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 20: Line 17:
|3.45
|3.45
|0.06
|0.06
|
|.15
|
|.12
|-
|-
|Gly
|Gly
Line 28: Line 25:
|23.26
|23.26
|0.43
|0.43
|
|.11
|
|.26
|-
|-
|Gly
|Gly
Line 36: Line 33:
|25.01
|25.01
|0.47
|0.47
|
|.34
|
|.49
|-
|-
|Gly
|Gly
Line 44: Line 41:
|1.88
|1.88
|0.03
|0.03
|
|.40
|
|.13
|-
|-
|Glu
|Glu
Line 52: Line 49:
|6.28
|6.28
|0.09
|0.09
|
|.31
|
|.17
|-
|-
|Glu
|Glu
Line 60: Line 57:
|66.34
|66.34
|0.91
|0.91
|
|.69
|
|.83
|-
|-
|Asp
|Asp
Line 68: Line 65:
|44.43
|44.43
|0.83
|0.83
|
|.63
|
|.74
|-
|-
|Asp
|Asp
Line 76: Line 73:
|8.96
|8.96
|0.17
|0.17
|
|.37
|
|.26
|-
|-
|Val
|Val
Line 84: Line 81:
|2.57
|2.57
|0.04
|0.04
|
|.37
|
|.15
|-
|-
|Val
|Val
Line 92: Line 89:
|17.24
|17.24
|0.28
|0.28
|
|.15
|
|.25
|-
|-
|Val
|Val
Line 100: Line 97:
|39.31
|39.31
|0.65
|0.65
|
|.26
|
|.52
|-
|-
|Val
|Val
Line 108: Line 105:
|1.40
|1.40
|0.02
|0.02
|
|.22
|
|.08
|-
|-
|Ala
|Ala
Line 116: Line 113:
|2.11
|2.11
|0.04
|0.04
|
|.36
|
|.15
|-
|-
|Ala
|Ala
Line 124: Line 121:
|25.22
|25.22
|0.46
|0.46
|
|.21
|
|.38
|-
|-
|Ala
|Ala
Line 132: Line 129:
|25.62
|25.62
|0.47
|0.47
|
|.16
|
|.34
|-
|-
|Ala
|Ala
Line 140: Line 137:
|2.12
|2.12
|0.04
|0.04
|
|.27
|
|.13
|-
|-
|Arg
|Arg
Line 148: Line 145:
|0.79
|0.79
|0.03
|0.03
|
|.02
|
|.05
|-
|-
|Arg
|Arg
Line 156: Line 153:
|22.17
|22.17
|0.80
|0.80
|
|.04
|
|.33
|-
|-
|Ser
|Ser
Line 164: Line 161:
|15.27
|15.27
|0.23
|0.23
|
|.15
|
|.23
|-
|-
|Ser
|Ser
Line 172: Line 169:
|3.80
|3.80
|0.06
|0.06
|
|.28
|
|.16
|-
|-
|Lys
|Lys
Line 180: Line 177:
|8.59
|8.59
|0.09
|0.09
|
|.23
|
|.15
|-
|-
|Lys
|Lys
Line 188: Line 185:
|88.38
|88.38
|0.91
|0.91
|
|.77
|
|.85
|-
|-
|Asn
|Asn
Line 196: Line 193:
|55.39
|55.39
|0.77
|0.77
|
|.45
|
|.62
|-
|-
|Asn  
|Asn  
Line 204: Line 201:
|16.93
|16.93
|0.23
|0.23
|
|.55
|
|.38
|-
|-
|Met
|Met
Line 212: Line 209:
|23.03
|23.03
|1.00
|1.00
|
|1.00
|
|1.00
|-
|-
|Ile
|Ile
Line 220: Line 217:
|31.53
|31.53
|0.32
|0.32
|
|.07
|
|.17
|-
|-
|Ile
|Ile
Line 228: Line 225:
|59.82
|59.82
|0.60
|0.60
|
|.51
|
|.62
|-
|-
|Ile
|Ile
Line 236: Line 233:
|8.01
|8.01
|0.08
|0.08
|
|.42
|
|.21
|-  
|-  
|Thr
|Thr
Line 244: Line 241:
|0.86
|0.86
|0.02
|0.02
|
|.27
|
|.10
|-
|-
|Thr
|Thr
Line 252: Line 249:
|29.47
|29.47
|0.55
|0.55
|
|.13
|
|.38
|-
|-
|Thr
|Thr
Line 260: Line 257:
|22.62
|22.62
|0.42
|0.42
|
|.17
|
|.38
|-
|-
|Thr
|Thr
Line 268: Line 265:
|1.11
|1.11
|0.02
|0.02
|
|.44
|
|.14
|-
|-
|Trp
|Trp
Line 276: Line 273:
|0.41
|0.41
|0.04
|0.04
|
|1.00
|
|1.00
|-
|-
|Trp
|Trp
Line 284: Line 281:
|10.13
|10.13
|0.96
|0.96
|
|0.0
|
|0.0
|-
|-
|Cys
|Cys
Line 292: Line 289:
|5.19
|5.19
|0.85
|0.85
|
|.45
|
|.68
|-
|-
|Cys
|Cys
Line 300: Line 297:
|0.93
|0.93
|0.15
|0.15
|
|.55
|
|.32
|-
|-
|End
|End
Line 308: Line 305:
|0.54
|0.54
|0.19
|0.19
|
|.07
|
|.14
|-
|-
|End
|End
Line 316: Line 313:
|2.24
|2.24
|0.81
|0.81
|
|.64
|
|.86
|-
|-
|Tyr
|Tyr
Line 324: Line 321:
|29.26
|29.26
|0.78
|0.78
|
|.57
|
|.68
|-
|-
|Tyr
|Tyr
Line 332: Line 329:
|8.02
|8.02
|0.22
|0.22
|
|.43
|
|.32
|-
|-
|Leu
|Leu
Line 340: Line 337:
|7.18
|7.18
|0.08
|0.08
|
|.13
|
|.16
|-
|-
|Leu
|Leu
Line 348: Line 345:
|64.03
|64.03
|0.71
|0.71
|
|.13
|
|.49
|-
|-
|Phe
|Phe
Line 356: Line 353:
|41.88
|41.88
|0.81
|0.81
|
|.57
|
|.70
|-
|-
|Phe
|Phe
Line 364: Line 361:
|9.73
|9.73
|0.19
|0.19
|
|.43
|
|.30
|-  
|-  
|Ser
|Ser
Line 372: Line 369:
|0.84
|0.84
|0.01
|0.01
|
|.16
|
|.05
|-
|-
|Ser
|Ser
Line 380: Line 377:
|30.16
|30.16
|0.46
|0.46
|
|.12
|
|.29
|-
|-
|Ser
|Ser
Line 388: Line 385:
|14.59
|14.59
|0.22
|0.22
|
|.15
|
|.22
|-
|-
|Ser
|Ser
|TCC
|TCC
|92.00
|92
|0.37
|0.37
|0.01
|0.01
|
|.15
|
|.05
|-
|-
|Arg
|Arg
Line 404: Line 401:
|0.02
|0.02
|0.00
|0.00
|
|.10
|
|0.0
|-
|-
|Arg
|Arg
|CGA
|CGA
|128.00
|128
|0.52
|0.52
|0.02
|0.02
|
|.06
|
|.06
|-
|-
|Arg
|Arg
Line 420: Line 417:
|4.06
|4.06
|0.15
|0.15
|
|.38
|
|.44
|-
|-
|Arg
|Arg
|CGC
|CGC
|67.00
|67
|0.27
|0.27
|0.01
|0.01
|
|.40
|
|.12
|-
|-
|Gln
|Gln
Line 436: Line 433:
|1.64
|1.64
|0.05
|0.05
|
|.65
|
|.24
|-
|-
|Gln
|Gln
Line 444: Line 441:
|28.72
|28.72
|0.95
|0.95
|
|.35
|
|.76
|-
|-
|His
|His
Line 452: Line 449:
|9.00
|9.00
|0.73
|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
|-
|-
|His    CAC      836.00      3.40      0.27
|Pro
|CCA
|Leu    CTG      182.00      0.74      0.01
|3516
|Leu    CTA      1690.00      6.88      0.08
|14.31
|Leu    CTT      2682.00    10.91      0.12
|0.57
|Leu    CTC        52.00      0.21      0.00
|.19
|.44
|Pro     CCG      203.00      0.83      0.03
|-
|Pro    CCA      3516.00    14.31      0.57
|Pro
|Pro    CCT      2306.00      9.38     0.37
|CCT
|Pro     CCC       157.00      0.64     0.03
|2306
|9.38
|0.37
|.16
|.32
|-
|Pro
|CCC
|157
|0.64
|0.03
|.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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