Mesoplasma florum:Codon usage: Difference between revisions

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The codon usage table for Mesoplasma florum is here:
The Mesoplasma florum codon usage table is here.  Also in this table are the probabilities for E. coli codons, and a compromise codon probability calculated by taking the geometric mean of the two genome codon probabilities and renormalizing such that the sum of probabilities of each codon for a specific amino acid is unity.
 
A computer readable version of this compromise codon table is here, suitable for use with the DNA2.0 Gene Designer software available [http://www.dna20.com/index.php?pageID=216 here].  [[media:mf-ec-codon.txt | Compromise codon table]]
Mesoplasma florum L1 [gbbct]: 683 CDS's (245761 codons)
AmAcid  Codon      Number    /1000    Fraction  ..
   


{| border="1"
{| border="1"
Line 21: Line 18:
|0.06
|0.06
|.15
|.15
|
|.12
|-
|-
|Gly
|Gly
Line 29: Line 26:
|0.43
|0.43
|.11
|.11
|
|.26
|-
|-
|Gly
|Gly
Line 37: Line 34:
|0.47
|0.47
|.34
|.34
|
|.49
|-
|-
|Gly
|Gly
Line 45: Line 42:
|0.03
|0.03
|.40
|.40
|
|.13
|-
|-
|Glu
|Glu
Line 53: Line 50:
|0.09
|0.09
|.31
|.31
|
|.17
|-
|-
|Glu
|Glu
Line 61: Line 58:
|0.91
|0.91
|.69
|.69
|
|.83
|-
|-
|Asp
|Asp
Line 69: Line 66:
|0.83
|0.83
|.63
|.63
|
|.74
|-
|-
|Asp
|Asp
Line 77: Line 74:
|0.17
|0.17
|.37
|.37
|
|.26
|-
|-
|Val
|Val
Line 85: Line 82:
|0.04
|0.04
|.37
|.37
|
|.15
|-
|-
|Val
|Val
Line 93: Line 90:
|0.28
|0.28
|.15
|.15
|
|.25
|-
|-
|Val
|Val
Line 101: Line 98:
|0.65
|0.65
|.26
|.26
|
|.52
|-
|-
|Val
|Val
Line 109: Line 106:
|0.02
|0.02
|.22
|.22
|
|.08
|-
|-
|Ala
|Ala
Line 117: Line 114:
|0.04
|0.04
|.36
|.36
|
|.15
|-
|-
|Ala
|Ala
Line 125: Line 122:
|0.46
|0.46
|.21
|.21
|
|.38
|-
|-
|Ala
|Ala
Line 133: Line 130:
|0.47
|0.47
|.16
|.16
|
|.34
|-
|-
|Ala
|Ala
Line 141: Line 138:
|0.04
|0.04
|.27
|.27
|
|.13
|-
|-
|Arg
|Arg
Line 149: Line 146:
|0.03
|0.03
|.02
|.02
|
|.05
|-
|-
|Arg
|Arg
Line 157: Line 154:
|0.80
|0.80
|.04
|.04
|
|.33
|-
|-
|Ser
|Ser
Line 165: Line 162:
|0.23
|0.23
|.15
|.15
|
|.23
|-
|-
|Ser
|Ser
Line 173: Line 170:
|0.06
|0.06
|.28
|.28
|
|.16
|-
|-
|Lys
|Lys
Line 181: Line 178:
|0.09
|0.09
|.23
|.23
|
|.15
|-
|-
|Lys
|Lys
Line 189: Line 186:
|0.91
|0.91
|.77
|.77
|
|.85
|-
|-
|Asn
|Asn
Line 197: Line 194:
|0.77
|0.77
|.45
|.45
|
|.62
|-
|-
|Asn  
|Asn  
Line 205: Line 202:
|0.23
|0.23
|.55
|.55
|
|.38
|-
|-
|Met
|Met
Line 213: Line 210:
|1.00
|1.00
|1.00
|1.00
|
|1.00
|-
|-
|Ile
|Ile
Line 221: Line 218:
|0.32
|0.32
|.07
|.07
|
|.17
|-
|-
|Ile
|Ile
Line 229: Line 226:
|0.60
|0.60
|.51
|.51
|
|.62
|-
|-
|Ile
|Ile
Line 237: Line 234:
|0.08
|0.08
|.42
|.42
|
|.21
|-  
|-  
|Thr
|Thr
Line 245: Line 242:
|0.02
|0.02
|.27
|.27
|
|.10
|-
|-
|Thr
|Thr
Line 253: Line 250:
|0.55
|0.55
|.13
|.13
|
|.38
|-
|-
|Thr
|Thr
Line 261: Line 258:
|0.42
|0.42
|.17
|.17
|
|.38
|-
|-
|Thr
|Thr
Line 269: Line 266:
|0.02
|0.02
|.44
|.44
|
|.14
|-
|-
|Trp
|Trp
Line 277: Line 274:
|0.04
|0.04
|1.00
|1.00
|
|1.00
|-
|-
|Trp
|Trp
Line 285: Line 282:
|0.96
|0.96
|0.0
|0.0
|
|0.0
|-
|-
|Cys
|Cys
Line 293: Line 290:
|0.85
|0.85
|.45
|.45
|
|.68
|-
|-
|Cys
|Cys
Line 301: Line 298:
|0.15
|0.15
|.55
|.55
|
|.32
|-
|-
|End
|End
Line 309: Line 306:
|0.19
|0.19
|.07
|.07
|
|.14
|-
|-
|End
|End
Line 317: Line 314:
|0.81
|0.81
|.64
|.64
|
|.86
|-
|-
|Tyr
|Tyr
Line 325: Line 322:
|0.78
|0.78
|.57
|.57
|
|.68
|-
|-
|Tyr
|Tyr
Line 333: Line 330:
|0.22
|0.22
|.43
|.43
|
|.32
|-
|-
|Leu
|Leu
Line 341: Line 338:
|0.08
|0.08
|.13
|.13
|
|.16
|-
|-
|Leu
|Leu
Line 349: Line 346:
|0.71
|0.71
|.13
|.13
|
|.49
|-
|-
|Phe
|Phe
Line 357: Line 354:
|0.81
|0.81
|.57
|.57
|
|.70
|-
|-
|Phe
|Phe
Line 365: Line 362:
|0.19
|0.19
|.43
|.43
|
|.30
|-  
|-  
|Ser
|Ser
Line 373: Line 370:
|0.01
|0.01
|.16
|.16
|
|.05
|-
|-
|Ser
|Ser
Line 381: Line 378:
|0.46
|0.46
|.12
|.12
|
|.29
|-
|-
|Ser
|Ser
Line 389: Line 386:
|0.22
|0.22
|.15
|.15
|
|.22
|-
|-
|Ser
|Ser
Line 397: Line 394:
|0.01
|0.01
|.15
|.15
|
|.05
|-
|-
|Arg
|Arg
Line 405: Line 402:
|0.00
|0.00
|.10
|.10
|
|0.0
|-
|-
|Arg
|Arg
Line 413: Line 410:
|0.02
|0.02
|.06
|.06
|
|.06
|-
|-
|Arg
|Arg
Line 421: Line 418:
|0.15
|0.15
|.38
|.38
|
|.44
|-
|-
|Arg
|Arg
Line 429: Line 426:
|0.01
|0.01
|.40
|.40
|
|.12
|-
|-
|Gln
|Gln
Line 437: Line 434:
|0.05
|0.05
|.65
|.65
|
|.24
|-
|-
|Gln
|Gln
Line 445: Line 442:
|0.95
|0.95
|.35
|.35
|
|.76
|-
|-
|His
|His
Line 453: Line 450:
|0.73
|0.73
|.57
|.57
|
|.65
|-
|-
|His
|His
Line 461: Line 458:
|0.27
|0.27
|.43
|.43
|
|.35
|-  
|-  
|Leu
|Leu
Line 469: Line 466:
|0.01
|0.01
|.50
|.50
|
|.11
|-
|-
|Leu
|Leu
Line 477: Line 474:
|0.08
|0.08
|.04
|.04
|
|.08
|-
|-
|Leu
|Leu
Line 485: Line 482:
|0.12
|0.12
|.10
|.10
|
|.17
|-
|-
|Leu
|Leu
Line 493: Line 490:
|0.00
|0.00
|.10
|.10
|
|0.0
|-
|-
|Pro
|Pro
Line 501: Line 498:
|0.03
|0.03
|.52
|.52
|
|.16
|-
|-
|Pro
|Pro
Line 509: Line 506:
|0.57
|0.57
|.19
|.19
|
|.44
|-
|-
|Pro
|Pro
Line 517: Line 514:
|0.37
|0.37
|.16
|.16
|
|.32
|-
|-
|Pro
|Pro
Line 525: Line 522:
|0.03
|0.03
|.12
|.12
|
|.08
|-
|-
|}
|}
[[Category:Mesoplasma florum]]

Latest revision as of 08:45, 17 September 2009

The Mesoplasma florum codon usage table is here. Also in this table are the probabilities for E. coli codons, and a compromise codon probability calculated by taking the geometric mean of the two genome codon probabilities and renormalizing such that the sum of probabilities of each codon for a specific amino acid is unity. A computer readable version of this compromise codon table is here, suitable for use with the DNA2.0 Gene Designer software available here. Compromise codon table

Amino acid Codon Number Number / 1000 Probability EC Probability Compromise Probability
Gly GGG 848 3.45 0.06 .15 .12
Gly GGA 5717 23.26 0.43 .11 .26
Gly GGT 6147 25.01 0.47 .34 .49
Gly GGC 461 1.88 0.03 .40 .13
Glu GAG 1543 6.28 0.09 .31 .17
Glu GAA 16303 66.34 0.91 .69 .83
Asp GAT 10918 44.43 0.83 .63 .74
Asp GAC 2203 8.96 0.17 .37 .26
Val GTG 632 2.57 0.04 .37 .15
Val GTA 4237 17.24 0.28 .15 .25
Val GTT 9660 39.31 0.65 .26 .52
Val GTC 344 1.40 0.02 .22 .08
Ala GCG 519 2.11 0.04 .36 .15
Ala GCA 6198 25.22 0.46 .21 .38
Ala GCT 6297 25.62 0.47 .16 .34
Ala GCC 522 2.12 0.04 .27 .13
Arg AGG 194 0.79 0.03 .02 .05
Arg AGA 5448 22.17 0.80 .04 .33
Ser AGT 3752 15.27 0.23 .15 .23
Ser AGC 935 3.80 0.06 .28 .16
Lys AAG 2110 8.59 0.09 .23 .15
Lys AAA 21721 88.38 0.91 .77 .85
Asn AAT 13612 55.39 0.77 .45 .62
Asn AAC 4161 16.93 0.23 .55 .38
Met ATG 5660 23.03 1.00 1.00 1.00
Ile ATA 7748 31.53 0.32 .07 .17
Ile ATT 14701 59.82 0.60 .51 .62
Ile ATC 1968 8.01 0.08 .42 .21
Thr ACG 211 0.86 0.02 .27 .10
Thr ACA 7243 29.47 0.55 .13 .38
Thr ACT 5558 22.62 0.42 .17 .38
Thr ACC 274 1.11 0.02 .44 .14
Trp TGG 101 0.41 0.04 1.00 1.00
Trp TGA 2489 10.13 0.96 0.0 0.0
Cys TGT 1275 5.19 0.85 .45 .68
Cys TGC 228 0.93 0.15 .55 .32
End TAG 132 0.54 0.19 .07 .14
End TAA 551 2.24 0.81 .64 .86
Tyr TAT 7191 29.26 0.78 .57 .68
Tyr TAC 1972 8.02 0.22 .43 .32
Leu TTG 1765 7.18 0.08 .13 .16
Leu TTA 15736 64.03 0.71 .13 .49
Phe TTT 10293 41.88 0.81 .57 .70
Phe TTC 2391 9.73 0.19 .43 .30
Ser TCG 206 0.84 0.01 .16 .05
Ser TCA 7413 30.16 0.46 .12 .29
Ser TCT 3585 14.59 0.22 .15 .22
Ser TCC 92 0.37 0.01 .15 .05
Arg CGG 6 0.02 0.00 .10 0.0
Arg CGA 128 0.52 0.02 .06 .06
Arg CGT 998 4.06 0.15 .38 .44
Arg CGC 67 0.27 0.01 .40 .12
Gln CAG 404 1.64 0.05 .65 .24
Gln CAA 7058 28.72 0.95 .35 .76
His CAT 2211 9.00 0.73 .57 .65
His CAC 836 3.40 0.27 .43 .35
Leu CTG 182 0.74 0.01 .50 .11
Leu CTA 1690 6.88 0.08 .04 .08
Leu CTT 2682 10.91 0.12 .10 .17
Leu CTC 52 0.21 0.00 .10 0.0
Pro CCG 203 0.83 0.03 .52 .16
Pro CCA 3516 14.31 0.57 .19 .44
Pro CCT 2306 9.38 0.37 .16 .32
Pro CCC 157 0.64 0.03 .12 .08
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