77.9%GC3 content

41.4Effective codons (Nc)

472Coding sequences

1/26GC3 rank here

Genetic code

NCBI table 11 (Bacterial, Archaeal and Plant Plastid), covering chromosomal coding sequences. Sense-codon assignments match the standard code; initiation differs. Which code applies where.

What distinguishes this table

The most constrained choice in M. tuberculosis is isoleucine: of its 3 synonymous codons, ATC takes 80% of the family. Glutamate sits at the other end, spread almost evenly across its options (evenness 0.93 against 0.56 for isoleucine). Those two families are where a codon-optimizer has the most and the least room to move.

Measured across all 59 sense codons, this table correlates most closely with M. bovis (bovine/elephant TB) (r = 1.000) and least with Ferret (r = 0.442). A sequence tuned for the first would need little adjustment to move here; one tuned for the second would need a great deal.

Relative to the average across the 26 organisms on this site, M. tuberculosis leans hardest on CCG (+0.392 against the mean) and avoids AAT most (-0.255). Those two are the codons that most distinguish this table from the others.

Preferred and avoided codons

Amino acid	Preferred	Freq	RSCU	Avoided	Freq	RSCU
Alanine A	GCC	0.451	1.80	GCT	0.079	0.32
Arginine R	CGC	0.393	2.35	AGA	0.017	0.10
Asparagine N	AAC	0.793	1.59	AAT	0.207	0.41
Aspartate D	GAC	0.733	1.47	GAT	0.267	0.53
Cysteine C	TGC	0.752	1.50	TGT	0.248	0.50
Glutamate E	GAG	0.649	1.30	GAA	0.351	0.70
Glutamine Q	CAG	0.745	1.49	CAA	0.255	0.51
Glycine G	GGC	0.504	2.02	GGA	0.109	0.44
Histidine H	CAC	0.710	1.42	CAT	0.290	0.58
Isoleucine I	ATC	0.801	2.40	ATA	0.051	0.15
Leucine L	CTG	0.523	3.14	TTA	0.014	0.09
Lysine K	AAG	0.767	1.53	AAA	0.233	0.47
Phenylalanine F	TTC	0.792	1.58	TTT	0.208	0.42
Proline P	CCG	0.549	2.20	CCT	0.059	0.24
Serine S	TCG	0.350	2.10	TCT	0.041	0.24
Threonine T	ACC	0.584	2.34	ACT	0.061	0.25
Tyrosine Y	TAC	0.717	1.43	TAT	0.283	0.57
Valine V	GTG	0.456	1.82	GTA	0.058	0.23

Full codon usage table

Amino acid	Codon	Frequency	RSCU
Alanine A	GCC	0.4508	1.803
	GCG	0.3711	1.484
	GCA	0.0990	0.396
	GCT	0.0790	0.316
Arginine R	CGC	0.3925	2.355
	CGG	0.3300	1.980
	CGT	0.1151	0.691
	CGA	0.0981	0.589
	AGG	0.0476	0.286
	AGA	0.0167	0.100
Asparagine N	AAC	0.7928	1.586
Asparagine N	AAT	0.2072	0.414
Aspartate D	GAC	0.7332	1.466
Aspartate D	GAT	0.2668	0.534
Cysteine C	TGC	0.7522	1.504
Cysteine C	TGT	0.2478	0.496
Glutamate E	GAG	0.6491	1.298
Glutamate E	GAA	0.3509	0.702
Glutamine Q	CAG	0.7448	1.490
Glutamine Q	CAA	0.2552	0.510
Glycine G	GGC	0.5039	2.016
	GGG	0.1991	0.796
	GGT	0.1882	0.753
	GGA	0.1088	0.435
Histidine H	CAC	0.7096	1.419
Histidine H	CAT	0.2904	0.581
Isoleucine I	ATC	0.8010	2.403
	ATT	0.1480	0.444
	ATA	0.0510	0.153
Leucine L	CTG	0.5228	3.137
	CTC	0.1819	1.091
	TTG	0.1745	1.047
	CTT	0.0569	0.341
	CTA	0.0495	0.297
	TTA	0.0143	0.086
Lysine K	AAG	0.7671	1.534
Lysine K	AAA	0.2329	0.466
Methionine M	ATG	1.0000	1.000
Phenylalanine F	TTC	0.7924	1.585
Phenylalanine F	TTT	0.2076	0.415
Proline P	CCG	0.5491	2.196
	CCC	0.2899	1.160
	CCA	0.1016	0.406
	CCT	0.0594	0.238
Serine S	TCG	0.3501	2.101
	AGC	0.2663	1.598
	TCC	0.2180	1.308
	AGT	0.0631	0.379
	TCA	0.0619	0.371
	TCT	0.0406	0.244
Threonine T	ACC	0.5840	2.336
	ACG	0.2733	1.093
	ACA	0.0813	0.325
	ACT	0.0615	0.246
Tryptophan W	TGG	1.0000	1.000
Tyrosine Y	TAC	0.7170	1.434
Tyrosine Y	TAT	0.2830	0.566
Valine V	GTG	0.4556	1.822
	GTC	0.3959	1.584
	GTT	0.0906	0.362
	GTA	0.0579	0.232

Provenance

Computed from 472 RefSeq coding sequences for Mycobacterium tuberculosis, sampled and counted codon by codon. Frequencies are relative within each amino acid family. Page generated 2026-08-09.

The full derivation of GC3, RSCU and the effective number of codons, along with the limits of each, is set out once in the methods note rather than repeated on every page.

Use this table

Nucleora codon-optimizes a coding sequence against this table directly, then folds the result and reports where structure would interfere with expression.

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