is da een prob van buffering van de data stream da hij maar 601Kb krijgt ipv 728??? L. -------- Original Message -------- Subject: Re: cytochrome P450s in Ectocarpus Date: Tue, 23 Oct 2007 10:09:29 -0500 From: David Nelson <drnelson1@gmail.com> To: lieven sterck <lieven.sterck@psb.ugent.be> References: <d862fa170710201348oba00fb2i5367e7ce2b09e4b@mail.gmail.com> <471C6F29.9000504@psb.ugent.be> <d862fa170710221017i4ef554c7x3b4840c2cc7ae337@mail.gmail.com> <d862fa170710221211g3d88a30fna570812c65112ca4@mail.gmail.com> <13689.157.193.202.129.1193094062.squirrel@webmail.psb.ugent.be> <d862fa170710221811g6819eed7lbaa4969e338fbca8@mail.gmail.com> <d862fa170710230750l60cd4d5fj8b138c24f51a70e8@mail.gmail.com> <471E0AEC.2080305@psb.ugent.be> Dear Lieven, Thanks so much. I doubt most of these P450s will have ESTs, but it would sure make my life easier. I noticed a problem in recovering your sequences from the blast pages. When I clicked on the F next to the sequence name I got a display of the nucleotide sequence. There was a button that said save as FASTA. When I did this and opened the file on my computer it was missing quite a lot of sequence. Of the contig_63 that was 728,000 bp I only got 601,000 bp. However, if I selected the sequence off the display page and pasted into a Word document I got all 728,000bp. So there is some problem with the save as FASTA command. You might want to do a couple of checks. David On 10/23/07, *lieven sterck* <lieven.sterck@psb.ugent.be <mailto:lieven.sterck@psb.ugent.be>> wrote: Hi David, I just received the cleaned ESTs a couple of days ago. I will make this set also available on the blast page. regards, lieven David Nelson wrote:
Dear Lieven,
How can I Blast ESTs for Ectocarpus?
David
On 10/22/07, *David Nelson* <drnelson1@gmail.com <mailto:drnelson1@gmail.com>> wrote:
Dear Lieven,
Thanks for the tip. I had been clicking on the name next to the F. I thought they were both the same, I did not try the F. It worked.
David
On 10/22/07, * Lieven Sterck* <lieven.sterck@psb.ugent.be <mailto:lieven.sterck@psb.ugent.be>> wrote:
Hi David,
I could send you the scaffolds. But you should be able to extract them yourself: on the blast result page click on the 'F' left of the sequence name (next to the '>' sign) this will lead you to the actual sequence of the hit.
I will get you an invitation to the annotation site first thing in the morning.
don't hesitate to contact me if something is unclear!! regards, lieven
> Dear Lieven, > > There are only 10 contigs with P450 sequences. > Some are pretty short weak matches and may be accidental. >> F sctg_6 CYP51C1 >> F sctg_63 CYP97E3 and CYP97E4 >> F sctg_25 CYP97F-like seq >> F sctg_362 most like CYP5021A1 >> F sctg_1 bacterial chromosome with 14 P450s, all assembled >> F sctg_10 C-helix and I-helix parts >> F sctg_471 2 sequences only partially assembled >> F sctg_60 2 sequences only have the PERF motif (accidental?) >> F sctg_193 only the I-helix motif >> F sctg_81 poor match may be accidental (heme signature region) > > The current version of the blast server will not return any DNA sequence > to > me. I am not given permission to see the genome yet, so could you please > send me 9 of the contigs above so I can continue to assemble these P450 > genes. I do not need the sctg_1 since I have already completed those 14 > bacterial P450s. > > If the files are too large, > I only need the parts of them shown below > >> F sctg_6 1,170,000-1,200,000 >> F sctg_10 780,000-820,000 >> F sctg_25 950,000-970,000 >> F sctg_60 400,000-460,000 >> F sctg_63 330,000-370,000 >> F sctg_81 170,000-220,000 >> F sctg_193 150,000-200,000 >> F sctg_362 70,000-90,000 >> F sctg_471 30,000-80,000 > > Thanks. > > David Nelson > > > On 10/22/07, David Nelson <drnelson1@gmail.com <mailto:drnelson1@gmail.com>> wrote: >> >> Dear All, >> >> Can you make the pull down choices for the expect value in the blast >> server go up to 100 rather than stopping at 10? This may be helpful for >> finding distantly related exons. >> >> David >> >> On 10/22/07, lieven sterck <lieven.sterck@psb.ugent.be <mailto:lieven.sterck@psb.ugent.be>> wrote: >> > >> > Hi David, >> > >> > That's correct! Scaffold sctg_1 is indeed from a bacterial symbiont >> > found associated with (or within) ectocarpus. >> > There are some more scaffolds from this organism, a list: >> > sctg_1 >> > sctg_1222 >> > sctg_1301 >> > sctg_1320 >> > sctg_1403 >> > sctg_1415 >> > sctg_1432 >> > sctg_1769 >> > sctg_1876 >> > sctg_397 >> > sctg_627 >> > sctg_822 >> > sctg_853 >> > sctg_870 >> > sctg_886 >> > sctg_893 >> > >> > these scaffolds have recently been removed from the official assembly. >> > GenoScope (responsible for the sequencing) is finishing and analyzing >> > this bacterial symbiont. >> > >> > best regards, >> > lieven >> > >> > >> > David Nelson wrote: >> > >> > Dear all, >> > >> > I have begun looking over the P450s in Ectocarpus. >> > The biggest surprise was sctg_1 which had 14 P450s but they seem to be >> > bacterial. >> > >> > Here are the 14 P450s with their best matches. I compared them to >> 3305 >> > bacterial sequences from the Global Ocean Sequencing Project at the J >> Craig >> > Venter Institute. Some were a better match to those seawater >> sequences than >> > to named P450s. >> > >> > Since the whole contig of 3.4 Mb seems to be bacterial and often like >> > Caulobacter, I searched Genbank for a rRNA from Caulobacter. I found >> one >> > from a >> > >> > Caulobacter endosymbiont of Tetranychus urticae >> > AY753176 >> > ribosomal RNA gene, partial sequence. >> > >> > I used this for a blastn search of Ectocarpus. >> > I found a 90% match on the same contig as the 14 P450s (see below) >> > There is a Caulobacter-like endosymbiont or contaminant in the algae >> > genome data. >> > >> > I blasted the Ectocarpus bacterial rRNA seq against Genbank and found >> > a Sargasso Sea bacterioplankton as the best match >> > >> > >F sctg_1 >> > 3017346 aaagatttatcgcccctggatgggcccgcgt tggattagctagttggtggggtaatggcc >> > 3017405 >> > 3017406 taccaaggcgacgatccatagctggtctgagaggatgatcagccacactggaactgagac >> > 3017465 >> > 3017466 acggtccagactcctacgggaggcagcagtggggaatattggacaatgggcgcaagcctg >> > 3017525 >> > 3017526 atccagccatgccgcgtgagtgatgaaggccctagggttgtaaaactctttcagtggtga >> > 3017585 >> > 3017586 agataatgacggtaaccacagaagaagctccggctaactccgtgccagcagccgcggtaa >> > 3017645 >> > 3017646 tacggagggagctagcgttgttcggaattactgggcgtaaagcgcacgtaggcggtctat >> > 3017705 >> > 3017706 aaagttgggggtgaaatcccggagctcaactccggaactgcct 3017748 >> > >> > only 6 nucleotide diffs to >> > >gb|AY162106.1| Alpha proteobacterium GMD21A06 small subunit >> ribosomal >> > RNA gene, >> > partial sequence >> > Length=1326 >> > >> > isolation_source="Sargasso Sea bacterioplankton >> > >> > Score = 710 bits (384), Expect = 0.0 >> > Identities = 397/403 (98%), Gaps = 1/403 (0%) >> > Strand=Plus/Plus >> > >> > Query 1 >> > AAAGATTTATCGCCCCTGGATGGGCCCGCGTTGGATTAGCTAGTTGGTGGGGTAATGGCC 60
>> > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| >> > Sbjct 174 >> > AAAGATTTATCGCCCCTGGATGGGCCCGCGTTGGATTAGCTAGTTGGTGGGGTAATGGCC 233 >> > >> > Query 61 >> > TACCAAGGCGACGATCCATAGCTGGTCTGAGAGGATGATCAGCCACACTGGAACTGAGAC 120 >> > ||||||||||||||||||||||||||||||||||||||||||||||||||| |||| >> ||| >> > Sbjct 234 >> > TACCAAGGCGACGATCCATAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGTGAC 293 >> > >> > Query 121 >> > ACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAGCCTG 180 >> > |||| ||||||||||||||||||||||||||||||||||||||||||||||||||| >> ||| >> > Sbjct 294 >> > ACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGCGCAAG-CTG 352 >> > >> > Query 181 >> > ATCCAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAACTCTTTCAGTGGTGA 240
>> > |||||||||||||||||||||||||||||||||||||||||||| >> ||||||||||||||| >> > Sbjct 353 >> > ATCCAGCCATGCCGCGTGAGTGATGAAGGCCCTAGGGTTGTAAAGCTCTTTCAGTGGTGA 412 >> > >> > Query 241 >> > AGATAATGACGGTAACCACAGAAGAAGCTCCGGCTAACTCCGTGCCAGCAGCCGCGGTAA 300 >> > |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| >> > Sbjct 413 >> > AGATAATGACGGTAACCACAGAAGAAGCTCCGGCTAACTCCGTGCCAGCAGCCGCGGTAA 472 >> > >> > Query 301 >> > TACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCACGTAGGCGGTCTAT 360 >> > ||||||||||||||||||||||||||||||||||||||||||||| >> |||||||||||||| >> > Sbjct 473 >> > TACGGAGGGAGCTAGCGTTGTTCGGAATTACTGGGCGTAAAGCGCGCGTAGGCGGTCTAT 532 >> > >> > Query 361 AAAGTTGGGGGTGAAATCCCGGAGCTCAACTCCGGAACTGCCT 403 >> > ||||||||||||||||||||||||||||||||||||||||||| >> > Sbjct 533 AAAGTTGGGGGTGAAATCCCGGAGCTCAACTCCGGAACTGCCT 575 >> > >> > >> > > F sctg_1 (14 P450s from a bacterial genome in the Ectocarpus data) >> > Length = 3415905 >> > >> > >67% to CYP108B1 Caulobacter crescentus AE005918 >> > 158936 FAKLRKDTPLGVAGPQGFEPFWVVTKHKDIVEVERNNEVFHNGDKSTTLVDANTDTA >> 158766 >> > 158765 VREMMGGSPHLIRSLVQMDNPDHKNYRGITAANFMPQELKALEVQVRKIAKSFVDHMEEL >> > 158586 >> > 158585 GRKNDGRCDFAKDVAFLYPLHVIMELLGVPQSDEPKMLKLTQELFGAADPELNRTGKE >> 158412 >> > >> > 158411 RDDPKEALAALSGTVAEFVEYFTAVTEDRRKTPRADIASVIANGKVNGEAIGIFEAMGYY >> > 158232 >> > 158231 IIVATAGHDTTSGTTAGTMWELAKDRQKFLQVKNDPKLIPLLVEESIRWVTPVKHFMRSA >> > 158052 >> > 158051 TQDTVLGGQEIKKGDWMMLCYQSGNRDEDVFDDPFEFKVNRQPNRHIAFGHGAHVCLGQH >> > 157872 >> > 157871 LARMEMRALWEELLPRLDSVELDGEPTRMLANFVCGPKSVPIK 157743 >> > >> > >59% to CYP153A2 Caulobacter crescentus CB15 GenPept AAK22050 >> > 1458133 LFERLRNEDPVHFFEHEEFGRFWSVTRHADIMSIDTNHQQFSSEPSIFLGNTNSDEDENF >> > 1458312 >> > 1458313 NPATFIAMDPPKHDAQRNAVNPAVAPPALRDLEPLIRQRVSAVLDSLPIGETFNWVDLVS >> > 1458492 >> > 1458493 IEITTQMLATLFDFPFEDRYMLTRWSDMTTANPETLAAMGLTIEDRRNAMYECLEIFG >> > 1458666 >> > 1458667 GLYAERAQLPPANDFISLMAHNEDMKNLDPMNLLGNLVLLIVGGNDTTRNSMSGGVLAL >> > 1458843 >> > 1458844 HENPAEFAKLKADPSIIPNMVSEIIRWQTPLAYMRRTANEDLEFRGKQIKQGDRIMMWYV >> > 1459023 >> > 1459024 SGNRDERAIERPNEFLIDRENARRHLSFGFGIHRCMGNRVGEMQVRILWEEILKRFDRVE >> > 1459203 >> > 1459204 VVGKPARTLSNFVMGFTELPVRL 1459272 >> > >> > >50% to CYP108B1 Caulobacter crescentus AE005918 >> > 1535639 IFTTLRQDNPLACVEVPGYDPHWMVTKYSDVKEITRQDNLFHSGDRPKILHSQAGEA >> > 1535809 >> > 1535810 LARSFTGGSPNLFQSLVQLDPPEHTAYRNVLQGEFMPGGIAKMKENVAKTAQEFVDQMAS >> > 1535989 >> > 1535990 LAPTCDFADDVAMNYPLQVVLDIVGVPREHHPKMLQLTQWLFSYADPDLKRPGSDIT >> > 1536160 >> > 1536161 DPEEIIKTWNVVFTQFHEFFMPLVEARRANPKEDIASLIANAKINGESMEERKMISYFG >> > 1536337 >> > 1536338 ILATAGHDTTSATTALGMKMLAENPDMLARLKEKPDLIPSFVEECIRWGSPVQHFIRSAT >> > 1536517 >> > 1536518 EDYVLRGQTIRKGDLLYISYLSANRDEEEFDDPFTFKMDRAPNRHVGFGFGGHVCLGQH >> > 1536694 >> > 1536695 LARLEIRTIWQTLLPRLTEVELTGPVKFTESEFVCGPKSVPIR 1536823 >> > >> > >41% to CYP107AA1 Bradyrhizobium japonicum USDA 110 GenPept BAC51802 >> > 56% to seawater bacterial sequence JCVI_PEP_1096696260773 >> > 2052084 PYPAMNQLREKDPVNETPVGPWRISRHADVVDVFRNAPTSQTLADGSSPNMDDQDRRGS >> > 2052260 >> > 2052261 FRDFMLNMDGPEHARLRRLVLGAFTPKALKHIEGEIDRVVDEAMHTALKQGGMEVVEDFA >> > 2052440 >> > 2052441 LRIPSRMICRIMGLPEEDIDQFTVWTAARTNAFFARFLPEDVVEHTRQAGEQMAD >> 2052605 >> > 2052606 YFEAQIKLRRANPREDLLTNLIQSEEKGDRLGDVELAIQAIGLLIAGFETTIGLIGNGTK >> > 2052785 >> > 2052786 ALIENPDQAELLKQNPDLAKNTVEECLRYDTPVLFNWRVLTEPYEVGGKTLPENAVLWMM >> > 2052965 >> > 2052966 LGAANHDPRVHDDPDTMDITRQGISHASFGGGAHTCLGNQLARMEASRAFHAFVS >> 2053130 >> > >> > >JCVI_PEP_1096696260773 /source_dna_id=JCVI_ORF_1096696260772 >> > /offset=0 >> > /translation_table=11 /length=353 /full_length=353 >> > Length = 353 >> > >> > Score = 956 (336.5 bits), Expect = 3.3e-98, P = 3.3e-98 >> > Identities = 183/326 (56%), Positives = 227/326 (69%) >> > >> > Query: 1 >> > PYPAMNQLREKDPVNETPVGPWRISRHADVVDVFRNAPTSQTLADGSSPNMDDQDRRGSF 60 >> > PYP + LRE DPVN TPVG WRISR+ DV VF +APTS T G SPN D D >> > +GSF >> > Sbjct: 28 >> > PYPKLAHLRENDPVNLTPVGTWRISRYEDVKAVFNDAPTSMTDKLGDSPNFDPLDTKGSF 87 >> > >> > Query: 61 >> > RDFMLNMDGPEHARLRRLVLGAFTPKALKHIEGEIDRVVDEAMHTALKQGGMEVVEDFAL 120 >> > +F+LN DG H RLR LV +F K ++ +E E+ + V A A GGM+VV >> A >> > >> > Sbjct: 88 >> > LEFVLNKDGDAHRRLRMLVQKSFGQKTVRLMEEEVAKTVAAAFDKAQADGGMDVVPALAH 147 >> > >> > Query: 121 >> > RIPSRMICRIMGLPEEDIDQFTVWTAARTNAFFARFLPEDVVEHTRQAGEQMADYFEAQI 180 >> > +PSRMIC+IMG+P +D F WTAARTNAFFA+FLP DV E TR AG M DYF >> A >> > I >> > Sbjct: 148 >> > EVPSRMICQIMGVPMQDRQIFNEWTAARTNAFFAKFLPPDVQERTRNAGAAMEDYFRALI 207 >> > >> > Query: 181 >> > KLRRANPREDLLTNLIQSEEKGDRLGDVELAIQAIGLLIAGFETTIGLIGNGTKALIENP 240 >> > R+ + +DLL+++I + E GD+ D EL IQAIG+++AG+ETTIGL+GNGT+A >> > +E+P >> > Sbjct: 208 >> > AERKRDLGDDLLSSMIMASEGGDKFTDDELIIQAIGVIVAGYETTIGLLGNGTRAFVEHP 267 >> > >> > Query: 241 >> > DQAELLKQNPDLAKNTVEECLRYDTPVLFNWRVLTEPYEVGGKTLPENAVLWMMLGAANH 300 >> > DQ L+ NP+L N +ECLRYDTP+LFNWRVL EPYE+ G TLP AV+W >> +LGAAN >> > >> > Sbjct: 268 >> > DQLAKLRNNPELVSNATDECLRYDTPILFNWRVLEEPYELSGVTLPAEAVIWQLLGAANR 327 >> > >> > Query: 301 DPRVHDDPDTMDITRQGISHASFGGG 326 >> > DP DPD DI R+ ++H SFGGG >> > Sbjct: 328 DPARFADPDQFDIEREDVAHQSFGGG 353 >> > >> > >37% to CYP107L2 SAV1987 AP005029 Streptomyces avermitilis >> > 2103582 DLHSYAFESNPEPTLAWLREHDPVHWSQHGYWFVTRYEDVRAVLGDPARFSSQKAGFGA >> > 2103406 >> > 2103405 NNPIGKDAKGPEGKSGKKASDAEKTMSKGLALSFNQQDPPDHSRVRKLVNQAFSRREISE >> > 2103226 >> > 2103225 RADKIQAVVDALMADVKAKGEFDLITDFAFHLPIIVASDIIGIPAEDRDLFRRNFELAA >> > 2103049 >> > 2103048 RLMAPKRSDEEWAEALTGAKWQSTYMGELIASRAREPRADLISALIQTSEDDQKLT >> 2102881 >> > >> > 2102880 GGEVASAIMTIFTAAGTTTERMISSGAFLLLTHPEQLAALRADHSLMDNVLEEILRFHHP >> > 2102701 >> > 2102700 NQSTSTNRRATQDVELGGKTIRAGDTVRVSLGSANRDAAQFDEPDAFNIQRTGTKHMSFG >> > 2102521 >> > 2102520 FGIHFCLGSALARYETKAALEALL 2102449 >> > >> > >57% to CYP153A2 Caulobacter crescentus at C-term >> > 70% to seawater bacterial sequence JCVI_PEP_1096681995831 >> > 2416172 MTTANQTSPNGAIDVNDIPLAELDVSQPHLFKNDTWRPWFARLRAEAPVHYLADSENG >> > 2416345 >> > 2416346 PFWSVTSHDMTKAVDANHKVFSSEEGGIAIVDPQPLDGEQLMRDPSFISMDEPKHATQRK >> > 2416525 >> > 2416526 AVSPAVAPKNLAELEPLIRERAADILDNLPVGETFNWVDRVSVELTARMLATLFDFPYER >> > 2416705 >> > 2416706 RRDLIRWSDVATAVPKVTGEANDMGARRDALIECATTFYQLWQERAAQPPKFDFVSM >> > 2416876 >> > 2416877 LAHGEATKHLSEDPLLMLGNIILLIVGGNDTTRNSISGGVVALNQYPEEYQKLRDTPAL >> > 2417053 >> > 2417054 IPNMVAETVRWQTPVIHMRRTALEDVELGGKTIRKGDKVVMWYLSGNRDEAVFPDADRLI >> > 2417233 >> > 2417234 IDRPNARQHVSFGFGVHRCMGNRLAEMQLRVLWEEIMKRFHTVEVVGEVERLSNNFI >> > 2417404 >> > 2417405 RGIASVPVRL 2417434 >> > >> > >JCVI_PEP_1096681995831 /source_dna_id=JCVI_ORF_1096681995830 >> > /offset=0 >> > /translation_table=11 /length=418 /full_length=418 >> > Length = 418 >> > >> > Score = 1567 (551.6 bits), Expect = 5.9e-163, P = 5.9e-163 >> > Identities = 290/409 (70%), Positives = 346/409 (84%) >> > >> > Query: 13 >> > IDVNDIPLAELDVSQPHLFKNDTWRPWFARLRAEAPVHYLADSENGPFWSVTSHDMTKAV 72 >> > ID + PL ELDVS P ++NDTWRP FARLR EAPVHYL+DS NGPFWSVTSH + >> K >> > V >> > Sbjct: 7 >> > IDNSSGPLRELDVSLPEHYENDTWRPMFARLRKEAPVHYLSDSVNGPFWSVTSHALIKEV 66 >> > >> > Query: 73 >> > DANHKVFSSEEGGIAIVDPQPLDGEQLMRDPSFISMDEPKHATQRKAVSPAVAPKNLAEL 132 >> > DAN+ +FSSE+GGI+IVD +P++G+ ++ +FI+MDEP+H+ QR AV+P+VAPKNL >> > EL >> > Sbjct: 67 >> > DANNSIFSSEKGGISIVDLKPVEGQ--VQGKNFIAMDEPEHSIQRSAVAPSVAPKNLVEL 124 >> > >> > Query: 133 >> > EPLIRERAADILDNLPVGETFNWVDRVSVELTARMLATLFDFPYERRRDLIRWSDVATAV 192 >> > EPLIRERA DIL+NLPVGETFNWV VS+ELTARML T+ DFPY++R >> L++WSD+AT >> > V >> > Sbjct: 125 >> > EPLIRERAVDILENLPVGETFNWVQEVSIELTARMLTTILDFPYDQRHKLVQWSDLATDV 184 >> > >> > Query: 193 >> > PKVTG-EANDMGARRDALIECATTFYQLWQERAAQPPKFDFVSMLAHGEATKHLSEDPLL 251 >> > P+VTG E DM AR D L+ CA FYQLW ++ QPP FD +SML + T ++ED >> > L >> > Sbjct: 185 >> > PQVTGKEGTDMQARYDELMNCAAAFYQLWVSKSGQPPSFDLISMLQNNPDTARMNEDMEL 244 >> > >> > Query: 252 >> > MLGNIILLIVGGNDTTRNSISGGVVALNQYPEEYQKLRDTPALIPNMVAETVRWQTPVIH 311 >> > LGN++LLIVGGNDTTRNSISGGV+ALNQYP+EYQKLRD PALIPNMV+E >> > +RWQTPVIH >> > Sbjct: 245 >> > FLGNMLLLIVGGNDTTRNSISGGVMALNQYPDEYQKLRDNPALIPNMVSEIIRWQTPVIH 304 >> > >> > Query: 312 >> > MRRTALEDVELGGKTIRKGDKVVMWYLSGNRDEAVFPDADRLIIDRPNARQHVSFGFGVH 371 >> > MRRTALED ELGG+ I+KG+KV+MWYLSGNRDE+VF D DRLIIDRPNAR >> > HV+FGFGVH >> > Sbjct: 305 >> > MRRTALEDYELGGQHIKKGEKVIMWYLSGNRDESVFEDPDRLIIDRPNARSHVAFGFGVH 364 >> > >> > Query: 372 RCMGNRLAEMQLRVLWEEIMKRFHTVEVVGEVERLSNNFIRGIASVPVRL 421 >> > RCMGNR+AE+QLRVLWEEIM+RFHT+EVVG++ RL NNFIRGI VPVR+ >> > Sbjct: 365 RCMGNRMAELQLRVLWEEIMERFHTIEVVGDITRLPNNFIRGIKEVPVRV 414 >> > >> > >58% to CYP153B4 Rhodopseudomonas palustris NZ_AAAF01000001 gene = >> > Rpal2887 >> > 2455381 FPIFEKMRAEEPVHYCAESTYGPYWSVTRYEDIMAVDTNHQVYSSEADFGGIVID >> 2455217 >> > 2455216 DRIAIDPETNYKSASFISMDQPKHDDQRKSVNGITNPNNLQYFGDIIRTRTVNMLDSLPV >> > 2455037 >> > 2455036 GEEFDWVPTVSIELTTQMLATLFDFPFEDRHKLTRWSDVITAEPESDIVENQE 2454878 >> > 2454877 ARVAELNEMAEYFVELQKGRINKPDSIDLLTMMTHSPAMAKMPPEEFMGNLALLIVGGN >> > 2454701 >> > 2454700 DTTRNSMSGSIFGMHLFPDEFKKMVDDPSLTDNAVAEIIRWQTPLSHMRRTALQDAVL >> > 2454527 >> > 2454526 GGKQIRKGDKVVMWYASGNRDTSIFDDPDKIIIDRKNARRHLSFGFGIHRCMGNRIGELQ >> > 2454347 >> > 2454346 LRILWEEILKRFSRVEVTGEPVLTHSNFVKGYASLPVKL 2454230 >> > >> > >59% to CYP153A2 Caulobacter crescentus CB15 GenPept AAK22050 >> > 2456653 FPIFEQMRQEDPVHYCAESTYGPYWSVTRYEDIMAVDTNHHVYSSDAHLGGIIID >> 2456489 >> > 2456488 DGIQNDPENDFKAVNFIAMDKPKHDEQRKSVNGITNPNNLQHFGEIIRKRTSNLLDSLPV >> > 2456309 >> > 2456308 GEEFDWVSTVSIELTTQMLATMFDFPFEDRHKLTRWSDVSTAEPGSGIVETQQQRI >> 2456141 >> > 2456140 DELMEMAAYFSDLQQSRKDKPDNIDLLTMMTHSPAMANMPPEEFLGNLSLLIVGGNDTT >> > 2455964 >> > 2455963 RNSMTGGVFGFSLFPEQWDKMVADPTLIDNAVAEIIRWQTPLAHMRRTALEDAILGG >> > 2455793 >> > 2455792 KQIRKGDKVVMWYASGNRDTSIFDDPDKIIIDRKNARRHLSFGFGIHRCMGNRIGELQLR >> > 2455613 >> > 2455612 ILWEEVLKRFSRIEVTGEPELTNSNFVKGYTSLPVKL 2455502 >> > >> > >68% to CYP153A2 Caulobacter crescentus CB15 GenPept AAK22050 >> > 2728456 PYFERLRKEAPVHKAYSPDFGEYWSVTRYEDIMAVDTNHHVFSSSWEHGGITLFDQISDF >> > 2728635 >> > 2728636 QLPMFIAMDPPKHDQQRITVQPIVAPNNLKNWEGLIRERTGQILDSLPRGEVFDWVDNVS >> > 2728815 >> > 2728816 VELTTMMLATLFDFPFEQRRKLTRWSDVATGRNNPEIVADDDQWRAELLECLEAFT >> 2728983 >> > 2728984 DIWNERINSDTPGNDLITMLTRGESTKNMDPMEYLGNIILLIVGGNDTTRNSMTASVYA >> > 2729160 >> > 2729161 LNKFAGEYDKLLAKPDLIPNLSSEIIRWQTPLAHMRRTALEDIVLNGAHIKKGDKVAMWY >> > 2729340 >> > 2729341 VSGNRDESVFEDADKVIIDRPNARRQMSFGYGIHRCVGNRLGELQIKILWEEILKRFPKI >> > 2729520 >> > 2729521 EVMEEPTRTKSVFVKGYTYMPVRI 2729592 >> > >> > >71% to CYP153A2 Caulobacter crescentus CB15 GenPept AAK22050 >> > 2729740 MPLEDINVADGALFQDDAIWPYFERLRKEAPVHKGHSDEFGDYWSVTRYEDIMAVDTNHH >> > 2729919 >> > 2729920 VFSSEGAITLADPLEDFRAPMFIAMDPPKHDKQRITVQPIVAPKNLQNWEGLIRERTGLI >> > 2730099 >> > 2730100 LDQLPRNETFDWVDKVSIELTTMMLATLFDFPFEERRRLTRWSDVATGRDNPEIYK >> 2730267 >> > 2730268 SEEQWRGELMECLEAFTGLWNDRVNSDTPGNDLISMLASGESTKNMDPMEYLGNIILLI >> > 2730444 >> > 2730445 VGGNDTTRNSMTGSVYALNKFAGEYDKLIADPSLIPNLSSEIIRWQTPLAHMRRTALEDI >> > 2730624 >> > 2730625 ELNGQMIKKGDKVAMWYVSGNRDTAVFENADDVIIDRPNARRQMSFGYGIHRCVGNRLGE >> > 2730804 >> > 2730805 LQIKILWEELLKRFPKIEVMEEPTRTRSPFVKGYTYMPVRI 2730927 >> > >> > >68% to CYP153A2 Caulobacter crescentus CB15 GenPept AAK22050 >> > 2731076 MPLNEINPARRDLFQNDVIWPYFERLRKEAPVHKAYDEDFGEYWSVTRYEDIMAVDTNHH >> > 2731255 >> > 2731256 VFSSDWTNGGITLFDAAEDFRLPMFIAMDPPKHDQQRITVQPIVAPNNLKNWEGLIRERT >> > 2731435 >> > 2731436 AYVLDSLPRGETFDWVDNVSIELTTMMLATLFDFPFEERRKLTFWSDMVTTDPKT >> 2731600 >> > 2731601 LEGGVEEKRGHLLACLEYFTGLWNERINSDTPGNDLITMLTRGESTKNMDPMEYLGNI >> > 2731774 >> > 2731775 ILLIVGGNDTTRNSMTASVYGLNKFPGEYDKLIADPSLIPNLSSEIIRWQTPLAHMRRTA >> > 2731954 >> > 2731955 LEDIELNGTMIKKGDKVAMWYVSGNRDADVFENADDIIIDRPNARRQMSFGYGIHRCVGN >> > 2732134 >> > 2732135 RLGELQIKILWEEILKRFPKIELMEEPTRTPGCFVKGYTYMPVRI 2732269 >> > >> > >68% to CYP153A2 Caulobacter crescentus CB15 GenPept AAK22050 >> > 2732420 MPLNEFNPAQRDLFQNDVIWPYFERLREEAPVHKCFDEEFGEYWSVSSYEHIMAVDTNHQ >> > 2732599 >> > 2732600 VFSSSWEHGGITLFDGPEDFQLPMFIAMDQPKHDEQRKTVQPIVAPNNLKSWEPLIRERT >> > 2732779 >> > 2732780 GMVLDSLPRGETFDWVDNVSIELTTMMLATLFDFPFEDRRKLTFWSDMVTTDAN 2732941 >> > 2732942 TLEGGEEEWKGHLLECLAYFTELWNQRINSDKPGNDLITMLTRGEATKNMDPMEYLGN >> > 2733115 >> > 2733116 IILLIVGGNDTTRNSMTGSVYALNKFPTEYDKLIADPGLIPNLSSEIIRWQTPLAHMRRT >> > 2733295 >> > 2733296 ALEDFELGGKMIKKGDKVAMWYVSGNRDKTVFENADDVIIDRANARRQMSFGYGIHRCVG >> > 2733475 >> > 2733476 NRLGELQIMILWEEILKRFPKIELMAEPTRSPGCFVKGYTYMPVRI 2733613 >> > >> > >33% to CYP107L1 AF087022 Streptomyces venezuelae cytochrome P. = >> pikC >> > gene >> > AF079139, 50% to seawater bacterial sequence JCVI_PEP_1096680833653 >> > 302400 PYPLYTRLRPHAPVQGYRDYPPGTVPGEDEPVNAWVLLDYDQVSKAARDHRTFSSRDPLQ >> > 302221 >> > 302220 EGSSAPTLMLVNHDNPEHDRLRNIVNLAFSRKRIEELSPYVSKMVHTLLDEVESASGGKV >> > 302041 >> > 302040 EAMSDICAALPARVMVHLLGLPNEIAAKFRHWGTAFMLSADLTPEERQTSNV 301885 >> > 301884 ELYTYFVEQVTAMDEALAAGKDVPDSLMRALLTAEADGEKLTRDEVIRFCLTLVVAGAE >> > 301708 >> > 301707 TTTFLLGNLLHHLATMPEMTERLRANRDDIEGFMNESLRHSGPPQRLFRIAEADVEVGGQ >> > 301528 >> > 301527 QIRKGDWVALFFAAANHDPAMFPDPEKFDIDRTNLNKQLTFGVGVHHCLGSALAKAEARE >> > 301348 >> > 301347 LMNALL 301330 >> > >> > >JCVI_PEP_1096680833653 /source_dna_id=JCVI_ORF_1096680833652 >> > /offset=0 >> > /translation_table=11 /length=250 /full_length=250 >> > Length = 250 >> > >> > Score = 586 ( 206.3 bits), Expect = 5.3e-59, P = 5.3e-59 >> > Identities = 118/234 (50%), Positives = 160/234 (68%) >> > >> > Query: 1 >> > AFPYPLYTRLRPHAPVQGYRDYPPGTVPGEDEPVNAWVLLDYDQVSKAARDHRTFSSRDP 60 >> > A PYP Y +LR +PV GY D PPGTVPG+DEP +W +L + V +AARD +TFSS >> > DP >> > Sbjct: 20 >> > ANPYPYYDQLRAASPVHGYVDLPPGTVPGQDEPKISWAVLRHADVVEAARDAQTFSSADP 79 >> > >> > Query: 61 >> > LQEGSSAPTLMLVNHDNPEHDRLRNIVNLAFSRKRIEELSPYVSKMVHTLLDEVESASGG 120 >> > LQ S+APTLMLVN D P H +LR I + AF+ +RI E P+V+++ +L + >> > GG >> > Sbjct: 80 >> > LQAESTAPTLMLVNDDPPRHSKLRAIAHKAFTPRRILEKGPWVAQVAAEIL----APCGG 135 >> > >> > Query: 121 >> > KV-EAMSDICAALPARVMVHLLGLPNEIAAKFRHWGTAFMLSADLTPEERQTSNVELYTY 179 >> > + + M+D+ LP RVM ++G+ + A +FR+W TAFMLSADLTP R+ SN E+ >> > + >> > Sbjct: 136 >> > RCFDFMTDVAPVLPTRVMAKVIGVDDAQAPRFRNWATAFMLSADLTPAAREASNREVAAF 195 >> > >> > Query: 180 FVEQVTAMDEALAAGKDVPDSLMRALLTAEADGEKLTRDEVIRFCLTLVVAGAET >> 234 >> > FV+ V + G D PD L+ AL+ ++DG++LTRDEV RFC+TL+VAGAET >> > Sbjct: 196 FVDHVNRRYALIERGGDPPDDLVTALILEDSDGQRLTRDEVTRFCITLLVAGAET >> 250 >> > >> > >48% to CYP191A1 Caulobacter crescentus CB15 GenPept AAK22930 >> > 75% to seawater bacterial sequence JCVI_PEP_1096682145269 >> > 3343360 PHEFYKTMRESAPVMWSDIRKGGDGFWSVSRYDDLKAVELAPTVFSSERGSINLGVAPKD >> > 3343181 >> > 3343180 KWKPEKLVSAALNALINLDAPRHMEMRIQQMDFFAPAYVATLRDKVSAKIDSLLDDMESK >> > 3343001 >> > 3343000 GPVVDMVPVFSEQLPLFTLCEMLGVDEEDRPKIAHWMHYLELASQYLTNPWQVIIKEPLF >> > 3342821 >> > 3342820 PFRFFKAVKDMFAYGEAIMADRRANPREDLLTAIAKTKLSDEELPQEFL 3342674 >> > 3342673 DGSWLLIIFAGNDTSRNSLSGTIRLMTEFPDQRQMVLDDPSLIPRMSQEALRMISPVRHM >> > 3342494 >> > 3342493 RRTAVEDTEINGQRIAKDEKVVLWYGAANRDPSMFPDPDRFDMMRDSVDKHLAFGHGVHK >> > 3342314 >> > 3342313 CLGSRIAQMQ 3342284 >> > >> > >JCVI_PEP_1096682145269 /source_dna_id=JCVI_ORF_1096682145268 >> > /offset=0 >> > /translation_table=11 /length=367 /full_length=367 >> > Length = 367 >> > >> > Score = 1279 (450.2 bits), Expect = 1.9e-132, P = 1.9e-132 >> > Identities = 236/312 (75%), Positives = 273/312 (87%) >> > >> > Query: 48 >> > ERGSINLGVAPKDKWKPEKLVSAALNALINLDAPRHMEMRIQQMDFFAPAYVATLRDKVS 107 >> > +RGSIN+ V + WKPEKL AA N+LINLDAP HMEMR+QQ +FF PAY+ >> TLRDKV >> > >> > Sbjct: 1 >> > QRGSINMMVGDRKLWKPEKLAPAAFNSLINLDAPAHMEMRMQQSEFFFPAYIETLRDKVE 60 >> > >> > Query: 108 >> > AKIDSLLDDMESKGPVVDMVPVFSEQLPLFTLCEMLGVDEEDRPKIAHWMHYLELASQYL 167 >> > AKID++LD++E +GPVVD +FSE+LPLFTLCEMLG+DEEDRP+I WMH+LELA >> > Q+L >> > Sbjct: 61 >> > AKIDAMLDELERQGPVVDFAKLFSEELPLFTLCEMLGIDEEDRPRIKLWMHHLELAGQFL 120 >> > >> > Query: 168 >> > TNPWQVIIKEPLFPFRFFKAVKDMFAYGEAIMADRRANPREDLLTAIAKTKLSDEELPQE 227 >> > NPWQ + EP+FPFRF K V++MFA+GE IM DRRANPR+DLLT IA++KL E >> > LPQE >> > Sbjct: 121 >> > ANPWQTFLSEPMFPFRFNKVVQEMFAFGERIMKDRRANPRDDLLTVIAQSKLEGELLPQE 180 >> > >> > Query: 228 >> > FLDGSWLLIIFAGNDTSRNSLSGTIRLMTEFPDQRQMVLDDPSLIPRMSQEALRMISPVR 287 >> > +LDGSWLLIIFAGNDTSRNSLSGTIRLMTEFP QR >> +VLDDPSLIP+MS+EALRM+SPV >> > >> > Sbjct: 181 >> > YLDGSWLLIIFAGNDTSRNSLSGTIRLMTEFPTQRTLVLDDPSLIPQMSEEALRMVSPVI 240 >> > >> > Query: 288 >> > HMRRTAVEDTEINGQRIAKDEKVVLWYGAANRDPSMFPDPDRFDMMRDSVDKHLAFGHGV 347 >> > HMRRTAVEDTEINGQ IAKDEKVVLWYGAANRDP +FPDPD F++ >> > RD+V+KHLAFGHGV >> > Sbjct: 241 >> > HMRRTAVEDTEINGQPIAKDEKVVLWYGAANRDPDIFPDPDTFNLHRDNVEKHLAFGHGV 300 >> > >> > Query: 348 HKCLGSRIAQMQ 359 >> > HKCLGSRIA+MQ >> > Sbjct: 301 HKCLGSRIAKMQ 312 >> > >> > >> > -- >> > David R. Nelson >> > Associate Professor >> > Dept. of Molecular Sciences >> > 858 Madison Ave. Suite G01 >> > University of Tennessee >> > Memphis TN 38163 >> > (901) 448-8303 phone >> > (901) 448-7360 fax >> > dnelson@utmem.edu <mailto:dnelson@utmem.edu> >> > >> > >> > -- >> > ============================================================== >> > Lieven Sterck Predoctoral fellow >> > >> > Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 >> > >> > VIB Department of Plant Systems Biology, UGent >> > Bioinformatics and Evolutionary Genomics Division >> > Technologiepark 927, B-9052 Gent, Belgium >> > Email: >> > lieven.sterck@psb.ugent.be <mailto:lieven.sterck@psb.ugent.be> >> > Website: http://bioinformatics.psb.ugent.be >> > >> > --------------------------------------------------------------
>> > Algal Genetics Group >> > UMR 7139 CNRS-UPMC >> > Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) >> > Station Biologique >> > Place Georges Teissier, BP74 >> > >> > 29682 Roscoff Cedex, France >> > Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html >> > >> > ==============================================================
>> > >> > >> >> >> -- >> David R. Nelson >> Associate Professor >> Dept. of Molecular Sciences >> 858 Madison Ave. Suite G01 >> University of Tennessee >> Memphis TN 38163 >> (901) 448-8303 phone >> (901) 448-7360 fax >> dnelson@utmem.edu <mailto:dnelson@utmem.edu> >> > > > > -- > David R. Nelson > Associate Professor > Dept. of Molecular Sciences > 858 Madison Ave. Suite G01 > University of Tennessee > Memphis TN 38163 > (901) 448-8303 phone > (901) 448-7360 fax > dnelson@utmem.edu <mailto:dnelson@utmem.edu> >
--
David R. Nelson Associate Professor Dept. of Molecular Sciences 858 Madison Ave. Suite G01 University of Tennessee Memphis TN 38163 (901) 448-8303 phone (901) 448-7360 fax dnelson@utmem.edu <mailto:dnelson@utmem.edu>
-- David R. Nelson Associate Professor Dept. of Molecular Sciences 858 Madison Ave. Suite G01 University of Tennessee Memphis TN 38163 (901) 448-8303 phone (901) 448-7360 fax dnelson@utmem.edu <mailto:dnelson@utmem.edu>
-- ============================================================== Lieven Sterck Predoctoral fellow Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be <mailto:lieven.sterck@psb.ugent.be> Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html <http://www.sb-roscoff.fr/UMR7139/en/genetics.html> ============================================================== -- David R. Nelson Associate Professor Dept. of Molecular Sciences 858 Madison Ave. Suite G01 University of Tennessee Memphis TN 38163 (901) 448-8303 phone (901) 448-7360 fax dnelson@utmem.edu <mailto:dnelson@utmem.edu> -- ============================================================== Lieven Sterck Predoctoral fellow Tel:+32 (0)9 3313821 Fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Division Technologiepark 927, B-9052 Gent, Belgium Email: lieven.sterck@psb.ugent.be Website: http://bioinformatics.psb.ugent.be -------------------------------------------------------------- Algal Genetics Group UMR 7139 CNRS-UPMC Végétaux Marins et Biomolécules (Marine Plants and Biomolecules) Station Biologique Place Georges Teissier, BP74 29682 Roscoff Cedex, France Website: http://www.sb-roscoff.fr/UMR7139/en/genetics.html ==============================================================