Mesoplasma florum:Recombination: Difference between revisions

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(New page: S. citri GII3-3X genome analysis Three groups of recT homologs: Group 1: * CAL00077 = CAK99381 * CAK98970 is an N-terminal deletion, CAK98971 is a C-terminal deletion * CAK98977 is a C-...)
 
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See Iyer 2002  PMID 11914131


S. citri GII3-3X genome analysis
S. citri GII3-3X genome analysis
Line 17: Line 20:
* CAK99166 identical to N terminus of CAK99906
* CAK99166 identical to N terminus of CAK99906


----


Group 1 gene order and homologs
* CAK99376
* CAK99376
** CAK99599
** CAK99599
Line 50: Line 55:
** CAK98970 (c terminal del)
** CAK98970 (c terminal del)


* CAK99382 endonuclease HNH gp54
* CAK99382 endonuclease HNH endonuclease gp54
** CAK98972
** CAK98972
** CAL00076
(CAL00075 is an n-adenine methylase)


* CAK99383 (random)
* CAK99383 (random)
----
Group 3 gene order and homologs
* CAK99903 no similar genes
* CAK99904
** CAK99287
** CAK99927
* CAK 99905  (sbcC?)
** CAK99286
** CAK99167 (N) CAK99168 (C)
** CAK99065
* CAK99906 (recT)
** CAK99285 (c)
** CAK99166 (n)
* CAK99907
** CAK99284
** CAK99165
** CAK99581
* CAK99908 n-6 adenine methylase
** CAK99164
** CAK99365
----
Group 2
* CAK99576
** CAK99904
* CAK99577
** CAK99904
* CAK99578  ssb
** CAK99924
** CAL00079
** CAK98392
** CAK99379
* CAK99579
** CAK99667
** CAK98393
* CAK99580  recT
** CAK98666
** CAK98394
* CAK99581
** CAK99907
** CAK99284
** CAK99294
** CAK99165
* CAK999582  pentapeptide
** CAL00071
** CAK99909
==CAL00077, CAK99381 protein and nucleotide sequences==
LOCUS      AM285338                855 bp    DNA    linear  BCT 01-JUL-2006
DEFINITION  Spiroplasma citri GII3-3X chromosome, contig ContigNP17.
ACCESSION  AM285338 REGION: complement(4198..5052)
VERSION    AM285338.1  GI:110005766
KEYWORDS    .
SOURCE      Spiroplasma citri
  ORGANISM  Spiroplasma citri
            Bacteria; Firmicutes; Mollicutes; Entomoplasmatales;
            Spiroplasmataceae; Spiroplasma.
REFERENCE  1
  AUTHORS  Carle,P., Saillard,C., Blanchard,A., Carrere,N., Carrere,S.,
            Duret,S., Eveillard,S., Gaurivaud,P., Gourgues,G., Gouzy,J.,
            Henry,A., Salar,P., Laigret,F., Bove,J.M., Renaudin,J. and
            Foissac,X.
  TITLE    The partial chromosome sequence of Spiroplasma citri GII3-3X
  JOURNAL  Unpublished
REFERENCE  2  (bases 1 to 855)
  AUTHORS  Foissac,X.
  TITLE    Direct Submission
  JOURNAL  Submitted (28-JUN-2006) Foissac X., UMR 1090 GDPP, INRA, Universite
            V. Segalen Bordeaux2, 71 avenue E. Bourlaux, BP81, Villenave
            d'Ornon, 33883, FRANCE
FEATURES            Location/Qualifiers
    source          1..855
                    /organism="Spiroplasma citri"
                    /mol_type="genomic DNA"
                    /strain="GII3-3X"
                    /specific_host="Circulifer haematoceps"
                    /db_xref="taxon:2133"
                    /country="Morocco"
                    /note="ContigNP17"
    gene            1..855
                    /gene="yqaK"
                    /locus_tag="SPICINP17_006"
    CDS            1..855
                    /gene="yqaK"
                    /locus_tag="SPICINP17_006"
                    /old_locus_tag="SCi01660"
                    /function="macromolecule metabolism; macromolecule
                    synthesis, modification; dna - replication, repair,
                    restr./modif."
                    /inference="ab initio prediction:FrameD"
                    /codon_start=1
                    /transl_table=4
                    /product="putative rect protein"
                    /protein_id="CAL00077.1"
                    /db_xref="GI:110005772"
                    /translation="MNNKIELILNNSKVNNWINEKLTNQKEINLFRKNILTIYNNNPN
                    LFDKEKINLMSVLSACVKAMLLDLPLDPNLGYAYIVPYNGKGQLQIGYKGYIQLAIRT
                    GKYLTINAIEVKQGELLNFDELEQEYNFKWITNENERTKKETIGYVAFFKLLNGYKKT
                    LYWSKEKCENHFKTYSKNYQTYGKFTAGSYEGMALKTVLTQLLRKWGIMSVEMQEAYQ
                    HDQAIIINNSKEFSDNPNIKNKEDNNVIELNNKKDELNLNLEQEFSSNEINDDEEIAK
                    AVNEMFSD"
ORIGIN     
        1 atgaataata aaattgaatt aatattaaat aattcaaaag ttaataattg aattaatgaa
      61 aaattaacaa atcagaaaga aattaattta tttcgtaaaa atatcttaac aatttataat
      121 aataatccca atttatttga taaagaaaaa ataaatttaa tgagtgtttt atctgcttgt
      181 gtaaaagcaa tgttattaga tttaccgtta gaccctaact taggatatgc ctatattgtt
      241 ccatataatg gaaaaggaca gttgcaaatt ggttataagg gttatattca gttagcaatc
      301 cgaacaggaa aatatttaac aataaacgca atagaagtaa aacaaggtga attattaaat
      361 tttgatgaat tagaacaaga atacaatttt aaatgaataa ccaacgaaaa tgaacgaaca
      421 aaaaaagaaa caatcggata tgttgcattt tttaaactac taaatggtta taaaaaaact
      481 ttatattgaa gtaaagaaaa atgcgaaaat cattttaaaa catattctaa gaattatcaa
      541 acttacggaa aatttacggc tggaagttat gaggggatgg cacttaaaac agtattaacc
      601 caacttttaa gaaaatgagg tattatgtca gttgaaatgc aagaagccta tcaacatgat
      661 caagcaataa ttattaataa cagcaaagag tttagtgata atcctaacat aaaaaataaa
      721 gaagataaca atgttattga attaaataac aaaaaagatg aattaaatct aaatttagaa
      781 caagaattta gcagtaatga aataaatgat gatgaagaaa ttgctaaagc tgttaatgaa
      841 atgttttctg attaa
//
>gi|110005766:c5052-4198 Spiroplasma citri GII3-3X chromosome, contig ContigNP17
ATGAATAATAAAATTGAATTAATATTAAATAATTCAAAAGTTAATAATTGAATTAATGAAAAATTAACAA
ATCAGAAAGAAATTAATTTATTTCGTAAAAATATCTTAACAATTTATAATAATAATCCCAATTTATTTGA
TAAAGAAAAAATAAATTTAATGAGTGTTTTATCTGCTTGTGTAAAAGCAATGTTATTAGATTTACCGTTA
GACCCTAACTTAGGATATGCCTATATTGTTCCATATAATGGAAAAGGACAGTTGCAAATTGGTTATAAGG
GTTATATTCAGTTAGCAATCCGAACAGGAAAATATTTAACAATAAACGCAATAGAAGTAAAACAAGGTGA
ATTATTAAATTTTGATGAATTAGAACAAGAATACAATTTTAAATGAATAACCAACGAAAATGAACGAACA
AAAAAAGAAACAATCGGATATGTTGCATTTTTTAAACTACTAAATGGTTATAAAAAAACTTTATATTGAA
GTAAAGAAAAATGCGAAAATCATTTTAAAACATATTCTAAGAATTATCAAACTTACGGAAAATTTACGGC
TGGAAGTTATGAGGGGATGGCACTTAAAACAGTATTAACCCAACTTTTAAGAAAATGAGGTATTATGTCA
GTTGAAATGCAAGAAGCCTATCAACATGATCAAGCAATAATTATTAATAACAGCAAAGAGTTTAGTGATA
ATCCTAACATAAAAAATAAAGAAGATAACAATGTTATTGAATTAAATAACAAAAAAGATGAATTAAATCT
AAATTTAGAACAAGAATTTAGCAGTAATGAAATAAATGATGATGAAGAAATTGCTAAAGCTGTTAATGAA
ATGTTTTCTGATTAA
* no CGG codons, four TGA codons
* GC percentage 24%
* Isochore here:
[[image:recT-SC-isochore.png]]
==Upstream promoter for recT gene==
aaaatgtaaa aatataaaat tatgcttttt tacaaaATTA CAtaaatata attgctattc
gTGTTATTTg tgaaaaataa aaaAGGAGAa aaaataaa
[[category:Mesoplasma florum]]

Latest revision as of 14:46, 8 April 2008

See Iyer 2002 PMID 11914131


S. citri GII3-3X genome analysis

Three groups of recT homologs:

Group 1:

  • CAL00077 = CAK99381
  • CAK98970 is an N-terminal deletion, CAK98971 is a C-terminal deletion
  • CAK98977 is a C-terminal truncation

Group 2:

  • CAK98666 = CAK99580
  • CAK98394 is a mutated version

Group 3:

  • CAK99285, CAK99906 similar, full length
  • CAK99166 identical to N terminus of CAK99906

Group 1 gene order and homologs

  • CAK99376
    • CAK99599
    • CAK99904
    • CAK99927
  • CAK99377
    • CAK99354
    • CAK99926
  • CAK99378
    • CAK99925
    • CAL00080
    • CAK98967
  • CAK99379 ssb
    • = CAK99924
    • = CAL00079
    • CAK99578
    • CAK98668
    • CAK98392
    • CAK98968
  • CAK99380
    • CAL00078
    • CAK98969
    • CAK99281
  • CAK99381 recT
    • CAL00077
    • CAK98971
    • CAK98970 (c terminal del)
  • CAK99382 endonuclease HNH endonuclease gp54
    • CAK98972
    • CAL00076

(CAL00075 is an n-adenine methylase)

  • CAK99383 (random)

Group 3 gene order and homologs

  • CAK99903 no similar genes
  • CAK99904
    • CAK99287
    • CAK99927
  • CAK 99905 (sbcC?)
    • CAK99286
    • CAK99167 (N) CAK99168 (C)
    • CAK99065
  • CAK99906 (recT)
    • CAK99285 (c)
    • CAK99166 (n)
  • CAK99907
    • CAK99284
    • CAK99165
    • CAK99581
  • CAK99908 n-6 adenine methylase
    • CAK99164
    • CAK99365

Group 2

  • CAK99576
    • CAK99904
  • CAK99577
    • CAK99904
  • CAK99578 ssb
    • CAK99924
    • CAL00079
    • CAK98392
    • CAK99379
  • CAK99579
    • CAK99667
    • CAK98393
  • CAK99580 recT
    • CAK98666
    • CAK98394
  • CAK99581
    • CAK99907
    • CAK99284
    • CAK99294
    • CAK99165
  • CAK999582 pentapeptide
    • CAL00071
    • CAK99909

CAL00077, CAK99381 protein and nucleotide sequences

LOCUS       AM285338                 855 bp    DNA     linear   BCT 01-JUL-2006
DEFINITION  Spiroplasma citri GII3-3X chromosome, contig ContigNP17.
ACCESSION   AM285338 REGION: complement(4198..5052)
VERSION     AM285338.1  GI:110005766
KEYWORDS    .
SOURCE      Spiroplasma citri
 ORGANISM  Spiroplasma citri
           Bacteria; Firmicutes; Mollicutes; Entomoplasmatales;
           Spiroplasmataceae; Spiroplasma.
REFERENCE   1
 AUTHORS   Carle,P., Saillard,C., Blanchard,A., Carrere,N., Carrere,S.,
           Duret,S., Eveillard,S., Gaurivaud,P., Gourgues,G., Gouzy,J.,
           Henry,A., Salar,P., Laigret,F., Bove,J.M., Renaudin,J. and
           Foissac,X.
 TITLE     The partial chromosome sequence of Spiroplasma citri GII3-3X
 JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 855)
 AUTHORS   Foissac,X.
 TITLE     Direct Submission
 JOURNAL   Submitted (28-JUN-2006) Foissac X., UMR 1090 GDPP, INRA, Universite
           V. Segalen Bordeaux2, 71 avenue E. Bourlaux, BP81, Villenave
           d'Ornon, 33883, FRANCE
FEATURES             Location/Qualifiers
    source          1..855
                    /organism="Spiroplasma citri"
                    /mol_type="genomic DNA"
                    /strain="GII3-3X"
                    /specific_host="Circulifer haematoceps"
                    /db_xref="taxon:2133"
                    /country="Morocco"
                    /note="ContigNP17"
    gene            1..855
                    /gene="yqaK"
                    /locus_tag="SPICINP17_006"
    CDS             1..855
                    /gene="yqaK"
                    /locus_tag="SPICINP17_006"
                    /old_locus_tag="SCi01660"
                    /function="macromolecule metabolism; macromolecule
                    synthesis, modification; dna - replication, repair,
                    restr./modif."
                    /inference="ab initio prediction:FrameD"
                    /codon_start=1
                    /transl_table=4
                    /product="putative rect protein"
                    /protein_id="CAL00077.1"
                    /db_xref="GI:110005772"
                    /translation="MNNKIELILNNSKVNNWINEKLTNQKEINLFRKNILTIYNNNPN
                    LFDKEKINLMSVLSACVKAMLLDLPLDPNLGYAYIVPYNGKGQLQIGYKGYIQLAIRT
                    GKYLTINAIEVKQGELLNFDELEQEYNFKWITNENERTKKETIGYVAFFKLLNGYKKT
                    LYWSKEKCENHFKTYSKNYQTYGKFTAGSYEGMALKTVLTQLLRKWGIMSVEMQEAYQ
                    HDQAIIINNSKEFSDNPNIKNKEDNNVIELNNKKDELNLNLEQEFSSNEINDDEEIAK
                    AVNEMFSD"
ORIGIN      
       1 atgaataata aaattgaatt aatattaaat aattcaaaag ttaataattg aattaatgaa
      61 aaattaacaa atcagaaaga aattaattta tttcgtaaaa atatcttaac aatttataat
     121 aataatccca atttatttga taaagaaaaa ataaatttaa tgagtgtttt atctgcttgt
     181 gtaaaagcaa tgttattaga tttaccgtta gaccctaact taggatatgc ctatattgtt
     241 ccatataatg gaaaaggaca gttgcaaatt ggttataagg gttatattca gttagcaatc
     301 cgaacaggaa aatatttaac aataaacgca atagaagtaa aacaaggtga attattaaat
     361 tttgatgaat tagaacaaga atacaatttt aaatgaataa ccaacgaaaa tgaacgaaca
     421 aaaaaagaaa caatcggata tgttgcattt tttaaactac taaatggtta taaaaaaact
     481 ttatattgaa gtaaagaaaa atgcgaaaat cattttaaaa catattctaa gaattatcaa
     541 acttacggaa aatttacggc tggaagttat gaggggatgg cacttaaaac agtattaacc
     601 caacttttaa gaaaatgagg tattatgtca gttgaaatgc aagaagccta tcaacatgat
     661 caagcaataa ttattaataa cagcaaagag tttagtgata atcctaacat aaaaaataaa
     721 gaagataaca atgttattga attaaataac aaaaaagatg aattaaatct aaatttagaa
     781 caagaattta gcagtaatga aataaatgat gatgaagaaa ttgctaaagc tgttaatgaa
     841 atgttttctg attaa
//

>gi|110005766:c5052-4198 Spiroplasma citri GII3-3X chromosome, contig ContigNP17
ATGAATAATAAAATTGAATTAATATTAAATAATTCAAAAGTTAATAATTGAATTAATGAAAAATTAACAA
ATCAGAAAGAAATTAATTTATTTCGTAAAAATATCTTAACAATTTATAATAATAATCCCAATTTATTTGA
TAAAGAAAAAATAAATTTAATGAGTGTTTTATCTGCTTGTGTAAAAGCAATGTTATTAGATTTACCGTTA
GACCCTAACTTAGGATATGCCTATATTGTTCCATATAATGGAAAAGGACAGTTGCAAATTGGTTATAAGG
GTTATATTCAGTTAGCAATCCGAACAGGAAAATATTTAACAATAAACGCAATAGAAGTAAAACAAGGTGA
ATTATTAAATTTTGATGAATTAGAACAAGAATACAATTTTAAATGAATAACCAACGAAAATGAACGAACA
AAAAAAGAAACAATCGGATATGTTGCATTTTTTAAACTACTAAATGGTTATAAAAAAACTTTATATTGAA
GTAAAGAAAAATGCGAAAATCATTTTAAAACATATTCTAAGAATTATCAAACTTACGGAAAATTTACGGC
TGGAAGTTATGAGGGGATGGCACTTAAAACAGTATTAACCCAACTTTTAAGAAAATGAGGTATTATGTCA
GTTGAAATGCAAGAAGCCTATCAACATGATCAAGCAATAATTATTAATAACAGCAAAGAGTTTAGTGATA
ATCCTAACATAAAAAATAAAGAAGATAACAATGTTATTGAATTAAATAACAAAAAAGATGAATTAAATCT
AAATTTAGAACAAGAATTTAGCAGTAATGAAATAAATGATGATGAAGAAATTGCTAAAGCTGTTAATGAA
ATGTTTTCTGATTAA
  • no CGG codons, four TGA codons
  • GC percentage 24%
  • Isochore here:

Upstream promoter for recT gene

aaaatgtaaa aatataaaat tatgcttttt tacaaaATTA CAtaaatata attgctattc
gTGTTATTTg tgaaaaataa aaaAGGAGAa aaaataaa
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