Mesoplasma florum:Recombination

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Bove,J.M., Renaudin,J. and Foissac,X. TITLE    The partial chromosome sequence of Spiroplasma citri GII3-3X JOURNAL  Unpublished REFERENCE  2  (bases 1 to 855) AUTHORS  Foissac,X. TITLE    Direct Submission JOURNAL  Submitted (28-JUN-2006) Foissac X., UMR 1090 GDPP, INRA, Universite V.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