Mesoplasma florum:Recombination: Difference between revisions
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* Isochore here: | * Isochore here: | ||
[[image:recT-SC-isochore.png]] | [[image:recT-SC-isochore.png]] | ||
==Upstream promoter for recT gene== | |||
aaaatgtaaa aatataaaat tatgcttttt tacaaaATTA CAtaaatata attgctattc | |||
gTGTTATTTg tgaaaaataa aaaAGGAGAa aaaataaa | |||
[[category:Mesoplasma florum]] | [[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