[Beg-bogas] [Fwd: Re: cytochrome P450s in Ectocarpus]

23 Oct 2007

      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
==============================================================

lieven sterck

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