ProDom-CG CG120

Release date = June 2004

Sequence and Family Data

Proteins used to build ProDom CG120:
A subset of the proteins used to build ProDom 2004.1
448751
(62 % of ProDom)

Number of complete genomes
120

domain families with at least 2 sequences
129667
(+36% since CG85)

domain families
365217
(+28% since CG85)

Families with a PDB link
6793

Families with a Prosite link (Patterns, Profiles)
16685

Families with a Pfam-A link
106269

Families with an InterPro link
124187

Proteins used to build ProDom CG120: A subset of the proteins used to build ProDom 2004.1	448751 (62 % of ProDom)
Number of complete genomes	120
domain families with at least 2 sequences	129667 (+36% since CG85)
domain families	365217 (+28% since CG85)
Families with a PDB link	6793
Families with a Prosite link (Patterns, Profiles)	16685
Families with a Pfam-A link	106269
Families with an InterPro link	124187

How is Prodom-CG built ?

ProDom-CG (Complete Genome) is a version of the ProDom database which holds only data originating from the complete genome sequencing projects. This release was builded using the following process:

Consider the complete genomes whose sequences are included inside Swissprot and Trembl (62 archeal or bacterial genomes, and 5 eukaryotic).
Start from Prodom Version 2003.1 (data of Jan 2003)
Keep only the sequences belonging to one of those genomes
Delete the ProDom families which are now empty
Calculate the multalignments and the consensus sequence for each remaining families.
Calculate the links towards other databases and the statistical data.

About the AC numbers

Because ProDom-CG was built from ProDom 2003.1, we could use an AC numbering scheme consistent with ProDom 2003.1:

The AC prefix is CG instead of PD
When a ProDom family is conserved inside ProDom-CG, its AC number is kept unchanged.
When a ProDom family is deleted for Prodom-CG, its AC number is marked as invalid in ProDom-CG

This enabled us to provide users of the Graphics User Interface with two more buttons:

From ProDom: access to the corresponding ProDom-CG family.
From ProDom-CG: access to the corresponding ProDom family. The button may be absent, meaning the this family was empty in ProDom-CG

Complete genomes found in ProDom-CG120

There are 16 archeal, 97 bacterial and 7 eukaryotic genomes in Prodom-CG.

Type	Organism	TaxId	Short name	nb of seq
				CG17	CG20	CG42	CG47	CG67	CG85	CG120
A	Aeropyrium pernix K1	56636	AERPE			2695	2700	2702	2702	2703
A	Archaeoglobus fulgidus	2234	ARCFU	2407	2407	2396	2400	2400	2400	2400
A	Halobacterium sp. (strain NRC-1)	64091	HALN1			2370	2425	2425	2425	2425
A	Methanosarcina acetivorans	2214	METAC						4469	4469
A	Methanococcus jannaschii	2190	METJA	1770	1770	1773	1771	1773	1775	1777
A	Methanopyrus kandleri	2320	METKA						1687	1687
A	Methanosarcina mazei	2209	METMA						3304	3304
A	Methanobacterium thermoautotrophicum	187420	METTH	1869	1869	1869	1869	464	1868	1868
A	Pyrococcus abyssi	29292	PYRAB			1765	1762	1762	1758	1784
A	Pyrobaculum aerophilum.	13773	PYRAE					2595	2599	2599
A	Pyrococcus furiosus	2261	PYRFU						2052	2052
A	Pyrococcus horikoshii	53953	PYRHO	2061	2061	2062	2066	2069	2070	2072
A	Sulfolobus solfataricus	2287	SULSO				2938	2938	2939	2939
A	Sulfolobus tokodaii	111955	SULTO					2818	2818	2818
A	Thermoplasma acidophilum	2303	THEAC			1478	1479	1479	1479	1479
A	Thermoplasma volcanium	50339	THEVO					1523	1523	1523
B	Agrobacterium tumefaciens (strain C58 / ATCC 33970)	176299	AGRT5					5391	5391	5392
B	Aquifex aeolicus	103690	ANASP					6069	6072	6072
B	Aquifex aeolicus	63363	AQUAE	1522	1522	1550	1549	1550	1551	1552
B	Bacillus anthracis (strain Ames)	198094	BACAA							5309
B	Bacillus cereus (strain ATCC 14579 / DSM 31)	226900	BACCR							5240
B	Bacillus halodurans	86665	BACHD			4066	3988	3987	4008	4007
B	Bacillus subtilis	1423	BACSU	4100	4100	4133	4119	4093	4099	4092
B	Bacteroides thetaiotaomicron	818	BACTN							4775
B	Bifidobacterium longum	216816	BIFLO							1724
B	Borrelia burgdorferi	139	BORBU	1255	1255	1251	1247	1247	1251	1558
B	Bradyrhizobium japonicum	375	BRAJA							8257
B	Brucella melitensis	29459	BRUME					3188	3187	3186
B	Brucella suis	29461	BRUSU							3247
B	Buchnera aphidicola	118099	BUCAI			568	573	573	572	572
B	Buchnera aphidicola	98794	BUCAP						560	560
B	Buchnera aphidicola (subsp. Baizongia pistaciae)	135842	BUCBP							507
B	Campylobacter jejuni	197	CAMJE			1613	1607	1607	1613	1613
B	Caulobacter crescentus	69394	CAUCR				3717	3717	3718	3718
B	Chlamydophila caviae	83557	CHLCV							1005
B	Chlamydia muridarum	83560	CHLMU			916	919	919	919	916
B	Chlamydia pneumoniae	83558	CHLPN		1052	1052	1052	1052	1052	1052
B	Chlorobium tepidum	1097	CHLTE						2244	2248
B	Chlamydia trachomatis	813	CHLTR	894	894	894	895	895	895	895
B	Clostridium acetobutylicum	1488	CLOAB					3836	3848	3848
B	Clostridium perfringens	1502	CLOPE					2722	2722	2722
B	Clostridium tetani	1513	CLOTE							2412
B	Corynebacterium efficiens	152794	COREF							2943
B	Corynebacterium glutamicum	1718	CORGL						3092	3092
B	Coxiella burnetii	777	COXBU							2021
B	Deinococcus radiodurans	1299	DEIRA			3084	3083	3083	3084	3084
B	Escherichia coli, and Escherichia coli O157:H7	83334	ECO57					5114	5139	5140
B	Escherichia coli O6	217992	ECOL6							5334
B	Escherichia coli	562	ECOLI	4289	4289	4301	4301	4330	4347	4347
B	Enterococcus faecalis (Streptococcus faecalis)	1351	ENTFA							3242
B	Fusobacterium nucleatum (subsp. nucleatum)	76856	FUSNN						2050	2050
B	Haemophilus	727	HAEIN	1709	1709	1712	1707	1710	1711	1711
B	Helicobacter pylori J99	85963	HELPJ			1488	1486	1486	1488	1488
B	Helicobacter pylori	210	HELPY	1565	1565	1554	1548	1548	1555	1555
B	Lactococcus lactis (subsp. lactis)	1360	LACLA			2222	2224	2224	2224	2224
B	Lactobacillus plantarum	1590	LACPL							3001
B	Leptospira interrogans	173	LEPIN							4692
B	Listeria innocua	1642	LISIN					3016	3017	3016
B	Listeria monocytogenes	1639	LISMO					2843	2845	2844
B	Mycoplasma genitalium	2097	MYCGE	480	480	483	485	485	486	486
B	Mycobacterium leprae	1769	MYCLE			1555	1590	1592	1592	1593
B	Mycoplasma penetrans	28227	MYCPE	677	677	687	687	687	687	1026
B	Mycoplasma pneumoniae	2104	MYCPN	677	677	687	687	687	687	687
B	Mycoplasma pulmonis	2107	MYCPU				772	772	778	772
B	Mycobacterium tuberculosis	1773	MYCTU	3918	3918	3874	3847	3854	3877	3877
B	Neisseria meningitidis (serogroup A)	65699	NEIMA			2039	2006	2006	2039	2039
B	Neisseria meningitidis (serogroup B)	491	NEIMB			1967	1964	1965	1966	1966
B	Nitrosomonas europaea	915	NITEU							2375
B	Oceanobacillus iheyensis	182710	OCEIH							3493
B	Pasteurella multocida	747	PASMU			2010	2014	2014	2015	2015
B	Pseudomonas aeruginosa	287	PSEAE			5556	5553	5554	5555	5556
B	Pseudomonas putida (strain KT2440)	160488	PSEPK							5314
B	Pseudomonas syringae (pv. tomato)	323	PSESM							5278
B	Ralstonia solanacearum	305	RALSO						5020	5020
B	Rhizobium loti (Mesorhizobium loti)	381	RHILO				7255	7259	7259	7259
B	Rhizobium meliloti (Sinorhizobium meliloti)	382	RHIME					6132	6149	6149
B	Rickettsia conorii, and Rickettsia rickettsii	781, 783	RICCN					1374	1374	1374
B	Rickettsia prowazekii	782	RICPR		834	835	834	834	834	834.
B	Salmonella typhi	601	SALTI					4683	4705	4708
B	Salmonella typhimurium	602	SALTY					4429	4532	4533
B	Shewanella oneidensis	70863	SHEON							4584
B	Shigella flexneri	623	SHIFL							4259
B	Staphylococcus aureus (strain Mu50 / ATCC 700699), and Staphylococcus aureus (strain N315), and Staphylococcus aureus (strain MW2)	158878, 158879, 196620	STAAM					2724	2727	2727
B	Staphylococcus aureus (strain N315)	158879	STAAN					2589	2592	2593
B	Staphylococcus aureus (strain MW2)	196620	STAAW						2659	2659
B	Staphylococcus epidermidis	1282	STAEP							2467
B	Streptococcus agalactiae (serotypes III and V)	216495, 216466	STRA3							1999
B	Streptococcus agalactiae (serotype V)	216466	STRA5							2106
B	Streptomyces avermitilis	33903	STRAW							7659
B	Streptococcus coelicolor	1902	STRCO						7798	8038
B	Streptococcus mutans	1309	STRMU							1953
B	Streptococcus pyogenes (serotype M3)	198466	STRP3						1830	1831
B	Streptococcus pyogenes (serotype M18)	186103	STRP8						1837	1837
B	Streptococcus pneumoniae	1313	STRPN					2077	2079	2079
B	Streptococcus pyogenes	1314	STRPY				1688	1688	1690	1690
B	Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	171101	STRR6							2038
B	Synechococcus elongatus (Thermosynechococcus elongatus)	32046	SYNEL							2452
B	Synechocystis sp. (strain PCC 6803)	1148	SYNY3		3166	3143	3138	3140	3140	3140
B	Thermotoga maritima	2336	THEMA			1847	1852	1852	1852	1852
B	Thermoanaerobacter tengcongensis	119072	THETN						2547	2547
B	Treponema pallidum	160	TREPA	1031	1031	1030	1029	1029	1029	1029
B	Tropheryma whipplei (strain TW08/27) (Whipple's bacillus)	218496	TROW8							781
B	Tropheryma whipplei (strain Twist) (Whipple's bacillus), and Tropheryma whipplei (Whipple's bacillus) (Tropheryma whippelii)	203267, 2039	TROWT							805
B	Ureaplasma parvum	134821	UREPA			611	603	603	611	611
B	Vibrio cholerae	666	VIBCH			3784	3784	3784	3785	3785
B	Vibrio parahaemolyticus	670	VIBPA							4821
B	Vibrio vulnificus	672	VIBVU							4483
B	Wigglesworthia glossinidia brevipalpis	36870	WIGBR							611
B	Xanthomonas axonopodis (pv. citri)	92829	XANAC						4358	4358
B	Xanthomonas campestris (pv. campestris)	340	XANCP						4129	4129
B	Xylella fastidiosa	2371	XYLFA			2774	2772	2773	2775	2775
B	Xylella fastidiosa (strain Temecula1 / ATCC 700964)	183190	XYLFT							2007
B	Yersinia pestis	632	YERPE					3853	3898	3899
E	Arabidopsis thaliana	3702	ARATH			28624	25306	25301	26019	26271
E	Caenorhabditis elegans	6239	CAEEL		16332	19810	17964	19804	20389	22769
E	Drosophila melanogaster	7227	DROME			16387	13600	13704	16693	16011
E	Homo sapiens	9606	HUMAN						29028	29435
E	Mus musculus (Mouse)	10090	MOUSE					16214	21310	28879
E	Schizosaccharomyces pombe	4896	SCHPO						5024	5040
E	Saccharomyces cerevisiae	4932	YEAST			6594	6081	6127	6219	6219

Global statistics

Distribution of the number of domains per sequence

NOTE - The sequences with more than 50 domains are not shown.

Distribution of the radius of gyration

NOTES -

The families with radius of gyration higher than 200 PAM are not shown
Only families with at least 2 sequences are used here

distribution of the diameter

NOTES -

The families with diameter higher than 500 PAM are not shown
Only families with at least 2 sequences are used here