ProDom-CG CG85

Release date = August 2003

Sequence and Family Data

Proteins used to build ProDom CG85:
A subset of the proteins used to build ProDom 2002.1
321971
(42 % of ProDom)

Number of complete genomes
85

domain families with at least 2 sequences
95138
(+22% since CG67)

domain families
283667
(+17 % since CG67)

PDB links
9154

Prosite links (Patterns, Profiles and Prefiles)
1423

Pfam-A links
4839

InterPro links
5824

Proteins used to build ProDom CG85: A subset of the proteins used to build ProDom 2002.1	321971 (42 % of ProDom)
Number of complete genomes	85
domain families with at least 2 sequences	95138 (+22% since CG67)
domain families	283667 (+17 % since CG67)
PDB links	9154
Prosite links (Patterns, Profiles and Prefiles)	1423
Pfam-A links	4839
InterPro links	5824

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-CG85

There are 16 archeal, 62 bacterial and 7 eukaryotic genomes in Prodom-CG.

Type	Organism	TaxId	Short name	nb of seq
				CG17	CG20	CG42	CG47	CG67	CG85
A	Aeropyrium pernix K1	56636	AERPE			2695	2700	2702	2702
A	Archaeoglobus fulgidus	2234	ARCFU	2407	2407	2396	2400	2400	2400
A	Halobacterium sp. (strain NRC-1)	64091	HALN1			2370	2425	2425	2425
A	Methanosarcina acetivorans	2214	METAC						4469
A	Methanococcus jannaschii	2190	METJA	1770	1770	1773	1771	1773	1775
A	Methanopyrus kandleri	2320	METKA						1687
A	Methanosarcina mazei	2209	METMA						3304
A	Methanobacterium thermoautotrophicum	187420	METTH	1869	1869	1869	1869	464	1868
A	Pyrococcus abyssi	29292	PYRAB			1765	1762	1762	1758
A	Pyrobaculum aerophilum.	13773	PYRAE					2595	2599
A	Pyrococcus furiosus	2261	PYRFU						2052
A	Pyrococcus horikoshii	53953	PYRHO	2061	2061	2062	2066	2069	2070
A	Sulfolobus solfataricus	2287	SULSO				2938	2938	2939
A	Sulfolobus tokodaii	111955	SULTO					2818	2818
A	Thermoplasma acidophilum	2303	THEAC			1478	1479	1479	1479
A	Thermoplasma volcanium	50339	THEVO					1523	1523
B	Agrobacterium tumefaciens (strain C58 / ATCC 33970)	176299	AGRT5					5391	5391
B	Aquifex aeolicus	103690	ANASP					6069	6072
B	Aquifex aeolicus	63363	AQUAE	1522	1522	1550	1549	1550	1551
B	Bacillus halodurans	86665	BACHD			4066	3988	3987	4008
B	Bacillus subtilis	1423	BACSU	4100	4100	4133	4119	4093	4099
B	Borrelia burgdorferi	139	BORBU	1255	1255	1251	1247	1247	1251
B	Brucella melitensis	29459	BRUME					3188	3187
B	Buchnera aphidicola	118099	BUCAI			568	573	573	572
B	Buchnera aphidicola	98794	BUCAP						560
B	Campylobacter jejuni	197	CAMJE			1613	1607	1607	1613
B	Caulobacter crescentus	69394	CAUCR				3717	3717	3718
B	Chlamydia muridarum	83560	CHLMU			916	919	919	919
B	Chlamydia pneumoniae	83558	CHLPN		1052	1052	1052	1052	1052
B	Chlorobium tepidum	1097	CHLTE						2244
B	Chlamydia trachomatis	813	CHLTR	894	894	894	895	895	895
B	Clostridium acetobutylicum	1488	CLOAB					3836	3848
B	Clostridium perfringens	1502	CLOPE					2722	2722
B	Corynebacterium glutamicum	1718	CORGL						3092
B	Deinococcus radiodurans	1299	DEIRA			3084	3083	3083	3084
B	Escherichia coli, and Escherichia coli O157:H7	83334	ECO57					5114	5139
B	Escherichia coli	562	ECOLI	4289	4289	4301	4301	4330	4347
B	Fusobacterium nucleatum (subsp. nucleatum)	76856	FUSNN						2050
B	Haemophilus	727	HAEIN	1709	1709	1712	1707	1710	1711
B	Helicobacter pylori J99	85963	HELPJ			1488	1486	1486	1488
B	Helicobacter pylori	210	HELPY	1565	1565	1554	1548	1548	1555
B	Lactococcus lactis (subsp. lactis)	1360	LACLA			2222	2224	2224	2224
B	Listeria innocua	1642	LISIN					3016	3017
B	Listeria monocytogenes	1639	LISMO					2843	2845
B	Mycoplasma genitalium	2097	MYCGE	480	480	483	485	485	486
B	Mycobacterium leprae	1769	MYCLE			1555	1590	1592	1592
B	Mycoplasma pneumoniae	2104	MYCPN	677	677	687	687	687	687
B	Mycoplasma pulmonis	2107	MYCPU				772	772	778
B	Mycobacterium tuberculosis	1773	MYCTU	3918	3918	3874	3847	3854	3877
B	Neisseria meningitidis (serogroup A)	65699	NEIMA			2039	2006	2006	2039
B	Neisseria meningitidis (serogroup B)	491	NEIMB			1967	1964	1965	1966
B	Pasteurella multocida	747	PASMU			2010	2014	2014	2015
B	Pseudomonas aeruginosa	287	PSEAE			5556	5553	5554	5555
B	Ralstonia solanacearum	305	RALSO						5020
B	Rhizobium loti (Mesorhizobium loti)	381	RHILO				7255	7259	7259
B	Rhizobium meliloti (Sinorhizobium meliloti)	382	RHIME					6132	6149
B	Rickettsia conorii, and Rickettsia rickettsii	781, 783	RICCN					1374	1374
B	Rickettsia prowazekii	782	RICPR		834	835	834	834	834
B	Salmonella typhi	601	SALTI					4683	4705
B	Salmonella typhimurium	602	SALTY					4429	4532
B	Staphylococcus aureus (strain Mu50 / ATCC 700699), and Staphylococcus aureus (strain N315)	158878, 158879	STAAM					2724	2727
B	Staphylococcus aureus (strain N315), and Staphylococcus aureus.	158879, 1280	STAAN					2589	2592
B	Staphylococcus aureus (strain MW2)	196620	STAAW						2659
B	Streptococcus coelicolor	1902	STRCO						7798
B	Streptococcus pyogenes (serotype M3)	198466	STRP3						1830
B	Streptococcus pyogenes (serotype M18)	186103	STRP8						1837
B	Streptococcus pneumoniae	1313	STRPN					2077	2079
B	Streptococcus pyogenes	1314	STRPY				1688	1688	1690
B	Synechocystis sp. (strain PCC 6803)	1148	SYNY3		3166	3143	3138	3140	3140
B	Thermotoga maritima	2336	THEMA			1847	1852	1852	1852
B	Thermoanaerobacter tengcongensis	119072	THETN						2547
B	Treponema pallidum	160	TREPA	1031	1031	1030	1029	1029	1029
B	Ureaplasma parvum	134821	UREPA			611	603	603	611
B	Vibrio cholerae	666	VIBCH			3784	3784	3784	3785
B	Xanthomonas axonopodis (pv. citri)	92829	XANAC						4358
B	Xanthomonas campestris (pv. campestris)	340	XANCP						4129
B	Xylella fastidiosa	2371	XYLFA			2774	2772	2773	2775
B	Yersinia pestis	632	YERPE					3853	3898
E	Arabidopsis thaliana	3702	ARATH			28624	25306	25301	26019
E	Caenorhabditis elegans	6239	CAEEL		16332	19810	17964	19804	20389
E	Drosophila melanogaster	7227	DROME			16387	13600	13704	16693
E	Homo sapiens	9606	HUMAN						29028
E	Mus musculus (Mouse)	10090	MOUSE					16214	21310
E	Schizosaccharomyces pombe	4896	SCHPO						5024
E	Saccharomyces cerevisiae	4932	YEAST			6594	6081	6127	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