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


    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:

     

    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:

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

    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 -

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


    distribution of the diameter

    NOTES -

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