kegg_metabolic — Metabolic networks from KEGG (2006)

Description

Metabolic networks of 109 organisms (bacteria, archaea and eukaryotes), extracted by M. Huss and P. Holme from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database in March 2006, and distributed by A. Clauset. Nodes are metabolites (substances) that take part in the enzymatic reactions annotated for the organism, and an undirected edge connects a reactant and a product of the same reaction, according to the reactant-product pairs listed in KEGG. The networks include a few self-loops. Each network is named after the KEGG organism code (e.g. eco for Escherichia coli K-12, hsa for Homo sapiens, sce for Saccharomyces cerevisiae). The metabolite names or KEGG compound identifiers are not included in the data.

Tags

Biological Metabolic Unweighted

Added

2020-08-11

Citation

• M. Huss & P. Holme, "Currency and commodity metabolites: their identification and relation to the modularity of metabolic networks." IET Syst. Biol. 1(5), 280-285 (2007) 10.1049/iet-syb:20060077 Sci-Hub

Upstream URL OK

http://santafe.edu/~aaronc/data/kegg2006_metabolic.zip

Networks

Tip: click on a column header to sort the list, or hover over it for a description.

Column legend

$\left<k\right>$

Mean degree

$\sigma_k$

Standard deviation of the degrees

$\lambda_h$

Largest eigenvalue of the Hashimoto (non-backtracking) matrix

$\tau$

Random walk mixing time

$r$

Degree assortativity

$c$

Global clustering coefficient

$\oslash$

(Pseudo-) diameter

$S$

Relative size of the largest component

NPs

Node properties

EPs

Edge properties

Show all columns

Name	Nodes	Edges	$\left<k\right>$	$\sigma_k$	$\lambda_h$	$\tau$	$r$	$c$	$\oslash$	$S$	Kind	Mode	NPs	EPs	gt	GraphML	GML	csv
aae	926	2,417	5.22	12.14	18.04	16.73	-0.18	0.05	10	0.95	Undirected	Unipartite			18 KiB	24 KiB	24 KiB	19 KiB
afu	909	2,113	4.65	11.13	15.79	43.79	-0.17	0.04	14	0.95	Undirected	Unipartite			17 KiB	24 KiB	24 KiB	19 KiB
ana	1,362	3,731	5.48	16.23	22.35	15.99	-0.19	0.04	10	0.96	Undirected	Unipartite			26 KiB	38 KiB	37 KiB	29 KiB
ape	805	1,959	4.87	10.71	15.51	15.17	-0.16	0.05	9	0.96	Undirected	Unipartite			15 KiB	21 KiB	21 KiB	16 KiB
atc	1,589	4,496	5.66	18.38	24.09	17.93	-0.19	0.04	11	0.97	Undirected	Unipartite			31 KiB	43 KiB	44 KiB	35 KiB
ath	1,561	4,466	5.72	18.04	24.17	17.79	-0.20	0.04	11	0.98	Undirected	Unipartite			30 KiB	43 KiB	43 KiB	33 KiB
atu	1,593	4,504	5.65	18.41	24.11	17.93	-0.19	0.04	11	0.97	Undirected	Unipartite			30 KiB	43 KiB	42 KiB	34 KiB
bas	664	1,578	4.75	9.18	13.71	35.36	-0.14	0.05	8	0.93	Undirected	Unipartite			12 KiB	17 KiB	17 KiB	13 KiB
bbu	505	1,184	4.69	8.70	13.32	15.14	-0.15	0.07	8	0.92	Undirected	Unipartite			9 KiB	13 KiB	13 KiB	10 KiB
bha	1,267	3,499	5.52	15.12	21.73	18.28	-0.18	0.05	11	0.97	Undirected	Unipartite			24 KiB	34 KiB	34 KiB	27 KiB
bja	1,746	5,078	5.82	19.40	25.65	15.13	-0.19	0.04	10	0.97	Undirected	Unipartite			33 KiB	46 KiB	44 KiB	36 KiB
blo	854	2,208	5.17	11.77	16.94	17.87	-0.16	0.05	8	0.95	Undirected	Unipartite			16 KiB	23 KiB	22 KiB	18 KiB
bme	1,574	4,383	5.57	17.40	23.82	17.94	-0.19	0.04	11	0.96	Undirected	Unipartite			31 KiB	43 KiB	43 KiB	35 KiB
bms	1,405	3,839	5.46	16.01	22.20	17.98	-0.18	0.04	11	0.96	Undirected	Unipartite			27 KiB	38 KiB	38 KiB	30 KiB
bsu	1,380	3,873	5.61	16.41	22.88	18.01	-0.17	0.04	11	0.97	Undirected	Unipartite			27 KiB	39 KiB	38 KiB	30 KiB
buc	638	1,605	5.03	9.21	14.08	54.92	-0.15	0.06	8	0.94	Undirected	Unipartite			12 KiB	17 KiB	17 KiB	13 KiB
cac	1,081	2,905	5.37	13.27	19.41	17.68	-0.15	0.05	9	0.96	Undirected	Unipartite			21 KiB	28 KiB	28 KiB	22 KiB
ccr	1,421	3,814	5.37	16.44	22.15	17.99	-0.18	0.04	11	0.95	Undirected	Unipartite			27 KiB	39 KiB	39 KiB	31 KiB
cef	1,166	3,226	5.53	14.90	20.94	18.24	-0.17	0.05	11	0.96	Undirected	Unipartite			22 KiB	31 KiB	31 KiB	25 KiB
cel	1,307	3,678	5.63	16.44	21.60	12.24	-0.19	0.04	9	0.97	Undirected	Unipartite			25 KiB	35 KiB	34 KiB	28 KiB
cgl	1,379	3,847	5.58	17.17	22.62	20.91	-0.19	0.04	11	0.97	Undirected	Unipartite			27 KiB	39 KiB	37 KiB	30 KiB
cje	851	2,219	5.22	11.88	17.61	18.75	-0.16	0.06	11	0.95	Undirected	Unipartite			16 KiB	23 KiB	23 KiB	18 KiB
cmu	650	1,526	4.70	9.06	13.54	21.09	-0.17	0.06	9	0.92	Undirected	Unipartite			12 KiB	17 KiB	17 KiB	13 KiB
cpa	659	1,580	4.80	9.20	14.11	21.06	-0.16	0.06	9	0.92	Undirected	Unipartite			13 KiB	18 KiB	18 KiB	14 KiB
cpe	1,068	2,834	5.31	13.30	19.33	17.70	-0.14	0.05	10	0.96	Undirected	Unipartite			20 KiB	29 KiB	29 KiB	22 KiB
cpj	660	1,584	4.80	9.23	14.16	29.66	-0.16	0.06	10	0.92	Undirected	Unipartite			12 KiB	17 KiB	17 KiB	13 KiB
cpn	660	1,585	4.80	9.23	14.14	21.06	-0.16	0.06	9	0.92	Undirected	Unipartite			12 KiB	17 KiB	17 KiB	13 KiB
cte	1,000	2,701	5.40	13.38	19.47	13.81	-0.19	0.05	8	0.94	Undirected	Unipartite			20 KiB	28 KiB	28 KiB	22 KiB
ctr	652	1,524	4.67	9.01	13.39	21.10	-0.16	0.05	9	0.92	Undirected	Unipartite			12 KiB	17 KiB	17 KiB	13 KiB
dme	1,372	3,798	5.54	16.29	21.48	20.90	-0.18	0.04	10	0.97	Undirected	Unipartite			26 KiB	36 KiB	36 KiB	29 KiB
dra	1,185	3,266	5.51	14.73	21.03	18.13	-0.17	0.05	11	0.96	Undirected	Unipartite			22 KiB	31 KiB	31 KiB	25 KiB
ecc	1,533	4,451	5.81	17.67	24.29	17.96	-0.17	0.04	11	0.97	Undirected	Unipartite			30 KiB	42 KiB	41 KiB	32 KiB
ece	1,604	4,742	5.91	18.87	25.15	17.96	-0.19	0.04	11	0.97	Undirected	Unipartite			31 KiB	43 KiB	42 KiB	34 KiB
ecj	1,635	4,843	5.92	18.98	25.28	17.82	-0.19	0.04	11	0.97	Undirected	Unipartite			33 KiB	47 KiB	47 KiB	37 KiB
eco	1,641	4,872	5.94	19.08	25.34	17.82	-0.19	0.04	11	0.97	Undirected	Unipartite			32 KiB	46 KiB	45 KiB	36 KiB
ecs	1,601	4,739	5.92	18.88	25.15	17.96	-0.19	0.04	11	0.97	Undirected	Unipartite			30 KiB	43 KiB	42 KiB	35 KiB
fnu	1,031	2,572	4.99	12.11	17.78	14.25	-0.14	0.05	9	0.96	Undirected	Unipartite			20 KiB	28 KiB	27 KiB	21 KiB
hal	808	2,080	5.15	12.03	17.23	18.40	-0.18	0.06	11	0.97	Undirected	Unipartite			15 KiB	21 KiB	21 KiB	16 KiB
hin	1,085	2,887	5.32	13.24	19.89	20.96	-0.15	0.06	11	0.97	Undirected	Unipartite			21 KiB	29 KiB	29 KiB	23 KiB
hpj	849	2,076	4.89	11.08	16.49	18.68	-0.15	0.05	11	0.96	Undirected	Unipartite			17 KiB	23 KiB	23 KiB	17 KiB
hpy	863	2,100	4.87	11.11	16.62	18.68	-0.15	0.05	11	0.95	Undirected	Unipartite			16 KiB	22 KiB	22 KiB	17 KiB
hsa	1,917	6,084	6.35	21.97	28.76	7.54	-0.20	0.04	8	0.97	Undirected	Unipartite			36 KiB	53 KiB	52 KiB	42 KiB
lil	1,234	3,219	5.22	13.77	19.21	20.96	-0.15	0.04	11	0.98	Undirected	Unipartite			24 KiB	34 KiB	34 KiB	26 KiB
lin	980	2,722	5.56	12.87	20.07	18.27	-0.16	0.06	11	0.95	Undirected	Unipartite			19 KiB	27 KiB	26 KiB	21 KiB
lla	966	2,528	5.23	12.06	18.14	17.73	-0.15	0.05	9	0.94	Undirected	Unipartite			19 KiB	26 KiB	26 KiB	20 KiB
lmo	1,004	2,787	5.55	13.01	20.27	18.27	-0.16	0.06	11	0.96	Undirected	Unipartite			19 KiB	27 KiB	27 KiB	21 KiB
mac	938	2,313	4.93	11.92	17.45	40.64	-0.17	0.05	11	0.96	Undirected	Unipartite			18 KiB	25 KiB	25 KiB	19 KiB
mge	358	846	4.73	7.29	10.42	28.29	-0.16	0.05	9	0.94	Undirected	Unipartite			7 KiB	9 KiB	9 KiB	7 KiB
mja	796	1,876	4.71	10.52	15.42	22.97	-0.16	0.05	9	0.95	Undirected	Unipartite			15 KiB	21 KiB	20 KiB	16 KiB
mka	754	1,748	4.64	10.60	15.03	32.43	-0.16	0.05	10	0.96	Undirected	Unipartite			14 KiB	19 KiB	19 KiB	15 KiB
mle	1,008	2,670	5.30	12.95	18.87	16.58	-0.16	0.05	9	0.95	Undirected	Unipartite			19 KiB	27 KiB	26 KiB	21 KiB
mlo	1,654	4,890	5.91	19.04	25.48	15.11	-0.18	0.04	9	0.97	Undirected	Unipartite			32 KiB	44 KiB	45 KiB	37 KiB
mma	1,008	2,480	4.92	12.45	17.80	40.25	-0.18	0.05	11	0.96	Undirected	Unipartite			19 KiB	27 KiB	26 KiB	20 KiB
mmu	1,863	5,886	6.32	21.59	28.26	7.53	-0.19	0.04	8	0.97	Undirected	Unipartite			38 KiB	53 KiB	53 KiB	42 KiB
mpe	579	1,348	4.66	8.98	12.95	14.51	-0.17	0.05	8	0.94	Undirected	Unipartite			11 KiB	15 KiB	15 KiB	12 KiB
mpn	375	897	4.78	7.38	10.61	21.80	-0.15	0.05	9	0.94	Undirected	Unipartite			7 KiB	11 KiB	10 KiB	8 KiB
mpu	385	934	4.85	7.87	11.15	14.50	-0.17	0.05	8	0.94	Undirected	Unipartite			7 KiB	10 KiB	10 KiB	8 KiB
mtc	1,443	4,059	5.63	16.90	22.93	15.68	-0.18	0.04	9	0.97	Undirected	Unipartite			28 KiB	39 KiB	38 KiB	31 KiB
mth	814	1,919	4.71	10.79	16.24	32.43	-0.15	0.06	10	0.95	Undirected	Unipartite			15 KiB	21 KiB	21 KiB	16 KiB
mtu	1,509	4,256	5.64	17.46	23.54	15.27	-0.18	0.04	9	0.97	Undirected	Unipartite			29 KiB	41 KiB	40 KiB	32 KiB
nma	1,017	2,707	5.32	13.17	19.21	20.94	-0.17	0.05	11	0.95	Undirected	Unipartite			19 KiB	28 KiB	27 KiB	22 KiB
nme	1,020	2,706	5.31	13.11	19.12	20.95	-0.17	0.05	11	0.95	Undirected	Unipartite			19 KiB	28 KiB	28 KiB	21 KiB
oih	1,340	3,729	5.57	15.59	22.13	20.61	-0.19	0.05	10	0.96	Undirected	Unipartite			26 KiB	38 KiB	38 KiB	29 KiB
pab	829	1,975	4.76	11.16	15.80	15.19	-0.17	0.05	9	0.97	Undirected	Unipartite			15 KiB	22 KiB	21 KiB	17 KiB
pae	1,581	4,606	5.83	18.27	24.98	17.90	-0.19	0.04	11	0.97	Undirected	Unipartite			31 KiB	41 KiB	40 KiB	33 KiB
pai	958	2,389	4.99	12.28	17.08	17.22	-0.18	0.04	9	0.96	Undirected	Unipartite			18 KiB	26 KiB	26 KiB	20 KiB
pfu	814	2,025	4.98	11.50	16.46	15.15	-0.18	0.05	9	0.97	Undirected	Unipartite			16 KiB	22 KiB	22 KiB	17 KiB
pho	733	1,748	4.77	10.67	15.24	15.19	-0.18	0.05	9	0.97	Undirected	Unipartite			14 KiB	20 KiB	20 KiB	15 KiB
pmu	1,167	3,306	5.67	15.41	21.38	20.96	-0.17	0.05	11	0.97	Undirected	Unipartite			22 KiB	32 KiB	31 KiB	25 KiB
rco	785	1,826	4.65	10.53	14.60	69.79	-0.18	0.05	9	0.94	Undirected	Unipartite			15 KiB	20 KiB	20 KiB	16 KiB
rno	1,646	4,911	5.97	20.13	25.77	7.40	-0.20	0.03	7	0.97	Undirected	Unipartite			31 KiB	46 KiB	45 KiB	36 KiB
rpr	754	1,751	4.64	10.43	14.25	69.73	-0.18	0.05	9	0.94	Undirected	Unipartite			14 KiB	20 KiB	19 KiB	16 KiB
rso	1,642	4,720	5.75	18.48	24.82	17.93	-0.19	0.04	11	0.97	Undirected	Unipartite			32 KiB	43 KiB	43 KiB	35 KiB
sag	875	2,215	5.06	11.75	18.31	14.40	-0.16	0.06	8	0.93	Undirected	Unipartite			17 KiB	23 KiB	23 KiB	18 KiB
sam	1,073	3,006	5.60	13.93	20.61	18.39	-0.18	0.06	11	0.96	Undirected	Unipartite			21 KiB	29 KiB	29 KiB	23 KiB
san	880	2,230	5.07	11.80	18.33	14.40	-0.15	0.06	8	0.93	Undirected	Unipartite			17 KiB	25 KiB	24 KiB	19 KiB
sau	1,080	3,009	5.57	13.91	20.61	18.39	-0.18	0.06	11	0.96	Undirected	Unipartite			21 KiB	28 KiB	28 KiB	23 KiB
sav	1,072	3,004	5.60	13.94	20.62	18.39	-0.18	0.06	11	0.96	Undirected	Unipartite			21 KiB	29 KiB	28 KiB	22 KiB
sce	1,378	4,106	5.96	17.91	23.58	16.93	-0.20	0.04	10	0.98	Undirected	Unipartite			27 KiB	38 KiB	37 KiB	30 KiB
sco	1,542	4,472	5.80	18.49	24.21	17.95	-0.20	0.04	11	0.98	Undirected	Unipartite			30 KiB	42 KiB	40 KiB	33 KiB
sfl	1,560	4,544	5.83	18.27	24.44	17.99	-0.19	0.04	11	0.97	Undirected	Unipartite			31 KiB	43 KiB	43 KiB	35 KiB
sme	1,705	5,023	5.89	19.65	25.94	15.09	-0.18	0.04	9	0.97	Undirected	Unipartite			32 KiB	46 KiB	45 KiB	37 KiB
smu	911	2,348	5.15	11.76	17.36	14.41	-0.15	0.05	8	0.94	Undirected	Unipartite			17 KiB	24 KiB	23 KiB	19 KiB
son	1,417	4,005	5.65	16.78	22.94	17.98	-0.17	0.04	11	0.97	Undirected	Unipartite			27 KiB	39 KiB	38 KiB	31 KiB
spg	822	2,026	4.93	10.79	16.49	14.40	-0.15	0.06	8	0.93	Undirected	Unipartite			16 KiB	23 KiB	22 KiB	17 KiB
spm	820	2,033	4.96	10.86	16.57	14.40	-0.15	0.06	8	0.93	Undirected	Unipartite			16 KiB	22 KiB	21 KiB	17 KiB
spn	892	2,319	5.20	12.28	18.07	14.40	-0.14	0.05	8	0.94	Undirected	Unipartite			17 KiB	25 KiB	24 KiB	19 KiB
spo	1,184	3,499	5.91	16.27	21.84	17.85	-0.20	0.05	10	0.98	Undirected	Unipartite			23 KiB	33 KiB	32 KiB	26 KiB
spr	910	2,374	5.22	12.41	18.29	14.40	-0.14	0.05	8	0.94	Undirected	Unipartite			17 KiB	25 KiB	24 KiB	20 KiB
spy	825	2,028	4.92	10.85	16.46	14.40	-0.15	0.05	8	0.93	Undirected	Unipartite			16 KiB	22 KiB	22 KiB	17 KiB
sso	1,035	2,576	4.98	13.01	18.23	15.13	-0.17	0.04	9	0.96	Undirected	Unipartite			19 KiB	28 KiB	27 KiB	21 KiB
stm	1,563	4,588	5.87	17.91	24.49	17.97	-0.17	0.04	11	0.97	Undirected	Unipartite			30 KiB	43 KiB	43 KiB	35 KiB
sto	973	2,365	4.86	12.15	17.38	15.14	-0.16	0.05	9	0.96	Undirected	Unipartite			18 KiB	26 KiB	25 KiB	20 KiB
sty	1,547	4,444	5.75	17.39	24.05	17.97	-0.17	0.04	11	0.97	Undirected	Unipartite			29 KiB	43 KiB	43 KiB	33 KiB
syn	1,264	3,415	5.40	15.21	21.29	17.98	-0.19	0.05	11	0.97	Undirected	Unipartite			24 KiB	33 KiB	33 KiB	26 KiB
tac	768	1,972	5.14	11.38	16.57	20.97	-0.18	0.06	9	0.96	Undirected	Unipartite			14 KiB	21 KiB	20 KiB	16 KiB
tel	1,159	3,067	5.29	14.09	19.97	15.85	-0.18	0.05	10	0.96	Undirected	Unipartite			22 KiB	30 KiB	30 KiB	24 KiB
tma	914	2,427	5.31	12.52	17.35	10.35	-0.16	0.05	9	0.96	Undirected	Unipartite			18 KiB	25 KiB	25 KiB	19 KiB
tpa	524	1,299	4.96	9.39	14.42	15.89	-0.15	0.07	8	0.92	Undirected	Unipartite			10 KiB	15 KiB	14 KiB	11 KiB
tte	991	2,615	5.28	12.68	19.14	14.40	-0.15	0.06	8	0.94	Undirected	Unipartite			19 KiB	27 KiB	26 KiB	21 KiB
tvo	778	2,010	5.17	11.80	16.63	20.97	-0.19	0.05	9	0.97	Undirected	Unipartite			15 KiB	21 KiB	20 KiB	16 KiB
uur	321	748	4.66	7.38	10.28	14.37	-0.17	0.05	8	0.93	Undirected	Unipartite			6 KiB	9 KiB	8 KiB	6 KiB
vch	1,422	4,051	5.70	16.96	23.08	18.02	-0.17	0.04	11	0.97	Undirected	Unipartite			27 KiB	37 KiB	36 KiB	29 KiB
wbr	775	2,113	5.45	12.19	17.07	21.01	-0.20	0.06	8	0.96	Undirected	Unipartite			15 KiB	22 KiB	21 KiB	16 KiB
xac	1,444	4,006	5.55	16.97	22.42	15.51	-0.17	0.04	10	0.97	Undirected	Unipartite			29 KiB	40 KiB	39 KiB	31 KiB
xcc	1,454	4,056	5.58	17.09	22.56	15.14	-0.17	0.04	10	0.97	Undirected	Unipartite			28 KiB	40 KiB	38 KiB	31 KiB
xfa	1,092	2,906	5.32	14.00	19.14	18.06	-0.17	0.04	10	0.96	Undirected	Unipartite			20 KiB	29 KiB	29 KiB	23 KiB
ype	1,474	4,204	5.70	17.15	23.62	15.44	-0.17	0.04	9	0.97	Undirected	Unipartite			29 KiB	40 KiB	39 KiB	31 KiB
ypk	1,452	4,102	5.65	16.89	23.39	15.50	-0.17	0.04	9	0.97	Undirected	Unipartite			28 KiB	39 KiB	38 KiB	31 KiB

Ridiculograms^*

^* These are automatically generated force-directed visualizations, and can be quite meaningless for networks both big and small. They should not be taken seriously as sources of scientific insight. See here for a discussion.