HGT-DB Vibrio cholerae chromosome 1

Horizontal Gene Transfer Database

Vibrio cholerae chromosome 1: 2742 proteins

See the statistical parameters of all the genome.
See the correspondence analysis of relative synonymous codon usages for Vibrio cholerae chromosome 1 genes.
See the extraneous regions in terms of G+C content.
See the list of the proposed horizontally transferred genes.
Download the tab-delimited file with all the statistical calculations for each gene. See the Abbreviations used.

Statistical parameters:

G+C content:

G+C(1) G+C(2) G+C(3) G+C(T)

mean value 57.0 38.4 48.9 48.1

st. dev. 5.2 4.0 6.6 3.6

skewness -0.8 -0.3 -1.1 -1.6

kurtosis 4.4 3.8 5.1 7.7

Amino acid content (in %):

AA Mean value SD AA Mean value SD

A 9.2 2.6 M 2.7 1.2

C 1.1 1.0 N 3.8 1.5

D 5.0 1.8 P 4.0 1.5

E 6.3 2.3 Q 5.2 2.2

F 4.0 1.7 R 5.0 1.9

G 6.6 2.1 S 6.1 1.9

H 2.4 1.3 T 5.1 1.5

I 6.1 1.9 V 7.2 2.0

K 5.0 2.0 W 1.3 1.0

L 10.9 2.9 Y 2.9 1.3

Codon usage (per thousand):

Codon Mean SD Codon Mean SD Codon Mean SD Codon Mean SD

GCT (A) 20.6 12.0 CAT (H) 13.3 9.4 CCT (P) 11.3 6.9 AGT (S) 11.5 8.2

GCC (A) 21.7 11.4 CAC (H) 11.0 7.8 CCC (P) 6.0 5.7 AGC (S) 13.8 8.3

GCG (A) 30.0 14.3 ATT (I) 31.1 12.6 CCG (P) 10.6 7.6 ACT (T) 13.0 8.2

GCA (A) 19.0 11.0 ATC (I) 25.2 12.3 CCA (P) 12.4 7.9 ACC (T) 19.5 9.9

TGT (C) 6.2 6.2 ATA (I) 4.1 6.3 CAG (Q) 18.0 11.4 ACG (T) 10.5 6.7

TGC (C) 4.8 5.6 AAG (K) 13.8 8.9 CAA (Q) 33.5 15.1 ACA (T) 7.4 6.6

GAT (D) 36.2 14.1 AAA (K) 36.3 15.6 CGT (R) 20.4 12.9 GTT (V) 16.3 11.3

GAC (D) 13.6 9.4 TTG (L) 23.2 12.1 CGC (R) 17.8 10.6 GTC (V) 14.4 8.5

GAG (E) 24.2 11.8 TTA (L) 19.9 11.8 CGG (R) 2.7 3.8 GTG (V) 29.4 13.8

GAA (E) 38.9 17.5 CTT (L) 12.7 7.6 CGA (R) 5.2 5.5 GTA (V) 11.1 7.9

TTT (F) 26.5 13.3 CTC (L) 14.9 9.2 AGG (R) 1.1 2.6 TGG (W) 13.0 10.1

TTC (F) 13.4 9.3 CTG (L) 29.1 14.5 AGA (R) 2.8 4.8 TAT (Y) 15.3 9.9

GGT (G) 25.8 14.8 CTA (L) 9.1 6.8 TCT (S) 11.2 8.2 TAC (Y) 13.4 8.5

GGC (G) 24.0 12.6 ATG (M) 27.1 11.9 TCC (S) 5.7 5.0 TGA (.) 0.8 1.8

GGG (G) 8.6 6.7 AAT (N) 19.0 11.6 TCG (S) 8.7 6.2 TAG (.) 0.6 1.6

GGA (G) 7.7 6.5 AAC (N) 18.7 10.7 TCA (S) 10.2 7.0 TAA (.) 2.4 2.4

Relative Synonymous Codon Usage (RSCU):

RSCU Mean SD RSCU Mean SD RSCU Mean SD RSCU Mean SD
GCT (A) 0.93 0.59 CAT (H) 1.03 0.58 CCT (P) 1.11 0.79 AGT (S) 1.07 0.79
GCC (A) 0.93 0.57 CAC (H) 0.88 0.57 CCC (P) 0.57 0.63 AGC (S) 1.37 0.91
GCG (A) 1.25 0.63 ATT (I) 1.51 0.56 CCG (P) 0.97 0.75 ACT (T) 1.04 0.74
GCA (A) 0.86 0.58 ATC (I) 1.24 0.58 CCA (P) 1.23 0.86 ACC (T) 1.47 0.80
TGT (C) 0.95 0.75 ATA (I) 0.22 0.38 CAG (Q) 0.67 0.38 ACG (T) 0.81 0.63
TGC (C) 0.72 0.70 AAG (K) 0.54 0.33 CAA (Q) 1.30 0.41 ACA (T) 0.63 0.67
GAT (D) 1.41 0.45 AAA (K) 1.44 0.35 CGT (R) 2.34 1.32 GTT (V) 0.94 0.66
GAC (D) 0.54 0.39 TTG (L) 1.28 0.69 CGC (R) 2.07 1.20 GTC (V) 0.79 0.53
GAG (E) 0.76 0.36 TTA (L) 1.09 0.68 CGG (R) 0.32 0.52 GTG (V) 1.61 0.74
GAA (E) 1.20 0.39 CTT (L) 0.73 0.54 CGA (R) 0.62 0.78 GTA (V) 0.63 0.51
TTT (F) 1.31 0.46 CTC (L) 0.79 0.54 AGG (R) 0.16 0.44 TGG (W) - -
TTC (F) 0.66 0.44 CTG (L) 1.57 0.87 AGA (R) 0.42 0.84 TAT (Y) 1.02 0.56
GGT (G) 1.49 0.77 CTA (L) 0.54 0.53 TCT (S) 1.12 0.95 TAC (Y) 0.91 0.55
GGC (G) 1.42 0.75 ATG (M) - - TCC (S) 0.55 0.56 TGA (.) - -
GGG (G) 0.54 0.54 AAT (N) 0.99 0.51 TCG (S) 0.83 0.69 TAG (.) - -
GGA (G) 0.50 0.54 AAC (N) 0.97 0.51 TCA (S) 1.03 0.82 TAA (.) - -

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	G+C(1)	G+C(2)	G+C(3)	G+C(T)
mean value	57.0	38.4	48.9	48.1
st. dev.	5.2	4.0	6.6	3.6
skewness	-0.8	-0.3	-1.1	-1.6
kurtosis	4.4	3.8	5.1	7.7

AA	Mean value	SD	AA	Mean value	SD
A	9.2	2.6	M	2.7	1.2
C	1.1	1.0	N	3.8	1.5
D	5.0	1.8	P	4.0	1.5
E	6.3	2.3	Q	5.2	2.2
F	4.0	1.7	R	5.0	1.9
G	6.6	2.1	S	6.1	1.9
H	2.4	1.3	T	5.1	1.5
I	6.1	1.9	V	7.2	2.0
K	5.0	2.0	W	1.3	1.0
L	10.9	2.9	Y	2.9	1.3

Codon	Mean	SD	Codon	Mean	SD	Codon	Mean	SD	Codon	Mean	SD
GCT (A)	20.6	12.0	CAT (H)	13.3	9.4	CCT (P)	11.3	6.9	AGT (S)	11.5	8.2
GCC (A)	21.7	11.4	CAC (H)	11.0	7.8	CCC (P)	6.0	5.7	AGC (S)	13.8	8.3
GCG (A)	30.0	14.3	ATT (I)	31.1	12.6	CCG (P)	10.6	7.6	ACT (T)	13.0	8.2
GCA (A)	19.0	11.0	ATC (I)	25.2	12.3	CCA (P)	12.4	7.9	ACC (T)	19.5	9.9
TGT (C)	6.2	6.2	ATA (I)	4.1	6.3	CAG (Q)	18.0	11.4	ACG (T)	10.5	6.7
TGC (C)	4.8	5.6	AAG (K)	13.8	8.9	CAA (Q)	33.5	15.1	ACA (T)	7.4	6.6
GAT (D)	36.2	14.1	AAA (K)	36.3	15.6	CGT (R)	20.4	12.9	GTT (V)	16.3	11.3
GAC (D)	13.6	9.4	TTG (L)	23.2	12.1	CGC (R)	17.8	10.6	GTC (V)	14.4	8.5
GAG (E)	24.2	11.8	TTA (L)	19.9	11.8	CGG (R)	2.7	3.8	GTG (V)	29.4	13.8
GAA (E)	38.9	17.5	CTT (L)	12.7	7.6	CGA (R)	5.2	5.5	GTA (V)	11.1	7.9
TTT (F)	26.5	13.3	CTC (L)	14.9	9.2	AGG (R)	1.1	2.6	TGG (W)	13.0	10.1
TTC (F)	13.4	9.3	CTG (L)	29.1	14.5	AGA (R)	2.8	4.8	TAT (Y)	15.3	9.9
GGT (G)	25.8	14.8	CTA (L)	9.1	6.8	TCT (S)	11.2	8.2	TAC (Y)	13.4	8.5
GGC (G)	24.0	12.6	ATG (M)	27.1	11.9	TCC (S)	5.7	5.0	TGA (.)	0.8	1.8
GGG (G)	8.6	6.7	AAT (N)	19.0	11.6	TCG (S)	8.7	6.2	TAG (.)	0.6	1.6
GGA (G)	7.7	6.5	AAC (N)	18.7	10.7	TCA (S)	10.2	7.0	TAA (.)	2.4	2.4

RSCU	Mean	SD	RSCU	Mean	SD	RSCU	Mean	SD	RSCU	Mean	SD
GCT (A)	0.93	0.59	CAT (H)	1.03	0.58	CCT (P)	1.11	0.79	AGT (S)	1.07	0.79
GCC (A)	0.93	0.57	CAC (H)	0.88	0.57	CCC (P)	0.57	0.63	AGC (S)	1.37	0.91
GCG (A)	1.25	0.63	ATT (I)	1.51	0.56	CCG (P)	0.97	0.75	ACT (T)	1.04	0.74
GCA (A)	0.86	0.58	ATC (I)	1.24	0.58	CCA (P)	1.23	0.86	ACC (T)	1.47	0.80
TGT (C)	0.95	0.75	ATA (I)	0.22	0.38	CAG (Q)	0.67	0.38	ACG (T)	0.81	0.63
TGC (C)	0.72	0.70	AAG (K)	0.54	0.33	CAA (Q)	1.30	0.41	ACA (T)	0.63	0.67
GAT (D)	1.41	0.45	AAA (K)	1.44	0.35	CGT (R)	2.34	1.32	GTT (V)	0.94	0.66
GAC (D)	0.54	0.39	TTG (L)	1.28	0.69	CGC (R)	2.07	1.20	GTC (V)	0.79	0.53
GAG (E)	0.76	0.36	TTA (L)	1.09	0.68	CGG (R)	0.32	0.52	GTG (V)	1.61	0.74
GAA (E)	1.20	0.39	CTT (L)	0.73	0.54	CGA (R)	0.62	0.78	GTA (V)	0.63	0.51
TTT (F)	1.31	0.46	CTC (L)	0.79	0.54	AGG (R)	0.16	0.44	TGG (W)	-	-
TTC (F)	0.66	0.44	CTG (L)	1.57	0.87	AGA (R)	0.42	0.84	TAT (Y)	1.02	0.56
GGT (G)	1.49	0.77	CTA (L)	0.54	0.53	TCT (S)	1.12	0.95	TAC (Y)	0.91	0.55
GGC (G)	1.42	0.75	ATG (M)	-	-	TCC (S)	0.55	0.56	TGA (.)	-	-
GGG (G)	0.54	0.54	AAT (N)	0.99	0.51	TCG (S)	0.83	0.69	TAG (.)	-	-
GGA (G)	0.50	0.54	AAC (N)	0.97	0.51	TCA (S)	1.03	0.82	TAA (.)	-	-