Chicken cytochrome bc1 sequences

Sequences are from NCBI non-redundant database,
the chicken genome project at Roslin Institute,
and the Univ. of Delaware Chick EST Database

References
1. Boardman PE, Sanz-Ezquerro J, Overton IM, Burt DW, Bosch E, Fong WT, Tickle C, Brown WRA, Wilson SA and Hubbard SJ. A Comprehensive Collection of Chicken cDNAs. Current Biology 2002 12:1965-1969

2. Burt D, Pourquie O. (2003) Genetics. Chicken genome--science nuggets to come soon. Science. (Jun 13) 300:1669.

Subunit 1: Entire to end of beef (446), all of mature sequence and last 15 residues of presequence (underlined, assuming cleavage as in beef )
[Full Report]
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GRVLRGLLPLTRNRGAATYAQTLQNIPETNV
TTLDNGLRVASEESSQPTCTVGVWIGAGSRYENEKNNGAGYFVEHLAFKGTKKRPCAAFE
KEVESMGAHFNGYTSREQTAFYIKALSKDMPKVVELLADVVQNCALEESQIEKERGVILQ
ELKEMDNDMTNVTFDYLHATAFQGTALARTVEGTTENIKHLTRADLASYIDTHFKAPRMV
LAAAGGISHKELVDAARQHFSGVSFTYKEDAVPILPRCRFTGSEIRARDDALPVAHVALA
VEGPGWADPDNVVLHVANAIIGRYDRTFGGGKHLSSRLAALAVEHKLCHSFQTFNTSYSD
TGLFGFHFVADPLSIDDMMXCAQGEWMRLCTSTTESEVKRAKNHLRSAMVAQLDGTTPVC
ETIGSHLLNYGRRISLEEWDSRISAVDARMVRDVCSKYIYDKCPALAAVGPIEQLLDYNR
IRSGMYWIRF

Subunit 2:
[Full Report]
Only two of the database hits seem to be core II
They cover 126-273 and 402-439(end) of bovine
Later Pangene obtained the entire sequence from Goldman's library.

Pangene/Goldman sequence:
MRRFSLPARSLAKRLYSLKVAPKVAVSAAAERVKLCPGAEDLEITKLPNGLIIASLENFS
PASRIGVFIKAGSRYETTANLGTAHLLRLASPLTTKGASSFRITRGIEAVGGSLSVYSTR
EKMTYCVECLRDHVDTVMEYLLNVTTAPEFRPWEVTDLQPQLKVDKAVAFQSPQVGVLEN
LHAAAYKTALANPLYCPDYRIGKITSEQLHHFVQNNFTSARMALVGIGVKHSDLKQVAEQ
FLNIRSGAGTSSAKATYWGGEIREQNGHSLVHAAVVTEGAAVGSAEANAFSVLQHVLGAG
PLIKRGSSVTSKLYQGVAKATTQPFDASAFNVNYSDSGLFGFYTISQAAHAGEVIRAAMN
QLKAAAQGGVTEEDVTKAKNQLKATYLMSVETAQGLLNEIGSEALLSGTHTAPSVVAQKI
DSVTSADVVNAAKKFVSGKKSMAASGDLGSTPFLDEL

Subunit 3 (Cytochrome b)
[Full Report]

        1 mapnirkshp llkminnsli dlpapsnisa wwnfgsllav clmtqiltgl llamhytadt
       61 slafssvaht crnvqygwli rnlhangasf fficiflhig rglyygsyly ketwntgvil
      121 lltlmatafv gyvlpwgqms fwgatvitnl fsaipyight lvewawggfs vdnptltrff
      181 alhfllpfai agitiihltf lhesgsnnpl gissdsdkip fhpyysfkdi lgltlmltpf
      241 ltlalfspnl lgdpenftpa nplvtpphik pewyflfaya ilrsipnklg gvlalaasvl
      301 ilflipflhk skqrtmtfrp lsqtlfwllv anlliltwig sqpvehpfii igqmaslsyf
      361 tillilfpti gtlenkmlny

Subunit 4 (cytochrome c1)
[Full Report]

1. pgp1n.pk001.b7 NCBI (U. Dela sequence) in frame 1,
GenBank Acc: BI390492

2. BBSRC 337515.1 in frame 3

Full sequence of mature chicken cyt c1 is:

GELELHPPAFPWSHGGPLSALDHSSVRRGFQVYKQVCSACHSMDYVAFRNLIGVTHTEAE  60
AKALAEEVEVQDGPDENGELFMRPGKISDYFPKPYPNPEAARADNNGALPPDLSYIVYAR 120
HGGEDYVFSLLTGYCDPPAGVVVREGLHYNPYFPGQAIGMAPPIYNEILEYDDGTPATMS 180
QIAKDVCTFLRWAAEPEHDQRKRMGLKMLLISALLTSLLYYMKRHKWSVLKSRKMAYRPP 240
K                                                            241

Subunit 5 (Rieske ISP):
[Full Report]

>precursor:
MLSVAARSGPFAPYLSAAAHAVPGPLKALAPAALRPEKVVLDLKRPLLCRESMSGRSARR 60
DLVAGISLNAPASVRYVHNDVTVPDFSAYRREDVMDATTSSQTSSEDRKGFSYLVTATAC
VATAYAAKNVVTQFISSLSASADVLALSKIEIKLSDIPEGKNVAFKWRGKPLFVRHRTQA
EINQEAEVDVSKLRDPQHDLDRVKKPEWVILVGVCTHLGCVPIANSGDFGGYYCPCHGSH
YDASGRIRKGPAPYNLEVPTYQFVGDDLVVVG

>presequence(su 9):
MLSVAARSGPFAPYLSAAAHAVPGPLKALAPAALRPEKVVLDLKRPLLCRESMSGRSARR 60
DLVAGISLNAPASVRY

>Mature sequence:
VHNDVTVPDFSAYRREDVMDATTSSQTSSEDRKGFSYLVTATACVATAYAAKNVVTQFIS
SLSASADVLALSKIEIKLSDIPEGKNVAFKWRGKPLFVRHRTQAEINQEAEVDVSKLRDP
QHDLDRVKKPEWVILVGVCTHLGCVPIANSGDFGGYYCPCHGSHYDASGRIRKGPAPYNL
EVPTYQFVGDDLVVVG

AARATVAGGGRLMDRIRKWYYNAAGFNKYGLMRDDTLYEDDDVKEALKRLPEDLYNERMF
RIKRALDLSLKHRILPKEQWVKYEEDKPYLEPYLKEVIRERLEREAWNKK

Subunit 7: 

[Full Report]

GIHFGNLARVRHIITYSLSPFEQRAIPNIFSDALPNVWRRFSSQVFKVAPPFLGAYLLYS
WGTQEFERLKRKNPADYENDQ

GEPEEEEEEELVDPLTTIREHCEQTEKCVKARERLELCDARVSSRSHTEEQCTEELFDFLHARDHCVAHKLFNKLK

Subunit 9:- see ISP (su 5) 
MLSVAARSGPFAPYLSAAAHAVPGPLKALAPAALRPEKVVLDLKRPLLCRESMSGRSARR 60
DLVAGISLNAPASVRY

LLRQAYSALFRRTSTFALTVVLGAVLFERAFDQGADAIFEHLNEGKLWKHIKHKYEASE

Subunit 11 

Closest matches with TblastN are not close:

UDELPATPK0035A5F udel.pat.pk0035.a5.f Length = 330 Frame = +1
(chromatin assembly factor)
Query:  14 ARNWVPTAQLWGAVGA---VG-LVSATDSRLILDWV 45
           A +W P  +LW  +G    VG L+SA+D   I  W+
Sbjct: 136 ASSWTPERRLWVVMGTXT*VGHLLSASDDHTICLWI 243

DKFZ426_9L9R1 REFORMAT of: dkfz426_9l9r1.dat Length = 658 Frame = -3
Query:   6 LGPRYRQLARNWVPTAQLWGAVGAVGLVSATDSRLILDWVP 46
                       L P W P WG + A G+ TD++++L W P
Sbjct: 146 LWPTMGSYGHQWGPRGHQWGPMAANGV--RTDTKVVL-WPP 33

WVPTASLWGAVGAVGLV
Aligning the second with other su11’s gives the motif:
(wiy)x(PA)xxxxwgxx(gas)xxg(lva)