Sponge genome CYPs

 

This file is a preliminary examination of the Sponge genome from

Reniera_sp sequenced at JGI and first released to the NCBI trace archive on

July 5, 2005.

 

Several genes have been assembled including a CYP51 and CYP20 ortholog.

 

Surprises include CYP27-like sequences in the mito clan and CYP9-like sequences

in the CYP3 clan.  These were absent in the hydra genome and were predicted to

be absent from sponge.  These sequences were thought to be found only in

bilateral animals, but they are in sponge.  There is a possibility that the

sponge genome includes some food organism’s genome sequence, but this is not

the best explanation for bilateral animal genes.  The other option is that

Hydra lost these genes in its evolution.  The choanoflagellate Monosiga ovata

Genome may clarify this question. 

 

gnl|ti|XXXXXXXXX numbers are trace archive numbers.

 

The set of Reniera genomic sequences was downloaded from the Trace Archive

as Database: fasta.reniera_sp__jgi-2005.001

473,144 sequences; 487,898,717 total letters

 

These sequences were searched on a stand alone blast server on my Mac G4.

Not all accession numbers are given here since my original file with all

this data is 189 pages long.  There are 241 unique accession numbers found in the

first round of searches.  Some of these have mate pairs that are also P450

blast hits, probably N- and C-terminals.  These will compress down to a small

number of genes as they become assembled.

 

D. Nelson July 11, 2005

 

>CYP51 sponge gnl|ti|858134330 BAYA5800.x1

66% to CYP51 fugu

MESSFSNIVSSVGPVAVLILTVLLVHYWWRRAGNK (0)

VKGNPPPPLIPSSLPFIGAAVSFGKDPINYLLAAHSKYGNVFSFNMVGSTFTYLIGSDST

SLFFNSRNESLNAEEVYSRLVTPVFGKGVAYDVPHD  (0)

LFVEQKKMLKYGLSVSHFRRYVPLIETETTKYFERWGDKGE

LDIFKALSELIILTASRCL ()

LGPEIRSVLNEEVAQLYTDLDGGFTHAAWLLPSWLPLPSFK ()

KRDKARERMAEIFTSVIKKRREMPNNQEDDILSYLITTTYK ()

DGRSLTDSEITGLLIGLLMAGQHTSSSTSSWLGFFLARHSDYQ (0)

TRAYEEQLEVCGSNCPPLDYDQ (0)

LKDLTFLDCCLKETLRLRPPIMTMMRMAKTEQ (0)

DVGGYTIPAGHQVCVSPTVNHQLNENWTDPQTFNPDRFVDEELSNSEKFSYVPFGA (1)

GRHRCIGESFAYVQIKTIWSVLLRKYQFELVGGVFPPVHYQTMIHTPTQPVIAYQLRQ*

 

>CYP20 ortholog

gnl|ti|859955098 BAYB135253.b1

gnl|ti|859355894 BAYB40512.g1

37  CNRGSYXXLIPGWNKEPSDPVLGDLAVAMSAGSLHHYLAKQHKEGSSPVVSFWWRNKRVVSICSQKSF 213

214 KDTENIYNRPSVIFAPCSDPLHGPNSIQSVNGDEWKRQRKMVHGTMRGDFLESFVPDLVV 393

394 IAHETAKTWASGEPIHLLKSITRMTLKAILMTSLGNIFENDEGIDELAALYHVCKCE 564

565 MDECILNIPPPQSQREKDFQSNLKILQGYLKQMMKARRSNLQSGRKSLPLMDALLNSGDP 744

745 EETIMSNVITFMGGFHTSGYFLTWTFYYLALHPEIQDKIMKEIVQKVGKEASSEKL

914 KEYVMSSDTYFEQFLDEAIRVSTVTSFSAHCPDKDVVVDGYHIPANTPI

565 IQSLGVAMHDPNVWDNPQKFDPNRFGSKHAKRGHEFRPFGVSTLRRCPANHFTYIMSSIY 744

745 VVILLQRFEFSTKDTNLTKKYGIATSPGHQIDFQVKTRG* 864

 

>gnl|ti|858479313 BAYA83845.b1

gnl|ti|858136366 BAYA7069.y1

gnl|ti|858508899 BAYA99290.b1

gnl|ti|859458170 BAYB64550.b1

>CYP20 like mid region aa 202-266

gnl|ti|858469316 BAYA80072.x1

gnl|ti|859485524 BAYB76641.g1

gnl|ti|858395077 BAYA59029.x1

gnl|ti|858308284 BAYA32249.x1

gnl|ti|859469211 BAYB60999.g1

>gnl|ti|859272310 BAYB18717.b1

gnl|ti|858479985 BAYA83845.g1 see .b1 above

gnl|ti|858340415 BAYA47943.y1

gnl|ti|859305065 BAYB27669.g1

gnl|ti|859949241 BAYB130068.b1

gnl|ti|858122273 BAYA1789.y1

gnl|ti|858324161 BAYA43946.x1

gnl|ti|858403097 BAYA59029.y1

CYP2 clan 27% to CYP20 danio

>Most like CYP20 or CYP4F

MIICIYTLCIIILMIYLFLVFSLGDLGLLSKHGSL

HQYLLHLHDNGRTPITVFWWGTQRVVSVCSPQLFKDTMKLTYRP (1)

KLLYELFEPMLTSHSIQYANGTDWEERRKFLYPTLRDEFLKDYIPIFIQ (0)

IADETASVWSSLSPDNNKIEFQEEFFTMTIKGITRTCYGNAFNNEEEVRKMAKVYHI

671 VWDEMEQRLHVGPPEAGSERERIFNESLGLVRDVILSVVKKRKDGTETEEVPFVD 850

851 ALLQSQVPDDQ 886

793 IISDAVTFMVGGLHTSGYLLVWATYYMSEHPEVLNGVVAEMRKEVGNDRSEKLYEYAYSTTS (2)

266 YLRKVLDETLRLSTLAPYAARYSEEDITVGEYSIPAGTPIIDALGVSLKNECLWKNVHK 442 (2)

686 FDPEHFGSCALQGKDSMAFSPFGMGRRKCPGYQFSYVEVSIFLTLLLQRFNLKPVSDKG 862

863 VGMVHGLVTSPSEPLYYTVHPIASDESTTEE*

 

 

>gnl|ti|858505615 BAYA104446.y1

CYP2clan.2

910 LNPEHLDSEPSQGKDSRAFSPLSMGRRKCPAYQFSYVEVSIFLTLLLQRFNRKPGSDKGV 731

730 VMVHGWVTSPQGATLLHGTSNSLGGINHGGMMESSVNGLLMFNPVGXLII*

 

>CYP27.a like (mito clan?)

gnl|ti|858130440 BAYA5747.y1

FLYTASAYFTFGADIDTTKSSL

PETQKFHEGFSTLVSTIDDFITALPLFKYFPSKMVKTLSKATDDLYSIGRKYIDLHQESESGYSLMDQLLKEGRMSKEEIIMSAIFLMASALDT

ISSNSSYLLYELSKRPDIQEKVYKQVISALGSTNAISGEVLQMMPYLGCVIKETQR (2)

ITPISPNHIRTVTKDVNLLGYNIPAQ (0)

TLTMYSTLAVSRNERF

FQNPLDFDPDRWNRDNIHSFSILPFGLGPKSCW (1)

GRKLAEFEMKVLLNLVRLTICLNPLRSYFP

 

>CYP27.b like (mito clan?) gnl|ti|859672470 BAYB104134.g1

GKMSAKDAISHSINMLAAGMDT

TAHTTAFVLYTLSKHPEVQEK

AYKQITSVLGDDEEPDGDSLQKMPYLGHHIKETQR

LYQVTPYTARWLETDVELLNYHIPAKVIV

KTAILGGMEAMSQNPTLYKDPLKFNPDRWSTDDIHPFTMLPFGFGPRACWG

 

>gnl|ti|858383600 BAYA50222.x1 28% to CYP27B fugu (mito clan)

RTGIRDGLNVRPFKVFKSGQEWKTLRSPRSKPILRLKVTRSPTNCMILPISKELTGWING

GKDSYITDIRNDLQRWALKGVVWFVFNEDLPVFEEGNEMAGDLAEASVNFINKISALFQS

LPWYKLYPTEALKNYEKAVKGMHGLGEKMMKSRFEQLQKLAQEGEVLNEERISLMEYLLI

EEKLTKEQALSQACDLLAAGVDTTSSTATFLLHHISKEPELQQALYDEVTSVCGLNGVPD

FNDLQKMPLVRNCVKETLRIYPVVGLLRKAQTNMVIDGYQVPKDTSFIFNLYLMGKDPKL

YPNPEVFNPYRWEEKKEKDGLVTFASLPFGAGVRMCYGRRLAELELHLLVANICRRFVLY

TDQSTLVTSRRSVYKADEPVRLNVIERNS*

 

 

>93% to 858383600 28% to CYP49A1 Drosophila (mito clan)

MNLLLRSSRSKLGLAPLSSLYRRHVSISLISEEDPSSVALWKSAKPFKEIPGPKCYPIVGAVP

SIYRSVTEDNPIDKVFSGWHEQYGSFYKTIAPKALGGPRS

ISTTDPDILKVLVRDEIKNKYPSRGSGVEEKASWIHNKINVPPFMFFTSGQEWKTLRSAM

SKPIIPRKVAMFSNQLYDAADQLGTHW

111 LNNRGKDSYITDIRNDLQRWALKGVVWFVFNEGLPVFEEGNQMAGDFAEASVNFINKLSV 290

291 VLRSLPWYKLYPTEALKNYKKAVNDMHALGEKMMKSRFEQLQKLAQEGEVLN 446

447 EERISLMEYLLIEEKLTKEQALSQACDLLAAGVDTTSSTATFLLHHISKEPELQQALYDE 626

627 VTSVCGLNGVPDFNDLQKMPLVRNCVKETLRIYPAVPLLRKAQTNMVIDGYQVPKDTSF 803

804 VFNLYLMGKDPELYPNPEVFNPYRWEEKKEKDGLVTFASLPFGTGVRMCYGRRLAELEL 980

981 HLLVANICRRFVLSTDQSTLVTSRQSIYKADEPVRLNVIERNS*

 

>gnl|ti|859304149 BAYB27137.g2 89% to  866269941 and 89% to 858383600

gnl|ti|858382446 BAYA49450.y1

gnl|ti|858123786 BAYA3305.y1

gnl|ti|858127618 BAYA3305.x1 yellow may be out of frame

    MSLLVRARLGLAPFSSLYCRHVSISLIDEEDPSSVALWKS

403 AKPFKEIPGPKCYPIVGAVPSIYARTEDTSKLKDIEWHEKYGSFFKTITPKALG 564

565 GSCSISTTDPDILKVLVRDEIKNKYPSRGSGLEEKVSWIHNKINIPPFMFFTSGQEWKTL 640

639 RSAMSKPIIPRKVAMFSNQLYDAADQLGTHWLNN

    REKDSYITDIRDDVQQWALKGVVWFIFNEDLPIFEEGNEMAGDFAKASIN 703

702 FFNKLAVINRSLPWYKLYPTEALKNYEKAVNDMHALGEKMMKSRFEQFQKLAQEGEVLN 526

525 EERISLMEYLLIEEKLTKEQALSQACDLLAAGVDTTSSTATFLLHHISKEPELQQALYDE 346

345 VTSVCGLNGVPDFNDLQKMPLVRNCVKETLRIYPSIPLFRKAQTKMVINGFQVPKDTSF 169

168 IFNLYLMGKDPKLYLNPEVFNPYRWEEKKEQDGLVTFASLPFGAGVR 28

    MCYGRRLAELELHLLVANICRRFVLSTDQSTLVTSRQSIYKADEPVRLNVIERNS*

 

>gnl|ti|858406544 BAYA62866.x1 gnl|ti|859472419 BAYB67088.b1

SENVSLSWASLHRHSSSAVYVNETDPSSLALWKSAKPFKQIPGPKCYPVIGALPTFLTRI

TKERPIGIVSLDWFKEYGSLYKLVIPGMSPALFTTDPDVFKVMVQNEASNKYPLRGFGFE

DKLGWVSHKIDVPPFMFFTGGQEWKTLRSAMAKPATPRKVATFSNQLYDAAQELGTHWLS

KKSKDFYITDIRGDLQRWGLKCVVWFVFNKDLPVFEEGNQMAHDFAKAAVNFNNNIGSML

QALPLYKLYPTAPFKNFKKAVNDMHAIGESMMKSRFEQLQKLAQEGEVLNEERVSLVEHL

LIEEKLTKEQALSQACDDLLSAGVDASSNTAVFLLHHISKEPELQQALYDEVTSVCGLNG 282

281 VPDFNDFQRMPLVRNCIKETLRLYPAAPIPRLAQTDMVVHGYKVPKNTSISFELFLIGR 105

104 DPKLYPNPESFNPYR 60

 

>gnl|ti|859698485 BAYB110373.g1 89% to 858406544

159 KVMVQNEASNKYPLRGFGLEDKFGWVSHKIDVPPFMFFTEGQEWKTLR 302

303 SAMAKPATPRKVATFSNQLYDAAEELGTHWLSKKGEDSYVTDIRDDLQQWALKGVVW 473

474 FVFNEELPVFKEGNQMADDFAKAAVNFTNSIGNMLQALPLYKLYPTAPFKNFKKAVYDMH 653

654 AIGESMMKTRFEQLQKLAQEGEVLNEERVSLVEHLLIEEKLTKEQALSQACD 809

810 LLSAGVDTSSNTAVFLLHHIAKEPELQQALYDEFTSVCGLNGIPDFNDFQRMPLVRKCIR 989

990 E 992

 

 

>CYP9 like gnl|ti|858495539 BAYA95490.y1

LKDFIQLLMDARADESSDEESSNKENMLNDLQIAGVCFDFMVGGYETTANALACTSYLLS

LNPDEQERLCEAIDNYYQENE  (0)

DASLYDASQNIPYLDWVIQEA

KHFTVNFYNLVGLVYAMKPVPLMV

GVTFLKGAKVMIPIQYLHYSPEHWEEPDAFKPSR (2?)

FSPEGKEGRNPLSHIPFGWGPRSCIGMRFALMEAKACLVSILRKYRFERSPDTQVGCR*

 

>CYP9.b gnl|ti|858286376 BAYA24583.y1

gnl|ti|858287525 name:BAYA24583.x1

MVNYTVSLPRLSFNYGLLVCVSSFFPILAASLLLVLVSAI

PLISFCYAPYRVLKRLGITHPPVRPFMGNALQVLK

839 DFLQLLMDTSAIDDDENKTNSSPKKLALTDQQIVGLCLDFMVAGQETTADALAYSSYL 666

665 LSLNPDEQERLCEAID 618

    XXXXXXXXXXX

537 YDASQNIPYLDWVIQEALRLYPPA 466

394 NRQCNETCTINGITFPKGSLVIFPIQYLHCSPDNWDEPEVFNPNR 257

212 FSPEGKEGRNPLSHIPFGWGPRSCIGMRFALMEAKACLVSILRKYRV 69

 

>CYP9.c gnl|ti|858383140 BAYA49761.y1

YDASHDIQYLDWVVSEGLRMYPPVTRISRYCSETSVINGVTIPKETCVQVPVKYLHYSPE

HWDQPDEFMPDR

EGKEGRHPLCYVPFGYGQRSCIGMRFALMEIKMAL

 

>CYP9.d gnl|ti|858422567 BAYA72010.x1 gnl|ti|858418346 BAYA72010.y1

919 QLTDDEIIALCTTFLLAGYETTSNLLAFTAYLLAMNPDKQEKLIQEIDKYYQDHKVI 740

GYIHLHQGAAIHLLEFIITHITRTFRICENTCTINGVTIPAGCYIVIPIQVLHQSVEHWEQPELFRPERF 437

SPDEKESRHPMCYMPFGAGPRNCIGMRFALMEAKMCLMNLLKKYKFERAPDTQ

VTEAEGCSVLLFSLILGSVKNSYWYYTVTS*

 

>CYP4C like gnl|ti|858493219 BAYA89713.y1 gnl|ti|858495906 BAYA89713.x1

MIRFCCWQRRLPLTSCIRWKATSTSSRVEDKAV

350 KPFSAIPSPPGSLPFVGHSRLLKDVTSFTKFAAKHSRELGPIFKLNMM 207

 

RLYPLIAFMPRMLDTDIDILGYHIPAK

TAILGGMEAMSQNPTLY

KDPLKFNPDRWSTDDIHPFTMLPFGFGPRACWG

HNDTVTTSSYIVIH

LIRHFKMESDFPKDRLPSSGLVLTRPSVPIRIKFTPCNQ*