ProDom-CG CG171

Release date = November 2005

Sequence and Family Data

Proteins used to build ProDom CG171:
A subset of the proteins used to build ProDom 2005.1
603067
(56.5 % of ProDom)

Number of complete genomes
171

domain families with at least 2 sequences
178675
(+39% since CG120)

domain families
499779
(+37% since CG120)

Families with a PDB link
10349

Families with a Prosite link (Patterns, Profiles)
30143

Families with a Pfam-A link
152952

Families with an InterPro link
175884

Proteins used to build ProDom CG171: A subset of the proteins used to build ProDom 2005.1	603067 (56.5 % of ProDom)
Number of complete genomes	171
domain families with at least 2 sequences	178675 (+39% since CG120)
domain families	499779 (+37% since CG120)
Families with a PDB link	10349
Families with a Prosite link (Patterns, Profiles)	30143
Families with a Pfam-A link	152952
Families with an InterPro link	175884

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 19 archeal, 97 bacterial and 9 eukaryotic genomes in Prodom-CG.

Type	Organism	TaxId	Short name	nb of seq
				CG17	CG20	CG42	CG47	CG67	CG85	CG120	CG171
A	Aeropyrium pernix K1	56636	AERPE			2695	2700	2702	2702	2703	2703
A	Archaeoglobus fulgidus	2234	ARCFU	2407	2407	2396	2400	2400	2400	2400	2400
A	Halobacterium sp. (strain NRC-1)	64091	HALN1			2370	2425	2425	2425	2425	2426
A	Methanosarcina acetivorans	2214	METAC						4469	4469	4470
A	Methanococcus jannaschii	2190	METJA	1770	1770	1773	1771	1773	1775	1777	1782
A	Methanopyrus kandleri	2320	METKA						1687	1687	1686
A	Methanosarcina mazei	2209	METMA						3304	3304	3304
A	Methanococcus maripaludis	39152	METMP								1721
A	Methanobacterium thermoautotrophicum	187420	METTH	1869	1869	1869	1869	464	1868	1868	1866
A	Nanoarchaeum equitans	160232	NANEQ								536
A	Picrophilus torridus	82076	PICTO								1534
A	Pyrococcus abyssi	29292	PYRAB			1765	1762	1762	1758	1784	1786
A	Pyrobaculum aerophilum.	13773	PYRAE					2595	2599	2599	2600
A	Pyrococcus furiosus	2261	PYRFU						2052	2052	2053
A	Pyrococcus horikoshii	53953	PYRHO	2061	2061	2062	2066	2069	2070	2072	2076
A	Sulfolobus solfataricus	2287	SULSO				2938	2938	2939	2939	2941
A	Sulfolobus tokodaii	111955	SULTO					2818	2818	2818	2819
A	Thermoplasma acidophilum	2303	THEAC			1478	1479	1479	1479	1479	1482
A	Thermoplasma volcanium	50339	THEVO					1523	1523	1523	1524
B	Acinetobacter sp. (strain ADP1).	62977	ACIAD								3302
B	Agrobacterium tumefaciens (strain C58 / ATCC 33970)	176299	AGRT5					5391	5391	5392	5397
B	Aquifex aeolicus	103690	ANASP					6069	6072	6072	6072
B	Aquifex aeolicus	63363	AQUAE	1522	1522	1550	1549	1550	1551	1552	1552
B	Bacillus anthracis	1392	BACAN								5611
B	Bacillus cereus (strain ATCC 10987)	222523	BACC1								5818
B	Bacillus cereus (strain ATCC 14579 / DSM 31)	226900	BACCR							5240	5241
B	Bacillus halodurans	86665	BACHD			4066	3988	3987	4008	4007	4007
B	Bacillus thuringiensis (subsp. konkukian)	180856	BACHK								5083
B	Bacillus subtilis	1423	BACSU	4100	4100	4133	4119	4093	4099	4092	4105
B	Bacteroides thetaiotaomicron	818	BACTN							4775	4775
B	Bartonella henselae (Rochalimaea henselae)	38323	BARHE								1465
B	Bartonella quintana (Rochalimaea quintana)	803	BARQU								1137
B	Bdellovibrio bacteriovorus	959	BDEBA								3577
B	Bifidobacterium longum	216816	BIFLO							1724	1724
B	Bordetella bronchiseptica (Alcaligenes bronchisepticus)	518	BORBR								4961
B	Borrelia burgdorferi	139	BORBU	1255	1255	1251	1247	1247	1251	1558	1558
B	Bordetella parapertussis	519	BORPA								4161
B	Bordetella pertussis	520	BORPE								3261
B	Bradyrhizobium japonicum	375	BRAJA							8257	8257
B	Brucella melitensis	29459	BRUME					3188	3187	3186	3182
B	Brucella suis	29461	BRUSU							3247	3253
B	Buchnera aphidicola	118099	BUCAI			568	573	573	572	572	572
B	Buchnera aphidicola	98794	BUCAP						560	560	561
B	Buchnera aphidicola (subsp. Baizongia pistaciae)	135842	BUCBP							507	507
B	Campylobacter jejuni	197	CAMJE			1613	1607	1607	1613	1613	1633
B	Candidatus Blochmannia floridanus	203907	CANBF								583
B	Caulobacter crescentus	69394	CAUCR				3717	3717	3718	3718	3718
B	Chlamydophila caviae	83557	CHLCV							1005	1005
B	Chlamydia muridarum	83560	CHLMU			916	919	919	919	916	916
B	Chlamydia pneumoniae	83558	CHLPN		1052	1052	1052	1052	1052	1052	1052
B	Chlorobium tepidum	1097	CHLTE						2244	2248	2248
B	Chlamydia trachomatis	813	CHLTR	894	894	894	895	895	895	895	895
B	Chromobacterium violaceum	536	CHRVO								4400
B	Clostridium acetobutylicum	1488	CLOAB					3836	3848	3848	3847
B	Clostridium perfringens	1502	CLOPE					2722	2722	2722	2722
B	Clostridium tetani	1513	CLOTE							2412	2414
B	Corynebacterium diphtheriae	1717	CORDI								2264
B	Corynebacterium efficiens	152794	COREF							2943	2947
B	Corynebacterium glutamicum	1718	CORGL						3092	3092	3093
B	Coxiella burnetii	777	COXBU							2021	2021
B	Deinococcus radiodurans	1299	DEIRA			3084	3083	3083	3084	3084	3084
B	Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)	882	DESVH								3507
B	Escherichia coli, and Escherichia coli O157:H7	83334	ECO57					5114	5139	5140	5276
B	Escherichia coli O6	217992	ECOL6							5334	5336
B	Escherichia coli	562	ECOLI	4289	4289	4301	4301	4330	4347	4347	4416
B	Enterococcus faecalis (Streptococcus faecalis)	1351	ENTFA							3242	3242
B	Erwinia carotovora subsp. atroseptica SCRI1043	218491	ERWCT								4449
B	Fusobacterium nucleatum (subsp. nucleatum)	76856	FUSNN						2050	2050	2049
B	Geobacter sulfurreducens	35554	GEOSL								3406
B	Gloeobacter violaceus	33072	GLOVI								4410
B	Haemophilus ducreyi	730	HAEDU								1694
B	Haemophilus	727	HAEIN	1709	1709	1712	1707	1710	1711	1711	1711
B	Halobacterium sp. (strain NRC-1 / ATCC 700922 / JCM 11081)	64091	HALN1								2426
B	Helicobacter hepaticus	32025	HELHP								1872
B	Helicobacter pylori J99	85963	HELPJ			1488	1486	1486	1488	1488	1488
B	Helicobacter pylori	210	HELPY	1565	1565	1554	1548	1548	1555	1555	1555
B	Lactobacillus johnsonii	33959	LACJO								1712
B	Lactococcus lactis (subsp. lactis)	1360	LACLA			2222	2224	2224	2224	2224	2224
B	Lactobacillus plantarum	1590	LACPL							3001	3001
B	Leifsonia xyli subsp. xyli str. CTCB07	281090	LEIXX								2003
B	Leptospira interrogans (serogroup Icterohaemorrhagiae / serovar OS Copenhageni)	44275	LEPIC								3649
B	Leptospira interrogans	173	LEPIN							4692	4692
B	Listeria innocua	1642	LISIN					3016	3017	3016	3017
B	Listeria monocytogenes (serotype 4b / strain F2365)	265669	LISMF								2814
B	Listeria monocytogenes	1639	LISMO					2843	2845	2844	2844
B	Mycoplasma gallisepticum	2096	MYCGA								727
B	Mycoplasma genitalium	2097	MYCGE	480	480	483	485	485	486	486	486
B	Mycobacterium leprae	1769	MYCLE			1555	1590	1592	1592	1593	1601
B	Mycoplasma mobile	2118	MYCMO								626
B	Mycoplasma mycoides (subsp. mycoides SC)	44101	MYCMS								977
B	Mycobacterium paratuberculosis	1770	MYCPA								4315
B	Mycoplasma penetrans	28227	MYCPE	677	677	687	687	687	687	1026	1029
B	Mycoplasma pneumoniae	2104	MYCPN	677	677	687	687	687	687	687	687
B	Mycoplasma pulmonis	2107	MYCPU				772	772	778	772	778
B	Mycobacterium tuberculosis	1773	MYCTU	3918	3918	3874	3847	3854	3877	3877	3949
B	Neisseria meningitidis (serogroup A)	65699	NEIMA			2039	2006	2006	2039	2039	2041
B	Neisseria meningitidis (serogroup B)	491	NEIMB			1967	1964	1965	1966	1966	1966
B	Nitrosomonas europaea	915	NITEU							2375	2374
B	Oceanobacillus iheyensis	182710	OCEIH							3493	3493
B	Onion yellows phytoplasma	100379	ONYPE								725
B	Parachlamydia sp. (strain UWE25) (subsp. Acanthamoeba sp.)	264201	PARUW								2024
B	Pasteurella multocida	747	PASMU			2010	2014	2014	2015	2015	2015
B	Photorhabdus luminescens (subsp. laumondii)	141679	PHOLL								4557
B	Photobacterium profundum (Photobacterium sp. (strain SS9))	74109	PHOPR								5324
B	Porphyromonas gingivalis (Bacteroides gingivalis)	837	PORGI								1864
B	Propionibacterium acnes	1747	PROAC								2292
B	Prochlorococcus marinus	1219	PROMA								1881
B	Prochlorococcus marinus (strain MIT 9313)	74547	PROMM								2257
B	Prochlorococcus marinus subsp. pastoris (strain CCMP 1378 / MED4)	59919	PROMP								1707
B	Pseudomonas aeruginosa	287	PSEAE			5556	5553	5554	5555	5556	5556
B	Pseudomonas putida (strain KT2440)	160488	PSEPK							5314	5314
B	Pseudomonas syringae (pv. tomato)	323	PSESM							5278	5420
B	Ralstonia solanacearum	305	RALSO						5020	5020	5020
B	Rhizobium loti (Mesorhizobium loti)	381	RHILO				7255	7259	7259	7259	7260
B	Rhodopirellula baltica	117	RHOBA								7271
B	Rhodopseudomonas palustris	1076	RHOPA								4798
B	Rhizobium meliloti (Sinorhizobium meliloti)	382	RHIME					6132	6149	6149	6149
B	Rickettsia conorii, and Rickettsia rickettsii	781, 783	RICCN					1374	1374	1374	1374
B	Rickettsia prowazekii	782	RICPR		834	835	834	834	834	834.	834
B	Salmonella typhi	601	SALTI					4683	4705	4708	4716
B	Salmonella typhimurium	602	SALTY					4429	4532	4533	4513
B	Shewanella oneidensis	70863	SHEON							4584	4584
B	Shigella flexneri	623	SHIFL							4259	4115
B	Staphylococcus aureus (strain Mu50 / ATCC 700699), and Staphylococcus aureus (strain N315), and Staphylococcus aureus (strain MW2)	158878, 158879, 196620	STAAM					2724	2727	2727	2710
B	Staphylococcus aureus (strain N315)	158879	STAAN					2589	2592	2593	2575
B	Staphylococcus aureus subsp. aureus MRSA252	282458	STAAR								2634
B	Staphylococcus aureus subsp. aureus MSSA476	282459	STAAS								2597
B	Staphylococcus aureus (strain MW2)	196620	STAAW						2659	2659	2654
B	Staphylococcus epidermidis	1282	STAEP							2467	2467
B	Streptococcus agalactiae (serotypes III and V)	216495, 216466	STRA3							1999	1999
B	Streptococcus agalactiae (serotype V)	216466	STRA5							2106	2106
B	Streptomyces avermitilis	33903	STRAW							7659	7662
B	Streptococcus coelicolor	1902	STRCO						7798	8038	8039
B	Streptococcus mutans	1309	STRMU							1953	1953
B	Streptococcus pyogenes (serotype M3)	198466	STRP3						1830	1831	1759
B	Streptococcus pyogenes (serotype M18)	186103	STRP8						1837	1837	1838
B	Streptococcus pneumoniae	1313	STRPN					2077	2079	2079	2079
B	Streptococcus pyogenes	1314	STRPY				1688	1688	1690	1690	1690
B	Streptococcus pneumoniae (strain ATCC BAA-255 / R6)	171101	STRR6							2038	2038
B	Synechococcus elongatus (Thermosynechococcus elongatus)	32046	SYNEL							2452	2452
B	Synechococcus sp. (strain WH8102)	84588	SYNPX								2512
B	Synechocystis sp. (strain PCC 6803)	1148	SYNY3		3166	3143	3138	3140	3140	3140	3505
B	Thermotoga maritima	2336	THEMA			1847	1852	1852	1852	1852	1852
B	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	262724	THET2								2201
B	Thermoanaerobacter tengcongensis	119072	THETN						2547	2547	2547
B	Treponema denticola	158	TREDE								2746
B	Treponema pallidum	160	TREPA	1031	1031	1030	1029	1029	1029	1029	1028
B	Tropheryma whipplei (strain TW08/27) (Whipple's bacillus)	218496	TROW8							781	781
B	Tropheryma whipplei (strain Twist) (Whipple's bacillus), and Tropheryma whipplei (Whipple's bacillus) (Tropheryma whippelii)	203267, 2039	TROWT							805	805
B	Ureaplasma parvum	134821	UREPA			611	603	603	611	611	611
B	Vibrio cholerae	666	VIBCH			3784	3784	3784	3785	3785	3785
B	Vibrio parahaemolyticus	670	VIBPA							4821	4821
B	Vibrio vulnificus	672	VIBVU							4483	4481
B	Vibrio vulnificus (strain YJ016)	196600	VIBVY								4990
B	Wigglesworthia glossinidia brevipalpis	36870	WIGBR							611	612
B	Wolbachia pipientis wMel	66077	WOLPM								1158
B	Wolinella succinogenes	844	WOLSU								2028
B	Xanthomonas axonopodis (pv. citri)	92829	XANAC						4358	4358	4358
B	Xanthomonas campestris (pv. campestris)	340	XANCP						4129	4129	4129
B	Xylella fastidiosa	2371	XYLFA			2774	2772	2773	2775	2775	2777
B	Xylella fastidiosa (strain Temecula1 / ATCC 700964)	183190	XYLFT							2007	2007
B	Yersinia pestis	632	YERPE					3853	3898	3899	3899
E	Arabidopsis thaliana	3702	ARATH			28624	25306	25301	26019	26271	26148
E	Ashbya gossypii (Yeast) (Eremothecium gossypii).	33169	ASHGO								4713
E	Caenorhabditis elegans	6239	CAEEL		16332	19810	17964	19804	20389	22769	21789
E	Drosophila melanogaster	7227	DROME			16387	13600	13704	16693	16011	20042
E	Homo sapiens	9606	HUMAN						29028	29435	33243
E	Mus musculus (Mouse)	10090	MOUSE					16214	21310	28879	29150
E	Plasmodium falciparum (isolate 3D7)	36329	PLAF7								5250
E	Schizosaccharomyces pombe	4896	SCHPO						5024	5040	4929
E	Saccharomyces cerevisiae	4932	YEAST			6594	6081	6127	6219	6219	6224

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