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         UniProtKB/Swiss-Prot protein knowledgebase release 2013_06 statistics





1.  INTRODUCTION



Release 2013_06 of 29-May-13 of UniProtKB/Swiss-Prot contains 540261 sequence entries,

comprising 191876607 amino acids abstracted from 219534 references. 



220 sequences have been added since release 2013_05, the sequence data of

159 existing entries has been updated and the annotations of

305232 entries have been revised.



Number of fragments: 9065

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 34285





Protein existence (PE):           entries     %



1: Evidence at protein level        79161   14.7%

2: Evidence at transcript level     64260   11.9%

3: Inferred from homology          379230   70.2%

4: Predicted                        15711    2.9%

5: Uncertain                         1899    0.4%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 12988



   The first twenty species represent 113431 sequences:    21 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5435

                            2x: 1883

                            3x:  987

                            4x:  641

                            5x:  470

                            6x:  394

                            7x:  285

                            8x:  219

                            9x:  204

                           10x:  119

                       11- 20x:  694

                       21- 50x:  404

                       51-100x:  212

                         >100x: 1041





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20257  Homo sapiens (Human)

       2      16613  Mus musculus (Mouse)

       3      12069  Arabidopsis thaliana (Mouse-ear cress)

       4       7854  Rattus norvegicus (Rat)

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

       6       5977  Bos taurus (Bovine)

       7       5089  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4431  Escherichia coli (strain K12)

       9       4188  Bacillus subtilis (strain 168)

      10       4126  Dictyostelium discoideum (Slime mold)

      11       3428  Caenorhabditis elegans

      12       3365  Xenopus laevis (African clawed frog)

      13       3195  Drosophila melanogaster (Fruit fly)

      14       3038  Oryza sativa subsp. japonica (Rice)

      15       2885  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2255  Gallus gallus (Chicken)

      17       2218  Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)

      18       2020  Mycobacterium tuberculosis

      19       2015  Escherichia coli O157:H7

      20       1787  Methanocaldococcus jannaschii  

      21       1771  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

      22       1707  Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

      23       1692  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      24       1684  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      25       1678  Shigella flexneri

      26       1412  Sus scrofa (Pig)

      27       1346  Salmonella typhi

      28       1245  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      29       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

      30       1170  Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)

      31       1036  Synechocystis sp. (strain PCC 6803 / Kazusa)

      32       1018  Yersinia pestis

      33       1015  Archaeoglobus fulgidus 

      34        950  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      35        930  Salmonella paratyphi A (strain ATCC 9150 / SARB42)

      36        926  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      37        925  Staphylococcus aureus (strain N315)

      38        923  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      39        909  Acanthamoeba polyphaga mimivirus (APMV)

      40        905  Kluyveromyces lactis   

      41        899  Staphylococcus aureus (strain COL)

      42        895  Staphylococcus aureus (strain MW2)

      43        889  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      44        889  Staphylococcus aureus (strain MSSA476)

      45        889  Oryctolagus cuniculus (Rabbit)

      46        888  Staphylococcus aureus (strain MRSA252)

      47        882  Salmonella choleraesuis (strain SC-B67)

      48        878  Shigella sonnei (strain Ss046)

      49        869  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      50        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      51        861  Candida glabrata   

      52        841  Escherichia coli O9:H4 (strain HS)

      53        835  Neurospora crassa 

      54        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      55        829  Shigella boydii serotype 4 (strain Sb227)

      56        825  Escherichia coli (strain UTI89 / UPEC)

      57        821  Shigella dysenteriae serotype 1 (strain Sd197)

      58        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      59        803  Canis familiaris (Dog) (Canis lupus familiaris)

      60        791  Escherichia coli (strain SMS-3-5 / SECEC)

      61        787  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      62        783  Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) 

      63        782  Aquifex aeolicus (strain VF5)

      64        775  Pasteurella multocida (strain Pm70)

      65        775  Emericella nidulans  

      66        771  Escherichia coli (strain K12 / DH10B)

      67        765  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      68        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      69        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      70        762  Escherichia coli (strain 55989 / EAEC)

      71        761  Escherichia coli O8 (strain IAI1)

      72        760  Shigella flexneri serotype 5b (strain 8401)

      73        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      74        758  Staphylococcus epidermidis (strain ATCC 12228)

      75        756  Escherichia coli (strain SE11)

      76        756  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      77        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      78        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      79        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      80        744  Photorhabdus luminescens subsp. laumondii (strain TT01)

      81        740  Staphylococcus aureus (strain NCTC 8325)

      82        736  Bacillus anthracis

      83        736  Bacillus halodurans 

      84        735  Yersinia enterocolitica serotype O:8 / biotype 1B (strain 8081)

      85        733  Vibrio vulnificus (strain CMCP6)

      86        731  Escherichia coli O81 (strain ED1a)

      87        721  Salmonella enteritidis PT4 (strain P125109)

      88        720  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      89        717  Vibrio vulnificus (strain YJ016)

      90        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      91        716  Zea mays (Maize)

      92        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      93        714  Salmonella paratyphi A (strain AKU_12601)

      94        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      95        713  Enterobacter sp. (strain 638)

      96        713  Salmonella agona (strain SL483)

      97        713  Escherichia coli O1:K1 / APEC

      98        713  Salmonella newport (strain SL254)

      99        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     100        712  Salmonella schwarzengrund (strain CVM19633)

     101        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     102        710  Salmonella heidelberg (strain SL476)

     103        702  Salmonella dublin (strain CT_02021853)

     104        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     105        696  Klebsiella pneumoniae (strain 342)

     106        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     107        693  Pseudomonas putida (strain KT2440)

     108        689  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     109        688  Pan troglodytes (Chimpanzee)

     110        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     111        683  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     112        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     113        675  Pseudomonas syringae pv. tomato (strain DC3000)

     114        670  Serratia proteamaculans (strain 568)

     115        668  Mycobacterium leprae (strain TN)

     116        667  Yersinia pestis (strain Pestoides F)

     117        666  Staphylococcus aureus (strain USA300)

     118        658  Rhizobium sp. (strain NGR234)

     119        658  Bradyrhizobium japonicum (strain USDA 110)

     120        656  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     121        653  Debaryomyces hansenii   

     122        652  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        646  Escherichia coli

     124        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     125        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     126        642  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     127        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     128        635  Shewanella oneidensis (strain MR-1)

     129        634  Yersinia pseudotuberculosis serotype IB (strain PB1/+)

     130        632  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     131        623  Oryza sativa subsp. indica (Rice)

     132        622  Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)

     133        616  Treponema pallidum (strain Nichols)

     134        613  Methanothermobacter thermautotrophicus  

     135        612  Staphylococcus haemolyticus (strain JCSC1435)

     136        606  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     137        605  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     138        602  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

     139        602  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     140        602  Photobacterium profundum (Photobacterium sp. (strain SS9))

     141        602  Staphylococcus saprophyticus subsp. saprophyticus 

     142        601  Salmonella paratyphi C (strain RKS4594)

     143        600  Yersinia pestis bv. Antiqua (strain Angola)

     144        591  Listeria innocua serovar 6a (strain CLIP 11262)

     145        590  Bacillus cereus (strain ATCC 10987)

     146        589  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     147        586  Rickettsia prowazekii (strain Madrid E)

     148        581  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     149        579  Neisseria meningitidis serogroup B (strain MC58)

     150        576  Brucella suis biovar 1 (strain 1330)

     151        572  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     152        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     153        568  Caenorhabditis briggsae

     154        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     155        566  Pseudomonas syringae pv. syringae (strain B728a)

     156        565  Helicobacter pylori (strain J99) (Campylobacter pylori J99)

     157        565  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     159        564  Pseudomonas aeruginosa (strain UCBPP-PA14)

     160        563  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     161        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     162        561  Bacillus cereus (strain ZK / E33L)

     163        557  Clostridium acetobutylicum 

     164        556  Xanthomonas axonopodis pv. citri (strain 306)

     165        552  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     166        552  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     167        552  Pseudomonas fluorescens (strain Pf0-1)

     168        546  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

     169        545  Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6)

     170        533  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     171        532  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     172        531  Erwinia tasmaniensis (strain DSM 17950 / Et1/99)

     173        529  Sodalis glossinidius (strain morsitans)

     174        529  Listeria monocytogenes serotype 4b (strain F2365)

     175        522  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     176        522  Xylella fastidiosa (strain 9a5c)

     177        515  Chromobacterium violaceum 

     178        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     179        513  Corynebacterium glutamicum 

     180        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     181        511  Pseudomonas aeruginosa (strain PA7)

     182        511  Vibrio cholerae serotype O1 (strain ATCC 39541 / Ogawa 395 / O395)

     183        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     184        508  Staphylococcus aureus (strain Newman)

     185        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     186        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     187        507  Geobacillus kaustophilus (strain HTA426)

     188        505  Streptomyces avermitilis 

     189        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     190        502  Deinococcus radiodurans 

     191        500  Pseudomonas entomophila (strain L48)

     192        499  Brucella abortus biovar 1 (strain 9-941)

     193        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     194        496  Bacillus clausii (strain KSM-K16)

     195        495  Burkholderia pseudomallei (strain K96243)

     196        495  Haemophilus influenzae (strain 86-028NP)

     197        494  Proteus mirabilis (strain HI4320)

     198        492  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     199        492  Bacillus amyloliquefaciens (strain FZB42)

     200        491  Xanthomonas campestris pv. campestris (strain 8004)

     201        490  Vibrio harveyi (strain ATCC BAA-1116 / BB120)

     202        487  Shewanella sp. (strain MR-7)

     203        486  Mannheimia succiniciproducens (strain MBEL55E)

     204        484  Pseudomonas aeruginosa (strain LESB58)

     205        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     206        484  Shewanella sp. (strain MR-4)

     207        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     208        481  Thermosynechococcus elongatus (strain BP-1)

     209        480  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     210        480  Acinetobacter sp. (strain ADP1)

     211        479  Pyrococcus horikoshii 

     212        478  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     213        475  Pseudomonas putida (strain F1 / ATCC 700007)

     214        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     215        474  Brucella abortus (strain 2308)

     216        473  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     217        473  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     218        469  Methanosarcina mazei  

     219        468  Pyrococcus abyssi (strain GE5 / Orsay)

     220        468  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     221        468  Clostridium perfringens (strain 13 / Type A)

     222        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     223        466  Shewanella frigidimarina (strain NCIMB 400)

     224        466  Pseudomonas putida (strain GB-1)

     225        466  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     226        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     227        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     228        463  Shewanella sp. (strain ANA-3)

     229        462  Burkholderia mallei (strain ATCC 23344)

     230        462  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     231        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     232        460  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     233        459  Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (Alcaligenes eutrophus) 

     234        459  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     235        458  Enterococcus faecalis (strain ATCC 700802 / V583)

     236        455  Staphylococcus aureus (strain JH1)

     237        454  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     238        454  Ovis aries (Sheep)

     239        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     240        453  Nicotiana tabacum (Common tobacco)

     241        453  Pseudomonas putida (strain W619)

     242        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     243        452  Shewanella baltica (strain OS185)

     244        451  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     245        451  Aeromonas salmonicida (strain A449)

     246        449  Thermoanaerobacter tengcongensis  

     247        449  Staphylococcus aureus (strain JH9)

     248        449  Hahella chejuensis (strain KCTC 2396)

     249        449  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)

     250        448  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19015 (  4%)

    Bacteria         328923 ( 61%)

    Eukaryota        175992 ( 33%)

    Viruses           16331 (  3%)





   Within Eukaryota:



   



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

     Human                  20258 ( 12%)           (  4%)

     Other Mammalia         45892 ( 26%)           (  8%)

     Other Vertebrata       17427 ( 10%)           (  3%)

     Viridiplantae          33903 ( 19%)           (  6%)

     Fungi                  30834 ( 18%)           (  6%)

     Insecta                 8686 (  5%)           (  2%)

     Nematoda                4303 (  2%)           (  1%)

     Other                  14689 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9054             1001-1100     3746

                 51- 100   41392             1101-1200     2593

                101- 150   57659             1201-1300     2020

                151- 200   57750             1301-1400     1882

                201- 250   56491             1401-1500     1509

                251- 300   49970             1501-1600      729

                301- 350   50155             1601-1700      568

                351- 400   43420             1701-1800      467

                401- 450   35502             1801-1900      427

                451- 500   28590             1901-2000      351

                501- 550   20344             2001-2100      212

                551- 600   14610             2101-2200      287

                601- 650   12264             2201-2300      294

                651- 700    8843             2301-2400      181

                701- 750    7294             2401-2500      138

                751- 800    5184             >2500         1090

                801- 850    4534

                851- 900    5025

                901- 950    3871

                951-1000    2750



   





   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: 2325





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  758

                       2x:  305

                       3x:  155

                       4x:  115

                       5x:   88

                       6x:   75

                       7x:   55

                       8x:   46

                       9x:   37

                      10x:   31

                  11- 20x:  182

                  21- 50x:  192

                  51-100x:   99

                    >100x:  187





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



   Nb    Citations   Journal name

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

    1        21137   Journal of Biological Chemistry

    2         9537   Proceedings of the National Academy of Sciences of the U.S.A.

    3         5718   Journal of Bacteriology

    4         5043   Biochemical and Biophysical Research Communications

    5         4601   Gene

    6         4571   Nucleic Acids Research

    7         4456   Biochemistry

    8         4365   FEBS Letters

    9         4229   The EMBO Journal

   10         3924   Molecular and Cellular Biology

   11         3717   Nature

   12         3571   Journal of Molecular Biology

   13         3243   European Journal of Biochemistry

   14         3221   Biochimica et Biophysica Acta

   15         3036   Cell

   16         2578   Journal of Virology

   17         2509   Genomics

   18         2502   Biochemical Journal

   19         2464   Science

   20         2053   Molecular Microbiology

   21         1880   Journal of Cell Biology

   22         1861   Plant Physiology

   23         1645   Plant Molecular Biology

   24         1596   Genes and Development

   25         1596   The American Journal of Human Genetics

   26         1538   Virology

   27         1508   Nature Genetics

   28         1453   Human Molecular Genetics

   29         1439   Oncogene

   30         1345   Molecular and General Genetics

   31         1340   Development

   32         1332   Molecular Biology of the Cell

   33         1311   Human Mutation

   34         1289   The Plant Cell

   35         1241   Journal of Biochemistry

   36         1191   Journal of Immunology

   37         1177   The Plant Journal

   38         1162   Molecular Cell

   39         1104   Genetics

   40         1085   Structure

   41         1029   Journal of General Virology

   42          978   Blood

   43          949   Journal of Cell Science

   44          948   Infection and Immunity

   45          928   Archives of Biochemistry and Biophysics

   46          861   Microbiology

   47          835   Developmental Biology

   48          810   Cancer Research

   49          795   Current Biology

   50          786   Yeast

   51          735   FEMS Microbiology Letters

   52          677   Acta Crystallographica, Section D

   53          659   Protein Science

   54          650   Journal of Neuroscience

   55          647   Toxicon

   56          641   Applied and Environmental Microbiology

   57          626   Human Genetics

   58          626   Nature Structural Biology

   59          622   Mechanisms of Development

   60          594   Neuron

   61          581   PLoS ONE

   62          576   Journal of Clinical Investigation

   63          546   American Journal of Physiology

   64          540   Current Genetics

   65          528   The Journal of Experimental Medicine

   66          497   Proteins

   67          485   Molecular Endocrinology

   68          479   Mammalian Genome

   69          476   Plant and Cell Physiology

   70          467   Journal of Neurochemistry

   71          459   Immunogenetics

   72          449   Nature Cell Biology

   73          448   Bioscience, Biotechnology, and Biochemistry

   74          443   The Journal of Clinical Endocrinology and Metabolism

   75          436   Endocrinology

   76          429   Molecular and Biochemical Parasitology

   77          416   Journal of Medical Genetics

   78          398   Journal of Molecular Evolution

   79          381   Experimental Cell Research

   80          379   Molecular Biology and Evolution

   81          377   DNA and Cell Biology

   82          365   DNA Sequence

   83          351   Peptides

   84          333   Nature Structural and Molecular Biology

   85          329   Brain Research. Molecular Brain Research

   86          328   RNA

   87          326   Developmental Cell

   88          325   Tissue Antigens

   89          320   Comparative Biochemistry and Physiology

   90          318   The FEBS Journal

   91          316   Antimicrobial Agents and Chemotherapy

   92          308   Journal of Investigative Dermatology

   93          305   Molecular Pharmacology

   94          304   Planta

   95          294   Biological Chemistry Hoppe-Seyler

   96          285   Biology of Reproduction

   97          280   Neurology

   98          279   Cytogenetics and Cell Genetics

   99          269   Virus Research

  100          268   Developmental Dynamics

  101          267   Genome Research

  102          259   Immunity

  103          257   Journal of General Microbiology

  104          257   Eukaryotic Cell

  105          257   EMBO Reports

  106          255   Biochimie

  107          251   Genes to Cells

  108          245   Molecular Plant-Microbe Interactions

  109          242   The FASEB Journal

  110          237   The New England Journal of Medicine

  111          234   European Journal of Immunology

  112          224   Annals of Neurology

  113          223   European Journal of Human Genetics

  114          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  115          217   Journal of the American Chemical Society

  116          215   DNA Research

  117          211   Journal of Human Genetics

  118          202   Investigative Ophthalmology and Visual Science

  119          200   Archives of Microbiology

  120          198   Acta Crystallographica, Section F

  121          196   Nature Immunology

  122          190   Journal of Experimental Botany

  123          190   Journal of Cellular Biochemistry

  124          190   Archives of Virology

  125          188   BMC Genomics

  126          187   American Journal of Medical Genetics. Part A

  127          186   Molecular and Cellular Endocrinology

  128          183   Molecular Immunology

  129          181   Glycobiology

  130          178   Clinical Genetics

  131          176   Journal of Medicinal Chemistry

  132          173   Diabetes

  133          172   Insect Biochemistry and Molecular Biology

  134          168   American Journal of Medical Genetics

  135          168   Circulation Research

  136          168   Molecular Phylogenetics and Evolution

  137          166   PLoS Genetics

  138          165   International Journal of Cancer

  139          165   Traffic

  140          160   Molecular Genetics and Metabolism

  141          159   Molecular Reproduction and Development

  142          159   DNA

  143          158   Phytochemistry

  144          155   Hemoglobin

  145          154   Bioorganicheskaia Khimiia

  146          154   Molecular Genetics and Genomics

  147          154   Biological Chemistry

  148          153   Protein Expression and Purification

  149          153   Molecular and Cellular Neuroscience

  150          152   Cell Cycle





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)                      1042620                 1.93                                         

   Journal                            836079     417690      1.55       1                                 

   Submitted to EMBL/GenBank/DDBJ     197416     176349      0.37       2                                 

   Submitted to other databases         6896       6423      0.01       3                                 

   Book citation                         724        710     <0.01       4                                 

   Plant Gene Register                   585        573     <0.01       5                                 

   Thesis                                420        417     <0.01       6                                 

   Unpublished observations              304        300     <0.01       7                                 

   Patent                                190        187     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 336296



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2428057                 4.49                                         

   ALLERGEN                              529        529     <0.01      27                                 

   ALTERNATIVE PRODUCTS                22021      22021      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        4985       4985      0.01      23                                 

   BIOTECHNOLOGY                         345        343     <0.01      28                                 

   CATALYTIC ACTIVITY                 243842     221020      0.45       5                                 

   CAUTION                              9356       9183      0.02      19                                 

   COFACTOR                           108466      98839      0.20       7                                 

   DEVELOPMENTAL STAGE                  9880       9880      0.02      17                                 

   DISEASE                              5244       3516      0.01      22                                 

   DISRUPTION PHENOTYPE                 5710       5710      0.01      20                                 

   DOMAIN                              39566      34855      0.07      10                                 

   ENZYME REGULATION                   11174      11174      0.02      15                                 

   FUNCTION                           421780     404496      0.78       2                                 

   INDUCTION                           15274      15274      0.03      14                                 

   INTERACTION                         10182      10182      0.02      16                                 

   MASS SPECTROMETRY                    5530       4227      0.01      21                                 

   MISCELLANEOUS                       32867      30394      0.06      12                                 

   PATHWAY                            131715     119862      0.24       6                                 

   PHARMACEUTICAL                         92         92     <0.01      29                                 

   POLYMORPHISM                          892        839     <0.01      24                                 

   PTM                                 44462      34746      0.08       8                                 

   RNA EDITING                           627        627     <0.01      25                                 

   SEQUENCE CAUTION                    41132      41132      0.08       9                                 

   SIMILARITY                         641761     515637      1.19       1                                 

   SUBCELLULAR LOCATION               327337     321367      0.61       3                                 

   SUBUNIT                            244522     244522      0.45       4                                 

   TISSUE SPECIFICITY                  38782      38782      0.07      11                                 

   TOXIC DOSE                            551        515     <0.01      26                                 

   WEB RESOURCE                         9433       7501      0.02      18                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3724819                 6.89                                         

   ACT_SITE                           142672      87185      0.26       9                                 

   BINDING                            293001      78108      0.54       4                                 

   CA_BIND                              3915       1636      0.01      35                                 

   CARBOHYD                           107343      27511      0.20      15                                 

   CHAIN                              547065     534045      1.01       1                                 

   COILED                              20253      13909      0.04      26                                 

   COMPBIAS                            54393      28852      0.10      18                                 

   CONFLICT                           127838      44786      0.24      12                                 

   CROSSLNK                             6802       3927      0.01      34                                 

   DISULFID                           109525      30083      0.20      14                                 

   DNA_BIND                            10374       9449      0.02      31                                 

   DOMAIN                             161416      96004      0.30       8                                 

   HELIX                              181084      17647      0.34       6                                 

   INIT_MET                            14256      14256      0.03      27                                 

   INTRAMEM                             2173        937     <0.01      37                                 

   LIPID                               11925       7565      0.02      30                                 

   METAL                              319394      78388      0.59       3                                 

   MOD_RES                            166685      60840      0.31       7                                 

   MOTIF                               35930      23285      0.07      24                                 

   MUTAGEN                             43729      10134      0.08      22                                 

   NON_CONS                             2043        751     <0.01      38                                 

   NON_STD                               354        279     <0.01      39                                 

   NON_TER                             12211       9330      0.02      29                                 

   NP_BIND                            121050      73759      0.22      13                                 

   PEPTIDE                             10305       7028      0.02      32                                 

   PROPEP                              12667      10898      0.02      28                                 

   REGION                             133571      68029      0.25      10                                 

   REPEAT                              95297      14072      0.18      16                                 

   SIGNAL                              38283      38273      0.07      23                                 

   SITE                                47105      26278      0.09      19                                 

   STRAND                             189520      16668      0.35       5                                 

   TOPO_DOM                           130529      27098      0.24      11                                 

   TRANSIT                              8369       8265      0.02      33                                 

   TRANSMEM                           356364      73570      0.66       2                                 

   TURN                                44034      14284      0.08      21                                 

   UNSURE                               3359        715      0.01      36                                 

   VAR_SEQ                             45074      19157      0.08      20                                 

   VARIANT                             85527      16750      0.16      17                                 

   ZN_FING                             29384      12913      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)               15982598                29.58                                                           

   Allergome                            1502        942     <0.01     101      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     112      Organism-specific databases                  

   ArrayExpress                        36167      36167      0.07      47      Gene expression databases                    

   Bgee                                38776      38776      0.07      45      Gene expression databases                    

   BindingDB                            5033       5033      0.01      85      Other                                        

   BioCyc                             311752     301069      0.58      20      Enzyme and pathway databases                 

   BRENDA                               4320       4310      0.01      91      Enzyme and pathway databases                 

   CAZy                                 7635       6875      0.01      74      Protein family/group databases               

   CGD                                   700        678     <0.01     113      Organism-specific databases                  

   ChEMBL                               5222       5222      0.01      82      Other                                        

   ChiTaRS                             12531      12526      0.02      69      Other                                        

   CleanEx                             30084      29443      0.06      51      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     125      2D gel databases                             

   ConoServer                            916        834     <0.01     107      Organism-specific databases                  

   CTD                                 70240      69562      0.13      39      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      79      Organism-specific databases                  

   dictyBase                            4203       4087      0.01      93      Organism-specific databases                  

   DIP                                 14222      14131      0.03      67      Protein-protein interaction databases        

   DisProt                               398        395     <0.01     120      3D structure databases                       

   DMDM                                16758      16755      0.03      63      Polymorphism databases                       

   DNASU                               18699      18628      0.03      59      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     124      2D gel databases                             

   DrugBank                             5319       1628      0.01      81      Other                                        

   EchoBASE                             4161       4161      0.01      94      Organism-specific databases                  

   EcoGene                              4292       4290      0.01      92      Organism-specific databases                  

   eggNOG                             430741     430741      0.80      10      Phylogenomic databases                       

   EMBL                               938828     529006      1.74       3      Sequence databases                           

   Ensembl                             83321      48412      0.15      35      Genome annotation databases                  

   EnsemblBacteria                    343291     325141      0.64      18      Genome annotation databases                  

   EnsemblFungi                        17644      17352      0.03      62      Genome annotation databases                  

   EnsemblMetazoa                      12380       9271      0.02      70      Genome annotation databases                  

   EnsemblPlants                       15977      14151      0.03      66      Genome annotation databases                  

   EnsemblProtists                      4499       4372      0.01      90      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     126      Organism-specific databases                  

   EuPathDB                              810        798     <0.01     109      Organism-specific databases                  

   EvolutionaryTrace                   16588      16588      0.03      64      Other                                        

   FlyBase                              5893       5519      0.01      78      Organism-specific databases                  

   Gene3D                             358846     274085      0.66      16      Family and domain databases                  

   GeneCards                           20041      19753      0.04      56      Organism-specific databases                  

   GeneFarm                             3181       3170      0.01      96      Organism-specific databases                  

   GeneID                             501164     470713      0.93       6      Genome annotation databases                  

   GeneTree                            38201      38182      0.07      46      Phylogenomic databases                       

   Genevestigator                      67362      67362      0.12      41      Gene expression databases                    

   GenoList                             7071       7059      0.01      75      Organism-specific databases                  

   GenomeRNAi                          21291      21290      0.04      54      Other                                        

   GermOnline                          41894      41320      0.08      44      Gene expression databases                    

   GlycoSuiteDB                          272        272     <0.01     123      PTM databases                                

   GO                                2431618     510574      4.50       1      Ontologies                                   

   Gramene                              6022       6022      0.01      77      Organism-specific databases                  

   H-InvDB                              5593       4772      0.01      80      Organism-specific databases                  

   HAMAP                              315755     315352      0.58      19      Family and domain databases                  

   HGNC                                19854      19686      0.04      57      Organism-specific databases                  

   HOGENOM                            385422     385422      0.71      13      Phylogenomic databases                       

   HOVERGEN                            75559      75559      0.14      37      Phylogenomic databases                       

   HPA                                 19093      14742      0.04      58      Organism-specific databases                  

   InParanoid                          69983      69983      0.13      40      Phylogenomic databases                       

   IntAct                              34942      34942      0.06      48      Protein-protein interaction databases        

   InterPro                          1823885     517288      3.38       2      Family and domain databases                  

   IPI                                 97313      67805      0.18      32      Sequence databases                           

   KEGG                               477492     450825      0.88       8      Genome annotation databases                  

   KO                                 375746     375352      0.70      14      Phylogenomic databases                       

   LegioList                             765        763     <0.01     111      Organism-specific databases                  

   Leproma                               671        668     <0.01     114      Organism-specific databases                  

   MaizeGDB                              499        494     <0.01     118      Organism-specific databases                  

   MEROPS                              11873      11873      0.02      72      Protein family/group databases               

   MGI                                 16526      16480      0.03      65      Organism-specific databases                  

   MIM                                 18059      13686      0.03      61      Organism-specific databases                  

   MINT                                31520      31520      0.06      50      Protein-protein interaction databases        

   mycoCLAP                              282        277     <0.01     122      Protein family/group databases               

   NextBio                             70854      70854      0.13      38      Other                                        

   neXtProt                            20098      20098      0.04      55      Organism-specific databases                  

   OGP                                   377        377     <0.01     121      2D gel databases                             

   OMA                                394711     394711      0.73      12      Phylogenomic databases                       

   Orphanet                             5193       2816      0.01      83      Organism-specific databases                  

   OrthoDB                             78225      78225      0.14      36      Phylogenomic databases                       

   PANTHER                            203572     189742      0.38      24      Family and domain databases                  

   Pathway_Interaction_DB               4568       1666      0.01      89      Enzyme and pathway databases                 

   PATRIC                             308958     308929      0.57      21      Genome annotation databases                  

   PaxDb                               66674      66674      0.12      42      Proteomic databases                          

   PDB                                 94830      19462      0.18      34      3D structure databases                       

   PDBsum                              94830      19462      0.18      33      3D structure databases                       

   PeptideAtlas                         5163       5163      0.01      84      Proteomic databases                          

   PeroxiBase                            771        755     <0.01     110      Protein family/group databases               

   Pfam                               722255     498909      1.34       4      Family and domain databases                  

   PharmGKB                            18374      18350      0.03      60      Organism-specific databases                  

   PhosphoSite                         33567      33567      0.06      49      PTM databases                                

   PhosSite                              659        647     <0.01     115      PTM databases                                

   PhylomeDB                           27569      27569      0.05      53      Phylogenomic databases                       

   PIR                                118719     108564      0.22      28      Sequence databases                           

   PIRSF                               99486      99292      0.18      30      Family and domain databases                  

   PMAP-CutDB                           1457       1457     <0.01     102      Other                                        

   PomBase                              5016       4959      0.01      86      Organism-specific databases                  

   PptaseDB                               40         40     <0.01     127      Protein family/group databases               

   PRIDE                              111021     111021      0.21      29      Proteomic databases                          

   PRINTS                             137283     120287      0.25      26      Family and domain databases                  

   ProDom                              29304      29125      0.05      52      Family and domain databases                  

   ProMEX                                819        819     <0.01     108      Proteomic databases                          

   PROSITE                            483155     304512      0.89       7      Family and domain databases                  

   ProtClustDB                        343981     343981      0.64      17      Phylogenomic databases                       

   ProteinModelPortal                 431994     431994      0.80       9      3D structure databases                       

   PseudoCAP                            1253       1244     <0.01     104      Organism-specific databases                  

   Reactome                            13102       7882      0.02      68      Enzyme and pathway databases                 

   REBASE                                403        403     <0.01     119      Protein family/group databases               

   RefSeq                             526828     471068      0.98       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1257       1036     <0.01     103      2D gel databases                             

   RGD                                  7768       7764      0.01      73      Organism-specific databases                  

   SABIO-RK                             2541       2541     <0.01      99      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      76      Organism-specific databases                  

   SignaLink                            2961       2961      0.01      97      Enzyme and pathway databases                 

   SMART                              167734     125565      0.31      25      Family and domain databases                  

   SMR                                207581     207581      0.38      23      3D structure databases                       

   STRING                             396551     396551      0.73      11      Protein-protein interaction databases        

   SUPFAM                             373776     288870      0.69      15      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     105      2D gel databases                             

   TAIR                                12086      12033      0.02      71      Organism-specific databases                  

   TCDB                                 3664       3648      0.01      95      Protein family/group databases               

   TIGRFAMs                           290396     269813      0.54      22      Family and domain databases                  

   TubercuList                          2033       1997     <0.01     100      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     117      2D gel databases                             

   UCSC                                59053      44633      0.11      43      Genome annotation databases                  

   UniGene                             98851      89812      0.18      31      Sequence databases                           

   UniPathway                         131590     119742      0.24      27      Enzyme and pathway databases                 

   VectorBase                            606        588     <0.01     116      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     106      2D gel databases                             

   WormBase                             4894       3945      0.01      87      Organism-specific databases                  

   Xenbase                              4736       4731      0.01      88      Organism-specific databases                  

   ZFIN                                 2800       2800      0.01      98      Organism-specific databases                  



Total number of cross-referenced databases: 127



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.25   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.56

   Arg (R) 5.53   Glu (E) 6.75   Lys (K) 5.84   Thr (T) 5.34

   Asn (N) 4.06   Gly (G) 7.07   Met (M) 2.42   Trp (W) 1.08

   Asp (D) 5.45   His (H) 2.27   Phe (F) 3.86   Tyr (Y) 2.92

   Cys (C) 1.37   Ile (I) 5.96   Pro (P) 4.70   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



4461 entries are encoded on a mitochondrion, and 3716 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: 74729