Corrigendum to “Novel domains of the prokaryotic two-component signal transduction systems”

Galperin, Michael Y.; Nikolskaya, Anastasia N.; Koonin, Eugene V.

doi:10.1111/j.1574-6968.2001.tb10887.x

In the above mentioned MiniReview, Table 2 was incorrect. It is now reproduced correctly below.

2

Inventory of signaling domains in complete prokaryotic genomes

Species^a	Genome size (kb)	Total number of proteins	Sensor module^b	Response module^b
			Cache	PAS	GAF	HisKin	CheY^c	Hpt	CheY^d	GGDEF	EAL	HD-GYP
Bacteria
*Mesorhizobium loti*	7036	6752	2	36	10	62	15	2	57	32	18	1
*Pseudomonas aeruginosa*	6264	5565	6	41	9	62^e	19	11	75	33	21	3
*Escherichia coli*	4639	4289	3	14	9	28^e	5	6	32	19	17	0
*Bacillus subtilis*	4215	4100	10	14	3	33^e	0	1	36	4	3	0
*Bacillus halodurans*	4202	4066	8	15	5	36^e	2	1	48	4	2	2
Mycobacterium tuberculosis	4412	3918	0	2	3	15	0	0	13	1	2	0
*Vibrio cholerae*	4033	3827	20	30	5	41^e	11	10	49	41	22	9
*Caulobacter crescentus*	4017	3737	3	26	6	62	28	2	45	11	10	0
Synechocystis sp.	3573	3169	2	26	28	42^e	17	7	41^e	23	13	2
Mycobacterium leprae	3268	2720	0	3	1	5	0	0	5	3	2	0
Xylella fastidiosa	2679	2766	0	4	1	14	5	2	20	3	3	1
*Deinococcus radiodurans*	2649	2580	0	7	3	21	5	0	25	16	5	4
*Lactococcus lactis*	2365	2266	0	2	1	7	0	0	7	0	0	0
Neisseria meningitidis	2184	2121	0	1	1	5	0	0	5	0	0	0
*Thermotoga maritima*	1861	1846	6	4	2	9	0	1	12	9+2^f	0	9
Haemophilus influenzae	1830	1709	0	1	0	4	0	2	6	0	0	0
Campylobacter jejuni	1641	1654	5	4	0	8	1	1	11	1+1	0	0
Helicobacter pylori	1668	1566	1	0	0	4	1	1	9	0	0	0
*Aquifex aeolicus*	1551	1522	1	7	4	4	0	0	5	11	7	1
Chlamydia pneumoniae	1230	1052	0	1	0	1	0	0	2	0	0	0
Treponema pallidum	1138	1031	1	0	2	1	0	1	4	1+1	0	3
Chlamydia trachomatis	1042	894	0	1	0	1	0	0	2	0	0	0
Borrelia burgdorferi	911	850	0	1	0	4	1	2	6	1	1	1
Rickettsia prowazekii	1111	834	0	0	0	4	0	0	5	1	1	0
Mycoplasma pneumoniae	816	689	0	0	0	0	0	0	0	0	0	0
Ureaplasma urealyticum	752	611	0	0	0	0	0	0	0	0	0	0
Buchnera sp. APS	641	564	0	0	0	0	0	0	0	0	0	0
Mycoplasma genitalium	580	484	0	0	0	0	0	0	0	0	0	0
Archaea
*Archaeoglobus fulgidus*	2178	2420	0	25	5	14	0	1	11	0	0	0
Halobacterium sp. NRC-1	2014	2058	0	15	7	14	3	1	6	0	0	0
*M. thermoautotrophicum*	1751	1869	0	15	4	16	3	0	8	0	0	0
*Pyrococcus abyssi*	1765	1765	1	1	0	1	0	0	2	0	0	0
*Pyrococcus horikoshii*	1739	∼1750	1	0	0	1	0	1	2	0	0	0
*Aeropyrum pernix*	1670	∼1720	0	0	0	0	0	0	0	0	0	0
*Methanococcus jannaschii*	1665	1715	0	0	0	0	0	0	0	0	0	0
*Thermoplasma acidophilum*	1565	1478	0	0	1	0	0	0	0	0	0	0

Species^a	Genome size (kb)	Total number of proteins	Sensor module^b	Response module^b
			Cache	PAS	GAF	HisKin	CheY^c	Hpt	CheY^d	GGDEF	EAL	HD-GYP
Bacteria
*Mesorhizobium loti*	7036	6752	2	36	10	62	15	2	57	32	18	1
*Pseudomonas aeruginosa*	6264	5565	6	41	9	62^e	19	11	75	33	21	3
*Escherichia coli*	4639	4289	3	14	9	28^e	5	6	32	19	17	0
*Bacillus subtilis*	4215	4100	10	14	3	33^e	0	1	36	4	3	0
*Bacillus halodurans*	4202	4066	8	15	5	36^e	2	1	48	4	2	2
Mycobacterium tuberculosis	4412	3918	0	2	3	15	0	0	13	1	2	0
*Vibrio cholerae*	4033	3827	20	30	5	41^e	11	10	49	41	22	9
*Caulobacter crescentus*	4017	3737	3	26	6	62	28	2	45	11	10	0
Synechocystis sp.	3573	3169	2	26	28	42^e	17	7	41^e	23	13	2
Mycobacterium leprae	3268	2720	0	3	1	5	0	0	5	3	2	0
Xylella fastidiosa	2679	2766	0	4	1	14	5	2	20	3	3	1
*Deinococcus radiodurans*	2649	2580	0	7	3	21	5	0	25	16	5	4
*Lactococcus lactis*	2365	2266	0	2	1	7	0	0	7	0	0	0
Neisseria meningitidis	2184	2121	0	1	1	5	0	0	5	0	0	0
*Thermotoga maritima*	1861	1846	6	4	2	9	0	1	12	9+2^f	0	9
Haemophilus influenzae	1830	1709	0	1	0	4	0	2	6	0	0	0
Campylobacter jejuni	1641	1654	5	4	0	8	1	1	11	1+1	0	0
Helicobacter pylori	1668	1566	1	0	0	4	1	1	9	0	0	0
*Aquifex aeolicus*	1551	1522	1	7	4	4	0	0	5	11	7	1
Chlamydia pneumoniae	1230	1052	0	1	0	1	0	0	2	0	0	0
Treponema pallidum	1138	1031	1	0	2	1	0	1	4	1+1	0	3
Chlamydia trachomatis	1042	894	0	1	0	1	0	0	2	0	0	0
Borrelia burgdorferi	911	850	0	1	0	4	1	2	6	1	1	1
Rickettsia prowazekii	1111	834	0	0	0	4	0	0	5	1	1	0
Mycoplasma pneumoniae	816	689	0	0	0	0	0	0	0	0	0	0
Ureaplasma urealyticum	752	611	0	0	0	0	0	0	0	0	0	0
Buchnera sp. APS	641	564	0	0	0	0	0	0	0	0	0	0
Mycoplasma genitalium	580	484	0	0	0	0	0	0	0	0	0	0
Archaea
*Archaeoglobus fulgidus*	2178	2420	0	25	5	14	0	1	11	0	0	0
Halobacterium sp. NRC-1	2014	2058	0	15	7	14	3	1	6	0	0	0
*M. thermoautotrophicum*	1751	1869	0	15	4	16	3	0	8	0	0	0
*Pyrococcus abyssi*	1765	1765	1	1	0	1	0	0	2	0	0	0
*Pyrococcus horikoshii*	1739	∼1750	1	0	0	1	0	1	2	0	0	0
*Aeropyrum pernix*	1670	∼1720	0	0	0	0	0	0	0	0	0	0
*Methanococcus jannaschii*	1665	1715	0	0	0	0	0	0	0	0	0	0
*Thermoplasma acidophilum*	1565	1478	0	0	1	0	0	0	0	0	0	0

^aThe names and data for non-obligate parasites are in bold. Complete genome sequences and corresponding references are available in the NCBI Entrez Genome division at http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/micr.html.

^bEach number represents the number of proteins in a given genome that contain the corresponding domain; multiple occurrences of the same domain (e.g., PAS, CheY) on a single polypeptide chain are counted as one. The numbers are from the COG database (http://www.ncbi.nlm.nih.gov/COG [4]) and/or from the results of iterative PSI-BLAST searches of domain-specific profiles against a database of proteins, encoded in completely sequenced microbial genomes [38,53,54]. These numbers were also compared against those in SMART [24] and those reported in [41]. Complete lists of proteins that contain each particular domain are available at ftp://ncbi.nlm.nih.gov/pub/galperin/TwoCompCensus.html.

^cCheY-like domains of the ‘hybrid’ sensor kinases (found on the same polypeptide chain with the His kinase domain, see [39]).

^dCheY-like domains found in the response regulators (associated with HTH, ATPase, CheB, GGDEF, or HD-GYP domains), as well as stand-alone CheY-like domains.

^eThese numbers do not include signaling proteins of the LytS family (COG3275, COG2972), predicted to be divergent His kinases [40]. The discrepancies with the numbers reported in [39] are due to the addition of Synechocystis sp. His kinase slr1212 and response regulators slr0687, sll1544, sll1879, and slr2041 and the exclusion of stand-alone Hpt domain slr0073 from the list of histidine kinases.

^fThese domains are likely to be inactivated.

2

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Inventory of signaling domains in complete prokaryotic genomes

Species^a	Genome size (kb)	Total number of proteins	Sensor module^b	Response module^b
			Cache	PAS	GAF	HisKin	CheY^c	Hpt	CheY^d	GGDEF	EAL	HD-GYP
Bacteria
*Mesorhizobium loti*	7036	6752	2	36	10	62	15	2	57	32	18	1
*Pseudomonas aeruginosa*	6264	5565	6	41	9	62^e	19	11	75	33	21	3
*Escherichia coli*	4639	4289	3	14	9	28^e	5	6	32	19	17	0
*Bacillus subtilis*	4215	4100	10	14	3	33^e	0	1	36	4	3	0
*Bacillus halodurans*	4202	4066	8	15	5	36^e	2	1	48	4	2	2
Mycobacterium tuberculosis	4412	3918	0	2	3	15	0	0	13	1	2	0
*Vibrio cholerae*	4033	3827	20	30	5	41^e	11	10	49	41	22	9
*Caulobacter crescentus*	4017	3737	3	26	6	62	28	2	45	11	10	0
Synechocystis sp.	3573	3169	2	26	28	42^e	17	7	41^e	23	13	2
Mycobacterium leprae	3268	2720	0	3	1	5	0	0	5	3	2	0
Xylella fastidiosa	2679	2766	0	4	1	14	5	2	20	3	3	1
*Deinococcus radiodurans*	2649	2580	0	7	3	21	5	0	25	16	5	4
*Lactococcus lactis*	2365	2266	0	2	1	7	0	0	7	0	0	0
Neisseria meningitidis	2184	2121	0	1	1	5	0	0	5	0	0	0
*Thermotoga maritima*	1861	1846	6	4	2	9	0	1	12	9+2^f	0	9
Haemophilus influenzae	1830	1709	0	1	0	4	0	2	6	0	0	0
Campylobacter jejuni	1641	1654	5	4	0	8	1	1	11	1+1	0	0
Helicobacter pylori	1668	1566	1	0	0	4	1	1	9	0	0	0
*Aquifex aeolicus*	1551	1522	1	7	4	4	0	0	5	11	7	1
Chlamydia pneumoniae	1230	1052	0	1	0	1	0	0	2	0	0	0
Treponema pallidum	1138	1031	1	0	2	1	0	1	4	1+1	0	3
Chlamydia trachomatis	1042	894	0	1	0	1	0	0	2	0	0	0
Borrelia burgdorferi	911	850	0	1	0	4	1	2	6	1	1	1
Rickettsia prowazekii	1111	834	0	0	0	4	0	0	5	1	1	0
Mycoplasma pneumoniae	816	689	0	0	0	0	0	0	0	0	0	0
Ureaplasma urealyticum	752	611	0	0	0	0	0	0	0	0	0	0
Buchnera sp. APS	641	564	0	0	0	0	0	0	0	0	0	0
Mycoplasma genitalium	580	484	0	0	0	0	0	0	0	0	0	0
Archaea
*Archaeoglobus fulgidus*	2178	2420	0	25	5	14	0	1	11	0	0	0
Halobacterium sp. NRC-1	2014	2058	0	15	7	14	3	1	6	0	0	0
*M. thermoautotrophicum*	1751	1869	0	15	4	16	3	0	8	0	0	0
*Pyrococcus abyssi*	1765	1765	1	1	0	1	0	0	2	0	0	0
*Pyrococcus horikoshii*	1739	∼1750	1	0	0	1	0	1	2	0	0	0
*Aeropyrum pernix*	1670	∼1720	0	0	0	0	0	0	0	0	0	0
*Methanococcus jannaschii*	1665	1715	0	0	0	0	0	0	0	0	0	0
*Thermoplasma acidophilum*	1565	1478	0	0	1	0	0	0	0	0	0	0

Species^a	Genome size (kb)	Total number of proteins	Sensor module^b	Response module^b
			Cache	PAS	GAF	HisKin	CheY^c	Hpt	CheY^d	GGDEF	EAL	HD-GYP
Bacteria
*Mesorhizobium loti*	7036	6752	2	36	10	62	15	2	57	32	18	1
*Pseudomonas aeruginosa*	6264	5565	6	41	9	62^e	19	11	75	33	21	3
*Escherichia coli*	4639	4289	3	14	9	28^e	5	6	32	19	17	0
*Bacillus subtilis*	4215	4100	10	14	3	33^e	0	1	36	4	3	0
*Bacillus halodurans*	4202	4066	8	15	5	36^e	2	1	48	4	2	2
Mycobacterium tuberculosis	4412	3918	0	2	3	15	0	0	13	1	2	0
*Vibrio cholerae*	4033	3827	20	30	5	41^e	11	10	49	41	22	9
*Caulobacter crescentus*	4017	3737	3	26	6	62	28	2	45	11	10	0
Synechocystis sp.	3573	3169	2	26	28	42^e	17	7	41^e	23	13	2
Mycobacterium leprae	3268	2720	0	3	1	5	0	0	5	3	2	0
Xylella fastidiosa	2679	2766	0	4	1	14	5	2	20	3	3	1
*Deinococcus radiodurans*	2649	2580	0	7	3	21	5	0	25	16	5	4
*Lactococcus lactis*	2365	2266	0	2	1	7	0	0	7	0	0	0
Neisseria meningitidis	2184	2121	0	1	1	5	0	0	5	0	0	0
*Thermotoga maritima*	1861	1846	6	4	2	9	0	1	12	9+2^f	0	9
Haemophilus influenzae	1830	1709	0	1	0	4	0	2	6	0	0	0
Campylobacter jejuni	1641	1654	5	4	0	8	1	1	11	1+1	0	0
Helicobacter pylori	1668	1566	1	0	0	4	1	1	9	0	0	0
*Aquifex aeolicus*	1551	1522	1	7	4	4	0	0	5	11	7	1
Chlamydia pneumoniae	1230	1052	0	1	0	1	0	0	2	0	0	0
Treponema pallidum	1138	1031	1	0	2	1	0	1	4	1+1	0	3
Chlamydia trachomatis	1042	894	0	1	0	1	0	0	2	0	0	0
Borrelia burgdorferi	911	850	0	1	0	4	1	2	6	1	1	1
Rickettsia prowazekii	1111	834	0	0	0	4	0	0	5	1	1	0
Mycoplasma pneumoniae	816	689	0	0	0	0	0	0	0	0	0	0
Ureaplasma urealyticum	752	611	0	0	0	0	0	0	0	0	0	0
Buchnera sp. APS	641	564	0	0	0	0	0	0	0	0	0	0
Mycoplasma genitalium	580	484	0	0	0	0	0	0	0	0	0	0
Archaea
*Archaeoglobus fulgidus*	2178	2420	0	25	5	14	0	1	11	0	0	0
Halobacterium sp. NRC-1	2014	2058	0	15	7	14	3	1	6	0	0	0
*M. thermoautotrophicum*	1751	1869	0	15	4	16	3	0	8	0	0	0
*Pyrococcus abyssi*	1765	1765	1	1	0	1	0	0	2	0	0	0
*Pyrococcus horikoshii*	1739	∼1750	1	0	0	1	0	1	2	0	0	0
*Aeropyrum pernix*	1670	∼1720	0	0	0	0	0	0	0	0	0	0
*Methanococcus jannaschii*	1665	1715	0	0	0	0	0	0	0	0	0	0
*Thermoplasma acidophilum*	1565	1478	0	0	1	0	0	0	0	0	0	0

^aThe names and data for non-obligate parasites are in bold. Complete genome sequences and corresponding references are available in the NCBI Entrez Genome division at http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/micr.html.

^bEach number represents the number of proteins in a given genome that contain the corresponding domain; multiple occurrences of the same domain (e.g., PAS, CheY) on a single polypeptide chain are counted as one. The numbers are from the COG database (http://www.ncbi.nlm.nih.gov/COG [4]) and/or from the results of iterative PSI-BLAST searches of domain-specific profiles against a database of proteins, encoded in completely sequenced microbial genomes [38,53,54]. These numbers were also compared against those in SMART [24] and those reported in [41]. Complete lists of proteins that contain each particular domain are available at ftp://ncbi.nlm.nih.gov/pub/galperin/TwoCompCensus.html.

^cCheY-like domains of the ‘hybrid’ sensor kinases (found on the same polypeptide chain with the His kinase domain, see [39]).

^dCheY-like domains found in the response regulators (associated with HTH, ATPase, CheB, GGDEF, or HD-GYP domains), as well as stand-alone CheY-like domains.

^eThese numbers do not include signaling proteins of the LytS family (COG3275, COG2972), predicted to be divergent His kinases [40]. The discrepancies with the numbers reported in [39] are due to the addition of Synechocystis sp. His kinase slr1212 and response regulators slr0687, sll1544, sll1879, and slr2041 and the exclusion of stand-alone Hpt domain slr0073 from the list of histidine kinases.

^fThese domains are likely to be inactivated.

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Corrigendum to “Novel domains of the prokaryotic two-component signal transduction systems”

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Corrigendum to “Novel domains of the prokaryotic two-component signal transduction systems”