UniProtKB/Swiss-Prot protein knowledgebase release 2014_09 statistics





1.  INTRODUCTION



Release 2014_09 of 01-Oct-14 of UniProtKB/Swiss-Prot contains 546439 sequence entries,

comprising 194445396 amino acids abstracted from 231080 references. 



208 sequences have been added since release 2014_08, the sequence data of

10 existing entries has been updated and the annotations of

538673 entries have been revised.



Number of fragments: 9125

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38126





Protein existence (PE):           entries     %



1: Evidence at protein level        84617   15.5%

2: Evidence at transcript level     62739   11.5%

3: Inferred from homology          385670   70.6%

4: Predicted                        11532    2.1%

5: Uncertain                         1881    0.3%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 13130



   The first twenty species represent 115153 sequences:  21.1 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5462

                            2x: 1896

                            3x: 1005

                            4x:  656

                            5x:  478

                            6x:  396

                            7x:  292

                            8x:  222

                            9x:  215

                           10x:  121

                       11- 20x:  708

                       21- 50x:  422

                       51-100x:  211

                         >100x: 1046





   2.2  Table of the most represented species



  ------  ---------  --------------------------------------------

  Number  Frequency  Species

  ------  ---------  --------------------------------------------

       1      20195  Homo sapiens (Human)

       2      16678  Mus musculus (Mouse)

       3      13199  Arabidopsis thaliana (Mouse-ear cress)

       4       7910  Rattus norvegicus (Rat)

       5       6621  Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

       6       5986  Bos taurus (Bovine)

       7       5103  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4433  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4127  Dictyostelium discoideum (Slime mold)

      11       3470  Caenorhabditis elegans

      12       3389  Xenopus laevis (African clawed frog)

      13       3266  Oryza sativa subsp. japonica (Rice)

      14       3236  Drosophila melanogaster (Fruit fly)

      15       2929  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2261  Gallus gallus (Chicken)

      17       2219  Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)

      18       2034  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2025  Escherichia coli O157:H7

      20       1887  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1779  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

      23       1707  Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

      24       1701  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      25       1688  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      26       1679  Shigella flexneri

      27       1414  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1271  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      30       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

      31       1170  Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)

      32       1048  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1021  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

      35        956  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      36        939  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      37        930  Salmonella paratyphi A (strain ATCC 9150 / SARB42)

      38        927  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      39        925  Staphylococcus aureus (strain N315)

      40        924  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      41        909  Acanthamoeba polyphaga mimivirus (APMV)

      42        905  Kluyveromyces lactis   

      43        899  Staphylococcus aureus (strain COL)

      44        895  Staphylococcus aureus (strain MW2)

      45        889  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      46        889  Staphylococcus aureus (strain MSSA476)

      47        889  Oryctolagus cuniculus (Rabbit)

      48        888  Staphylococcus aureus (strain MRSA252)

      49        882  Salmonella choleraesuis (strain SC-B67)

      50        878  Shigella sonnei (strain Ss046)

      51        875  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        841  Escherichia coli O9:H4 (strain HS)

      55        838  Neurospora crassa 

      56        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      57        829  Shigella boydii serotype 4 (strain Sb227)

      58        825  Escherichia coli (strain UTI89 / UPEC)

      59        822  Shigella dysenteriae serotype 1 (strain Sd197)

      60        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      61        810  Canis familiaris (Dog) (Canis lupus familiaris)

      62        791  Escherichia coli (strain SMS-3-5 / SECEC)

      63        790  Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) 

      64        788  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      65        786  Emericella nidulans  

      66        783  Aquifex aeolicus (strain VF5)

      67        776  Pasteurella multocida (strain Pm70)

      68        771  Escherichia coli (strain K12 / DH10B)

      69        771  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      70        767  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      71        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      72        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      73        762  Escherichia coli (strain 55989 / EAEC)

      74        761  Escherichia coli O8 (strain IAI1)

      75        760  Shigella flexneri serotype 5b (strain 8401)

      76        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      77        758  Staphylococcus epidermidis (strain ATCC 12228)

      78        756  Escherichia coli (strain SE11)

      79        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      80        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      81        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      82        747  Zea mays (Maize)

      83        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      84        742  Staphylococcus aureus (strain NCTC 8325)

      85        737  Bacillus halodurans 

      86        736  Bacillus anthracis

      87        736  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      88        733  Vibrio vulnificus (strain CMCP6)

      89        731  Escherichia coli O81 (strain ED1a)

      90        722  Salmonella enteritidis PT4 (strain P125109)

      91        717  Vibrio vulnificus (strain YJ016)

      92        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      93        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      94        715  Enterobacter sp. (strain 638)

      95        714  Salmonella paratyphi A (strain AKU_12601)

      96        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      97        713  Salmonella agona (strain SL483)

      98        713  Escherichia coli O1:K1 / APEC

      99        713  Salmonella newport (strain SL254)

     100        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     101        712  Salmonella schwarzengrund (strain CVM19633)

     102        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     103        710  Salmonella heidelberg (strain SL476)

     104        702  Pseudomonas putida (strain KT2440)

     105        702  Salmonella dublin (strain CT_02021853)

     106        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     107        696  Klebsiella pneumoniae (strain 342)

     108        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     109        691  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     110        689  Pan troglodytes (Chimpanzee)

     111        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     112        684  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     113        680  Oryza sativa subsp. indica (Rice)

     114        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

     116        671  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     117        670  Serratia proteamaculans (strain 568)

     118        668  Mycobacterium leprae (strain TN)

     119        667  Yersinia pestis (strain Pestoides F)

     120        666  Staphylococcus aureus (strain USA300)

     121        660  Bradyrhizobium diazoefficiens 

     122        659  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        658  Escherichia coli

     124        658  Rhizobium sp. (strain NGR234)

     125        653  Debaryomyces hansenii   

     126        644  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     127        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     128        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     129        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     130        638  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     131        636  Shewanella oneidensis (strain MR-1)

     132        634  Yersinia pseudotuberculosis serotype IB (strain PB1/+)

     133        622  Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)

     134        619  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

     137        609  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     138        607  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     139        606  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     140        602  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

     141        602  Photobacterium profundum (Photobacterium sp. (strain SS9))

     142        602  Staphylococcus saprophyticus subsp. saprophyticus 

     143        601  Salmonella paratyphi C (strain RKS4594)

     144        600  Yersinia pestis bv. Antiqua (strain Angola)

     145        591  Bacillus cereus (strain ATCC 10987)

     146        591  Listeria innocua serovar 6a (strain CLIP 11262)

     147        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     148        589  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     149        586  Rickettsia prowazekii (strain Madrid E)

     150        579  Neisseria meningitidis serogroup B (strain MC58)

     151        576  Brucella suis biovar 1 (strain 1330)

     152        573  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     153        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     154        568  Caenorhabditis briggsae

     155        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     156        567  Caulobacter crescentus (strain ATCC 19089 / CB15)

     157        567  Pseudomonas syringae pv. syringae (strain B728a)

     158        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     159        565  Pseudomonas aeruginosa (strain UCBPP-PA14)

     160        564  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     161        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     162        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     163        561  Bacillus cereus (strain ZK / E33L)

     164        558  Clostridium acetobutylicum 

     165        556  Xanthomonas axonopodis pv. citri (strain 306)

     166        553  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     167        553  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     168        552  Pseudomonas fluorescens (strain Pf0-1)

     169        546  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

     170        545  Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6)

     171        538  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     172        535  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     173        531  Erwinia tasmaniensis (strain DSM 17950 / Et1/99)

     174        529  Sodalis glossinidius (strain morsitans)

     175        529  Listeria monocytogenes serotype 4b (strain F2365)

     176        525  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     177        522  Xylella fastidiosa (strain 9a5c)

     178        515  Chromobacterium violaceum 

     179        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     180        515  Corynebacterium glutamicum 

     181        513  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     182        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        511  Pseudomonas aeruginosa (strain PA7)

     184        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     185        508  Staphylococcus aureus (strain Newman)

     186        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     187        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     188        507  Deinococcus radiodurans 

     189        507  Geobacillus kaustophilus (strain HTA426)

     190        506  Streptomyces avermitilis 

     191        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     192        500  Pseudomonas entomophila (strain L48)

     193        499  Brucella abortus biovar 1 (strain 9-941)

     194        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     195        496  Bacillus clausii (strain KSM-K16)

     196        495  Burkholderia pseudomallei (strain K96243)

     197        495  Haemophilus influenzae (strain 86-028NP)

     198        494  Proteus mirabilis (strain HI4320)

     199        494  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     200        492  Bacillus amyloliquefaciens subsp. plantarum 

     201        491  Xanthomonas campestris pv. campestris (strain 8004)

     202        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     203        490  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     204        488  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     205        488  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     206        487  Shewanella sp. (strain MR-7)

     207        486  Mannheimia succiniciproducens (strain MBEL55E)

     208        484  Pseudomonas aeruginosa (strain LESB58)

     209        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     210        484  Shewanella sp. (strain MR-4)

     211        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     212        483  Methanosarcina mazei  

     213        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     214        482  Thermosynechococcus elongatus (strain BP-1)

     215        481  Pyrococcus horikoshii 

     216        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     217        477  Pseudomonas putida (strain F1 / ATCC 700007)

     218        477  Brucella abortus (strain 2308)

     219        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     220        476  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     221        475  Pyrococcus abyssi (strain GE5 / Orsay)

     222        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     223        468  Clostridium perfringens (strain 13 / Type A)

     224        467  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     225        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     226        466  Shewanella frigidimarina (strain NCIMB 400)

     227        466  Pseudomonas putida (strain GB-1)

     228        464  Nicotiana tabacum (Common tobacco)

     229        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     230        464  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     231        463  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     232        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     233        463  Shewanella sp. (strain ANA-3)

     234        462  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     235        462  Burkholderia mallei (strain ATCC 23344)

     236        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     237        460  Enterococcus faecalis (strain ATCC 700802 / V583)

     238        459  Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Ralstonia eutropha 

     239        457  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     240        456  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     241        455  Staphylococcus aureus (strain JH1)

     242        455  Ovis aries (Sheep)

     243        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     244        453  Pseudomonas putida (strain W619)

     245        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     246        452  Shewanella baltica (strain OS185)

     247        451  Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

     248        451  Aeromonas salmonicida (strain A449)

     249        450  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)

     250        450  Dechloromonas aromatica (strain RCB)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19276 (  4%)

    Bacteria         331679 ( 61%)

    Eukaryota        179005 ( 33%)

    Viruses           16479 (  3%)





   Within Eukaryota:



   



    Category            sequences (% of Eukaryota) (% of the complete database)

     Human                  20196 ( 11%)           (  4%)

     Other Mammalia         46075 ( 26%)           (  8%)

     Other Vertebrata       17748 ( 10%)           (  3%)

     Viridiplantae          35612 ( 20%)           (  7%)

     Fungi                  31293 ( 17%)           (  6%)

     Insecta                 8767 (  5%)           (  2%)

     Nematoda                4346 (  2%)           (  1%)

     Other                  14968 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9102             1001-1100     3799

                 51- 100   41810             1101-1200     2644

                101- 150   58215             1201-1300     2047

                151- 200   58139             1301-1400     1919

                201- 250   56994             1401-1500     1533

                251- 300   50586             1501-1600      751

                301- 350   50757             1601-1700      577

                351- 400   43977             1701-1800      481

                401- 450   36051             1801-1900      439

                451- 500   28944             1901-2000      356

                501- 550   20653             2001-2100      217

                551- 600   14810             2101-2200      297

                601- 650   12406             2201-2300      300

                651- 700    8973             2301-2400      185

                701- 750    7397             2401-2500      141

                751- 800    5293             >2500         1111

                801- 850    4609

                851- 900    5085

                901- 950    3925

                951-1000    2791



   





   The average sequence length in UniProtKB/Swiss-Prot is 355 amino acids.



   The shortest sequence is   GWA_SEPOF (P83570):     2 amino acids.

   The longest sequence is  TITIN_MOUSE (A2ASS6): 35213 amino acids.





4.  JOURNAL CITATIONS



   Note: the following citation statistics reflect the number of distinct

         journal citations.



   Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2436





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  798

                       2x:  315

                       3x:  164

                       4x:  119

                       5x:   90

                       6x:   79

                       7x:   59

                       8x:   47

                       9x:   31

                      10x:   42

                  11- 20x:  191

                  21- 50x:  196

                  51-100x:  111

                    >100x:  194





   4.2  List of the most cited journals in UniProtKB/Swiss-Prot



   Nb    Citations   Journal name

   --    ---------   -------------------------------------------------------------

    1        22187   Journal of Biological Chemistry

    2        10076   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6029   Journal of Bacteriology

    4         5200   Biochemical and Biophysical Research Communications

    5         4717   Biochemistry

    6         4702   Nucleic Acids Research

    7         4664   Gene

    8         4504   FEBS Letters

    9         4376   The EMBO Journal

   10         4053   Molecular and Cellular Biology

   11         3925   Nature

   12         3830   Journal of Molecular Biology

   13         3327   Biochimica et Biophysica Acta

   14         3289   European Journal of Biochemistry

   15         3194   Cell

   16         2709   Journal of Virology

   17         2622   Science

   18         2604   Biochemical Journal

   19         2517   Genomics

   20         2206   Molecular Microbiology

   21         2029   Plant Physiology

   22         1971   Journal of Cell Biology

   23         1751   The American Journal of Human Genetics

   24         1703   Plant Molecular Biology

   25         1673   Genes and Development

   26         1584   Virology

   27         1570   Nature Genetics

   28         1546   Human Molecular Genetics

   29         1481   The Plant Cell

   30         1472   Oncogene

   31         1430   Molecular Biology of the Cell

   32         1414   Development

   33         1359   Molecular and General Genetics

   34         1357   Human Mutation

   35         1331   The Plant Journal

   36         1278   Molecular Cell

   37         1275   Journal of Biochemistry

   38         1221   Journal of Immunology

   39         1158   Structure

   40         1147   Genetics

   41         1043   Journal of General Virology

   42         1023   Blood

   43         1017   Journal of Cell Science

   44         1008   Infection and Immunity

   45          964   Archives of Biochemistry and Biophysics

   46          937   Microbiology

   47          919   PLoS ONE

   48          866   Developmental Biology

   49          865   Current Biology

   50          828   Cancer Research

   51          811   Yeast

   52          767   FEMS Microbiology Letters

   53          739   Acta Crystallographica, Section D

   54          711   Applied and Environmental Microbiology

   55          701   Journal of Neuroscience

   56          698   Protein Science

   57          692   Toxicon

   58          640   Human Genetics

   59          634   Nature Structural Biology

   60          628   Mechanisms of Development

   61          627   Neuron

   62          599   Journal of Clinical Investigation

   63          588   American Journal of Physiology

   64          553   The Journal of Experimental Medicine

   65          549   Current Genetics

   66          538   Proteins

   67          534   Plant and Cell Physiology

   68          504   Molecular Endocrinology

   69          485   Journal of Neurochemistry

   70          483   Mammalian Genome

   71          480   Nature Cell Biology

   72          470   Bioscience, Biotechnology, and Biochemistry

   73          469   Journal of Medical Genetics

   74          463   Endocrinology

   75          460   Immunogenetics

   76          449   The Journal of Clinical Endocrinology and Metabolism

   77          441   Molecular and Biochemical Parasitology

   78          403   Journal of Molecular Evolution

   79          398   Experimental Cell Research

   80          388   Nature Structural and Molecular Biology

   81          382   Molecular Biology and Evolution

   82          379   DNA and Cell Biology

   83          377   Peptides

   84          368   DNA Sequence

   85          363   The FEBS Journal

   86          359   RNA

   87          357   Developmental Cell

   88          342   Eukaryotic Cell

   89          342   Antimicrobial Agents and Chemotherapy

   90          331   Brain Research. Molecular Brain Research

   91          329   Planta

   92          327   Journal of Investigative Dermatology

   93          326   Comparative Biochemistry and Physiology

   94          325   Tissue Antigens

   95          322   Molecular Pharmacology

   96          299   Biology of Reproduction

   97          294   Biological Chemistry Hoppe-Seyler

   98          293   Neurology

   99          283   Developmental Dynamics

  100          281   Cytogenetics and Cell Genetics

  101          281   EMBO Reports

  102          276   Biochimie

  103          276   The FASEB Journal

  104          276   Immunity

  105          271   Genes to Cells

  106          270   Genome Research

  107          270   Virus Research

  108          263   Journal of General Microbiology

  109          262   The New England Journal of Medicine

  110          257   Molecular Plant-Microbe Interactions

  111          254   PLoS Genetics

  112          247   Journal of the American Chemical Society

  113          241   Acta Crystallographica, Section F

  114          240   European Journal of Human Genetics

  115          237   Annals of Neurology

  116          235   European Journal of Immunology

  117          221   Investigative Ophthalmology and Visual Science

  118          219   DNA Research

  119          219   Journal of Experimental Botany

  120          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  121          216   BMC Genomics

  122          215   Nature Immunology

  123          214   Archives of Microbiology

  124          214   Journal of Human Genetics

  125          205   Journal of Cellular Biochemistry

  126          201   American Journal of Medical Genetics. Part A

  127          198   Journal of Medicinal Chemistry

  128          196   Glycobiology

  129          195   Molecular and Cellular Endocrinology

  130          193   Clinical Genetics

  131          193   Archives of Virology

  132          191   Molecular Immunology

  133          186   Diabetes

  134          184   Circulation Research

  135          183   Cell Cycle

  136          176   Insect Biochemistry and Molecular Biology

  137          175   Applied Microbiology and Biotechnology

  138          175   Traffic

  139          175   PLoS Pathogens

  140          174   Phytochemistry

  141          173   Molecular Genetics and Metabolism

  142          170   International Journal of Cancer

  143          170   Protein Expression and Purification

  144          169   Molecular Phylogenetics and Evolution

  145          168   American Journal of Medical Genetics

  146          162   PLoS Biology

  147          161   Biological Chemistry

  148          160   Molecular Reproduction and Development

  149          159   DNA

  150          159   Molecular and Cellular Neuroscience





5.  STATISTICS FOR SOME LINE TYPES



The following table summarizes the total number of some UniProtKB/Swiss-Prot lines,

as well as the number of entries with at least one such line, and the

frequency of the lines.



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry

------------------------------------  -------- ---------  ---------



References (RL)                      1085771                 1.99                                         

   Journal                            892416     433966      1.63       1                                 

   Submitted to EMBL/GenBank/DDBJ     183312     162392      0.34       2                                 

   Submitted to other databases         7031       6533      0.01       3                                 

   Book citation                        1467       1453     <0.01       4                                 

   Plant Gene Register                   593        581     <0.01       5                                 

   Thesis                                424        421     <0.01       6                                 

   Unpublished observations              331        327     <0.01       7                                 

   Patent                                191        188     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 353952



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

------------------------------------  -------- ---------  ---------  ----

Comments (CC)                        2513080                 4.60                                         

   ALLERGEN                              664        664     <0.01      25                                 

   ALTERNATIVE PRODUCTS                23784      23784      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5975       5975      0.01      21                                 

   BIOTECHNOLOGY                         409        407     <0.01      28                                 

   CATALYTIC ACTIVITY                 251490     226574      0.46       5                                 

   CAUTION                              9898       9712      0.02      18                                 

   COFACTOR                           115758     105910      0.21       7                                 

   DEVELOPMENTAL STAGE                 10343      10343      0.02      17                                 

   DISEASE                              5707       3843      0.01      23                                 

   DISRUPTION PHENOTYPE                 7653       7653      0.01      20                                 

   DOMAIN                              42184      36705      0.08       9                                 

   ENZYME REGULATION                   12855      12855      0.02      16                                 

   FUNCTION                           435559     417683      0.80       2                                 

   INDUCTION                           16709      16709      0.03      14                                 

   INTERACTION                         13030      13030      0.02      15                                 

   MASS SPECTROMETRY                    5777       4403      0.01      22                                 

   MISCELLANEOUS                       33847      31256      0.06      12                                 

   PATHWAY                            133472     121461      0.24       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1037        980     <0.01      24                                 

   PTM                                 47152      36389      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42015      42015      0.08      10                                 

   SIMILARITY                         657224     521622      1.20       1                                 

   SUBCELLULAR LOCATION               334181     327790      0.61       3                                 

   SUBUNIT                            256103     256103      0.47       4                                 

   TISSUE SPECIFICITY                  40721      40721      0.07      11                                 

   TOXIC DOSE                            589        547     <0.01      27                                 

   WEB RESOURCE                         8219       6880      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

------------------------------------  -------- ---------  ---------  ----

Features (FT)                        3937219                 7.21                                         

   ACT_SITE                           149756      91685      0.27      10                                 

   BINDING                            326581      86724      0.60       4                                 

   CA_BIND                              3972       1669      0.01      35                                 

   CARBOHYD                           109277      28053      0.20      15                                 

   CHAIN                              553835     540090      1.01       1                                 

   COILED                              20778      14312      0.04      26                                 

   COMPBIAS                            56107      29888      0.10      18                                 

   CONFLICT                           130244      45547      0.24      13                                 

   CROSSLNK                             7170       4091      0.01      34                                 

   DISULFID                           115125      31365      0.21      14                                 

   DNA_BIND                            10720       9739      0.02      31                                 

   DOMAIN                             171457     103910      0.31       8                                 

   HELIX                              197759      18950      0.36       6                                 

   INIT_MET                            17742      17742      0.03      27                                 

   INTRAMEM                             2248        981     <0.01      37                                 

   LIPID                               12217       7832      0.02      30                                 

   METAL                              344408      85342      0.63       3                                 

   MOD_RES                            173777      62678      0.32       7                                 

   MOTIF                               37759      24496      0.07      24                                 

   MUTAGEN                             49968      11440      0.09      19                                 

   NON_CONS                             2069        759     <0.01      38                                 

   NON_STD                               357        282     <0.01      39                                 

   NON_TER                             12284       9390      0.02      29                                 

   NP_BIND                            131198      77504      0.24      12                                 

   PEPTIDE                             10490       7174      0.02      32                                 

   PROPEP                              12990      11186      0.02      28                                 

   REGION                             161319      77442      0.30       9                                 

   REPEAT                              97452      14349      0.18      16                                 

   SIGNAL                              39309      39299      0.07      23                                 

   SITE                                49751      27698      0.09      20                                 

   STRAND                             207220      17884      0.38       5                                 

   TOPO_DOM                           133188      27650      0.24      11                                 

   TRANSIT                              8697       8584      0.02      33                                 

   TRANSMEM                           361235      74667      0.66       2                                 

   TURN                                48115      15363      0.09      22                                 

   UNSURE                               3427        731      0.01      36                                 

   VAR_SEQ                             49663      20838      0.09      21                                 

   VARIANT                             87879      16902      0.16      17                                 

   ZN_FING                             29676      13113      0.05      25                                 



Total number of feature keys: 39







                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank      Category

------------------------------------  -------- ---------  ---------  ----      -------------------------------------------

Cross-references (DR)               16722461                30.60                                                           

   Allergome                            1633       1061     <0.01     104      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     117      Organism-specific databases                  

   ArrayExpress                        21909      21909      0.04      57      Gene expression databases                    

   Bgee                                38829      38829      0.07      49      Gene expression databases                    

   BindingDB                            4993       4993      0.01      91      Chemistry                                    

   BioCyc                             324370     307211      0.59      19      Enzyme and pathway databases                 

   BioGrid                             39408      39063      0.07      48      Protein-protein interaction databases        

   BRENDA                               4348       4336      0.01      94      Enzyme and pathway databases                 

   CAZy                                 7747       6970      0.01      77      Protein family/group databases               

   CCDS                                44892      33288      0.08      45      Sequence databases                           

   CGD                                   916        894     <0.01     112      Organism-specific databases                  

   ChEMBL                               5684       5684      0.01      84      Chemistry                                    

   ChiTaRS                             12556      12552      0.02      72      Other                                        

   CleanEx                             30068      29429      0.06      53      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     129      2D gel databases                             

   ConoServer                            949        866     <0.01     110      Organism-specific databases                  

   CTD                                 72093      71399      0.13      37      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      85      Organism-specific databases                  

   dictyBase                            4203       4087      0.01      96      Organism-specific databases                  

   DIP                                 15726      15661      0.03      70      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     121      3D structure databases                       

   DMDM                                16407      16407      0.03      69      Polymorphism databases                       

   DNASU                               18751      18681      0.03      64      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     128      2D gel databases                             

   DrugBank                             6742       1649      0.01      79      Chemistry                                    

   EchoBASE                             4161       4161      0.01      97      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      95      Organism-specific databases                  

   eggNOG                             430696     430696      0.79      12      Phylogenomic databases                       

   EMBL                               958021     535227      1.75       3      Sequence databases                           

   Ensembl                             81491      48856      0.15      35      Genome annotation databases                  

   EnsemblBacteria                    349059     330442      0.64      18      Genome annotation databases                  

   EnsemblFungi                        19027      18687      0.03      62      Genome annotation databases                  

   EnsemblMetazoa                      12163       9437      0.02      73      Genome annotation databases                  

   EnsemblPlants                       18719      15991      0.03      65      Genome annotation databases                  

   EnsemblProtists                      4481       4356      0.01      93      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     130      Organism-specific databases                  

   EuPathDB                              808        808     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16464      16464      0.03      68      Other                                        

   FlyBase                              5938       5564      0.01      83      Organism-specific databases                  

   Gene3D                             466339     343933      0.85       8      Family and domain databases                  

   GeneCards                           20886      19789      0.04      59      Organism-specific databases                  

   GeneFarm                             3313       3301      0.01      98      Organism-specific databases                  

   GeneID                             496704     469284      0.91       6      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     109      Organism-specific databases                  

   GeneTree                            38242      38228      0.07      50      Phylogenomic databases                       

   Genevestigator                      68222      68222      0.12      40      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      75      Other                                        

   GenoList                             7074       7062      0.01      78      Organism-specific databases                  

   GenomeRNAi                          21399      21399      0.04      58      Other                                        

   GO                                2556998     517800      4.68       1      Ontologies                                   

   Gramene                              6223       6223      0.01      81      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2012       2012     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      86      Organism-specific databases                  

   HAMAP                              323826     320907      0.59      20      Family and domain databases                  

   HGNC                                19980      19817      0.04      61      Organism-specific databases                  

   HOGENOM                            385511     385511      0.71      16      Phylogenomic databases                       

   HOVERGEN                            75646      75646      0.14      36      Phylogenomic databases                       

   HPA                                 22351      15981      0.04      56      Organism-specific databases                  

   InParanoid                          70961      70961      0.13      39      Phylogenomic databases                       

   IntAct                              42220      42220      0.08      47      Protein-protein interaction databases        

   InterPro                          1900432     525623      3.48       2      Family and domain databases                  

   KEGG                               476517     447720      0.87       7      Genome annotation databases                  

   KO                                 376559     376065      0.69      17      Phylogenomic databases                       

   LegioList                             765        763     <0.01     116      Organism-specific databases                  

   Leproma                               671        668     <0.01     118      Organism-specific databases                  

   MaizeGDB                              503        498     <0.01     123      Organism-specific databases                  

   MaxQB                               27059      27057      0.05      55      Proteomic databases                          

   MEROPS                              11917      11917      0.02      74      Protein family/group databases               

   MGI                                 16593      16549      0.03      67      Organism-specific databases                  

   MIM                                 18790      14006      0.03      63      Organism-specific databases                  

   MINT                                31579      31579      0.06      52      Protein-protein interaction databases        

   mycoCLAP                              328        320     <0.01     126      Protein family/group databases               

   NextBio                             71201      71201      0.13      38      Other                                        

   neXtProt                            20047      20047      0.04      60      Organism-specific databases                  

   OGP                                   376        376     <0.01     125      2D gel databases                             

   OMA                                403216     403216      0.74      13      Phylogenomic databases                       

   Orphanet                             6018       3167      0.01      82      Organism-specific databases                  

   OrthoDB                            389204     389204      0.71      15      Phylogenomic databases                       

   PANTHER                            172058     166189      0.31      24      Family and domain databases                  

   PATRIC                             307654     307624      0.56      21      Genome annotation databases                  

   PaxDb                               66594      66594      0.12      41      Proteomic databases                          

   PDB                                109119      21109      0.20      31      3D structure databases                       

   PDBsum                             109119      21109      0.20      30      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      88      Proteomic databases                          

   PeroxiBase                            769        753     <0.01     115      Protein family/group databases               

   Pfam                               738783     506964      1.35       4      Family and domain databases                  

   PharmGKB                            18384      18356      0.03      66      Organism-specific databases                  

   PhosphoSite                         33559      33559      0.06      51      PTM databases                                

   PhosSite                              605        596     <0.01     120      PTM databases                                

   PhylomeDB                           93315      93315      0.17      34      Phylogenomic databases                       

   PIR                                121606     111395      0.22      29      Sequence databases                           

   PIRSF                              102184     101222      0.19      33      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     105      Other                                        

   PomBase                              5139       5103      0.01      89      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     131      Protein family/group databases               

   PRIDE                              122276     122276      0.22      28      Proteomic databases                          

   PRINTS                             136752     120451      0.25      26      Family and domain databases                  

   PRO                                 57983      57983      0.11      43      Other                                        

   ProDom                              28667      28488      0.05      54      Family and domain databases                  

   ProMEX                                874        874     <0.01     113      Proteomic databases                          

   PROSITE                            444061     286848      0.81       9      Family and domain databases                  

   ProteinModelPortal                 440204     440204      0.81      11      3D structure databases                       

   PseudoCAP                            1279       1270     <0.01     106      Organism-specific databases                  

   Reactome                            56803      19933      0.10      44      Enzyme and pathway databases                 

   REBASE                                409        409     <0.01     124      Protein family/group databases               

   RefSeq                             645006     478388      1.18       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1258       1037     <0.01     107      2D gel databases                             

   RGD                                  7831       7827      0.01      76      Organism-specific databases                  

   SABIO-RK                             2897       2897      0.01     100      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      80      Organism-specific databases                  

   SignaLink                            2969       2961      0.01      99      Enzyme and pathway databases                 

   SMART                              169776     127141      0.31      25      Family and domain databases                  

   SMR                                218390     218390      0.40      23      3D structure databases                       

   STRING                             402594     402593      0.74      14      Protein-protein interaction databases        

   SUPFAM                             441758     339632      0.81      10      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     108      2D gel databases                             

   TAIR                                13194      13138      0.02      71      Organism-specific databases                  

   TCDB                                 5319       5299      0.01      87      Protein family/group databases               

   TIGRFAMs                           291083     270908      0.53      22      Family and domain databases                  

   TreeFam                             44745      44740      0.08      46      Phylogenomic databases                       

   TubercuList                          2062       2026     <0.01     102      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     122      2D gel databases                             

   UCSC                                58684      44731      0.11      42      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     127      PTM databases                                

   UniGene                            102420      92444      0.19      32      Sequence databases                           

   UniPathway                         133305     121299      0.24      27      Enzyme and pathway databases                 

   VectorBase                            613        595     <0.01     119      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     111      2D gel databases                             

   WormBase                             5038       4000      0.01      90      Organism-specific databases                  

   Xenbase                              4767       4761      0.01      92      Organism-specific databases                  

   ZFIN                                 2766       2766      0.01     101      Organism-specific databases                  



Total number of cross-referenced databases: 131



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.26   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.57

   Arg (R) 5.53   Glu (E) 6.74   Lys (K) 5.83   Thr (T) 5.34

   Asn (N) 4.05   Gly (G) 7.08   Met (M) 2.41   Trp (W) 1.09

   Asp (D) 5.46   His (H) 2.27   Phe (F) 3.86   Tyr (Y) 2.92

   Cys (C) 1.37   Ile (I) 5.95   Pro (P) 4.71   Val (V) 6.87



   Asx (B) 0.000  Glx (Z) 0.000  Xaa (X) 0.00



   



   Legend: gray = aliphatic, red = acidic, green = small hydroxy,

           blue = basic, black = aromatic, white = amide, yellow = sulfur





   6.2  Classification of the amino acids by their frequency



   Leu, Ala, Gly, Val, Glu, Ser, Ile, Lys, Arg, Asp, Thr, Pro, Asn, Gln,

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4465 entries are encoded on a mitochondrion, and 3780 are encoded on a plasmid.



12188 entries are encoded on a plastid, 

of which 21 are encoded on apicoplasts, 

11623 on chloroplasts, 

51 on organellar chromatophores,

145 on cyanelles, 

149 on non-photosynthetic plastids and 

199 on unspecified types of plastid.



Number of entries with at least one sequence correction: 76051