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*