6 (CYTOCHROME C552) - MONORAPHIDIUM BRAUNII.
   CYC6_SPIMA       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - SPI
   CYC6_ANASQ       CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
   CYC6_MICAE       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - MIC
   CYC6_PLEBO       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PLE
   CYC6_PETFA       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PET
   CYC6_APHFL       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - APH
   CYC6_SYNP7       CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
   CYC6_ANAVA       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANA
   CYC6_CHLRE       CYTOCHROME C6 PRECURSOR (CYTOCHROME C552) - CHLAMYDOMONAS RE
   CYC6_BRYMA       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - BRY
   CYC6_ALAES       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ALA
   CYC6_ANANI       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - ANA
   CYC6_SYNY3       CYTOCHROME C6 PRECURSOR (SOLUBLE CYTOCHROME F) (CYTOCHROME C
   CYC6_MONLU       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - PAV
   Q43945           GENES FIXN, FIXO, FIXQ, FIXP AND FIXG - AZORHIZOBIUM CAULINO
   Q51682           CCOP - PARACOCCUS DENITRIFICANS.
   Q53114           CBB3-TYPE CYTOCHROME C OXIDASE CCOP SUBUNIT - RHODOBACTER SP
   Q03075           CYTOCHROME C - BRADYRHIZOBIUM JAPONICUM.
   CYC6_EUGGR       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUG
   CYC6_EUGVI       CYTOCHROME C6 (SOLUBLE CYTOCHROME F) (CYTOCHROME C553) - EUG
   Q05577           FIXP PROTEIN - RHIZOBIUM MELILOTI.
   P72287           FIXPC - RHIZOBIUM LEGUMINOSARUM.
   Q52689           CCOP - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
   O69780           DI-HEME CYTOCHROME C - RHIZOBIUM ETLI.
   CYC4_PSEST       CYTOCHROME C4 PRECURSOR - PSEUDOMONAS STUTZERI (PSEUDOMONAS 
   O30730           DI-HEME CYTOCHROME CP - RHODOBACTER CAPSULATUS (RHODOPSEUDOM
   CYCA_GLUSU       ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR (CYTOCH
   O34215           CYTOCHROME C PRECURSOR - ERWINIA CYPRIPEDII.
   CYC4_PSEAE       CYTOCHROME C4 - PSEUDOMONAS AERUGINOSA.
   C554_PARSP       CYTOCHROME C-554(548) (C554) - PARACOCCUS SP. (STRAIN ATCC 1
   CYC4_AZOVI       CYTOCHROME C4 PRECURSOR - AZOTOBACTER VINELANDII.
   CYCA_ACEPO       ALCOHOL DEHYDROGENASE CYTOCHROME C SUBUNIT PRECURSOR - ACETO
   Q46444           QUINOHAEMOPROTEIN ETHANOL DEHYDROGENASE TYPE I PRECURSOR (EC
   Q57536           CYTOCHROME C SUBUNIT OF ALCOHOL DEHYDROGENASE - ACETOBACTER 
   C553_DESVM       CYTOCHROME C-553 PRECURSOR (C553) - DESULFOVIBRIO VULGARIS (
   C553_DESDN       CYTOCHROME C-553 (C553) - DESULFOVIBRIO DESULFURICANS (STRAI
   O34404           CYTOCHROME C OXIDASE POLYPEPTIDE II (EC 1.9.3.1) - BACILLUS 
   COX2_BACSU       CYTOCHROME C OXIDASE POLYPEPTIDE II PRECURSOR (EC 1.9.3.1) (
   CYSD_CHLLT       CYTOCHROME SUBUNIT OF SULFIDE DEHYDROGENASE (FC) (FCSD) (FLA
   C553_DESVH       CYTOCHROME C-553 PRECURSOR (C553) (LOW POTENTIAL CYTOCHROME 
   C554_THINE       CYTOCHROME C-554(547) (C554) - THIOBACILLUS NEAPOLITANUS.

SCAN HISTORY OWL28_0 2 160 NSINGLE SPTR37_9f 2 100 NSINGLE INITIAL MOTIF SETS CYTCHROMECIC1 Length of motif = 12 Motif number = 1 Class IC cytochrome c motif I - 1 PCODE ST INT KMCKSCHGADGS C553_DESDN 11 11 KSCVGCHGADGS C553_DESVM 8 8 AVCGACHGADGN CYC4_PSEAE 12 12 AVCGACHGPDGN CYC4_AZOVI 12 12 AVCGACHGVDGN PSU05988 32 32 GTCVACHGTDGQ C554_PARSP 12 12 ASCASCHGMQAQ C554_THINE 13 13 ANCAACHAGGNN CYC6_PORTE 12 12 ANCASCHAGGKN CYC6_ANASP 37 37 GNCAACHAGGAN CYC6_BRYMA 13 13 ANCASCHMGGKN CYC6_MICAE 8 8 ANCSACHAGGNN CYC6_ALAES 12 12 NNCSSCHVNGGN CYC6_EUGVI 8 8 GNCAACHMGGRN CYC6_CHLRE 70 70 ANCAACHASGGG CYC6_PLEBO 12 12 GNCAACHNGGLN CYC6_SYNY3 47 47 ANCAQCHVGGGN CYC6_APHFL 12 12 CYTCHROMECIC2 Length of motif = 23 Motif number = 2 Class IC cytochrome c motif II - 1 PCODE ST INT KGMMERVVKSLTDEDIEVLATHI C553_DESDN 55 32 KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 54 34 VLEMTGLLTNLSNEDLADIAAYF CYC4_PSEAE 54 30 VLEMTGMLDNFSDQDLADLAAYF CYC4_AZOVI 63 39 VLEMTGMLDPLSDQDLEDIAAYF PSU05988 83 39 AALMTPMAQGLSDEDIADIAAYY C554_PARSP 57 33 SAIMAPNAAGLSEQDMDNLSAYI C554_THINE 65 40 KNAMPAFGGRLVDEDIEDAANYV CYC6_PORTE 55 31 KNAMPAFKGRLKPEQIEDVAAYV CYC6_ANASP 80 31 KGAMPAWSDRLDDEEIDGVVAYV CYC6_BRYMA 58 33 MGAMPAFGGRLSAEDIEAVANYV CYC6_MICAE 51 31 KNAMPAFGSRLAETDIEDVANFV CYC6_ALAES 55 31 KGPMPAWEGVLDESEIKEVTDYV CYC6_EUGVI 53 33 KGAMPAWADRLSEEEIQAVAEYV CYC6_CHLRE 115 33 KGAMPAFKGRLSDDQIQSVALYV CYC6_PLEBO 55 31 NGAMPGFKGRISDSDMEDVAAYV CYC6_SYNY3 90 31 KGAMPAFGIRLKAEQIENVAAYV CYC6_APHFL 55 31 FINAL MOTIF SETS CYTCHROMECIC1 Length of motif = 12 Motif number = 1 Class IC cytochrome c motif I - 2 PCODE ST INT 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 32 32 KECAICHRNDGG CYCA_ACEPO 328 328 ANCVFCHGVPGV Q46444 633 633 EQCAICHRNDGG Q57536 329 329 KSCVGCHGADGS C553_DESVM 31 31 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 CYTCHROMECIC2 Length of motif = 23 Motif number = 2 Class IC cytochrome c motif II - 2 PCODE ST INT 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 83 39 AVAMPGYSKSLSAQQIADVVNFI CYCA_ACEPO 381 41 VRGMPDFTGKLSGDDVESLKAFI Q46444 675 30 AVAMPDYKNILSDQQIADVVNFI Q57536 382 41 KAVMTNLVKRYSDEEMKAMADYM C553_DESVM 77 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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