UniProtKB/Swiss-Prot protein knowledgebase release 2015_07 statistics





1.  INTRODUCTION



Release 2015_07 of 24-Jun-15 of UniProtKB/Swiss-Prot contains 548872 sequence entries,

comprising 195617763 amino acids abstracted from 237751 references. 



307 sequences have been added since release 2015_06, the sequence data of

11 existing entries has been updated and the annotations of

316192 entries have been revised.



Number of fragments: 9121

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38834





Protein existence (PE):           entries     %



1: Evidence at protein level        85772   15.6%

2: Evidence at transcript level     61870   11.3%

3: Inferred from homology          387762   70.6%

4: Predicted                        11507    2.1%

5: Uncertain                         1961    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: 13216



   The first twenty species represent 116485 sequences:  21.2 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5498

                            2x: 1895

                            3x: 1027

                            4x:  657

                            5x:  488

                            6x:  398

                            7x:  291

                            8x:  229

                            9x:  213

                           10x:  123

                       11- 20x:  711

                       21- 50x:  427

                       51-100x:  213

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20207  Homo sapiens (Human)

       2      16716  Mus musculus (Mouse)

       3      14041  Arabidopsis thaliana (Mouse-ear cress)

       4       7926  Rattus norvegicus (Rat)

       5       6718  Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

       6       5994  Bos taurus (Bovine)

       7       5119  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4433  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4131  Dictyostelium discoideum (Slime mold)

      11       3581  Caenorhabditis elegans

      12       3397  Xenopus laevis (African clawed frog)

      13       3362  Oryza sativa subsp. japonica (Rice)

      14       3247  Drosophila melanogaster (Fruit fly)

      15       2946  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2262  Gallus gallus (Chicken)

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

      18       2084  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2027  Escherichia coli O157:H7

      20       1890  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1785  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       1680  Shigella flexneri

      27       1415  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1292  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      30       1243  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

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

      32       1054  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1026  Archaeoglobus fulgidus 

      34       1022  Yersinia pestis

      35        981  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      36        957  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      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        926  Staphylococcus aureus (strain N315)

      40        925  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      41        910  Kluyveromyces lactis   

      42        909  Acanthamoeba polyphaga mimivirus (APMV)

      43        899  Staphylococcus aureus (strain COL)

      44        895  Staphylococcus aureus (strain MW2)

      45        892  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        878  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        843  Neurospora crassa 

      55        841  Escherichia coli O9:H4 (strain HS)

      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        812  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        790  Emericella nidulans  

      65        788  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      66        784  Aquifex aeolicus (strain VF5)

      67        776  Pasteurella multocida (strain Pm70)

      68        772  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      69        771  Escherichia coli (strain K12 / DH10B)

      70        771  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      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        752  Zea mays (Maize)

      82        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      83        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      84        743  Staphylococcus aureus (strain NCTC 8325)

      85        741  Bacillus halodurans 

      86        739  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  Escherichia coli O1:K1 / APEC

      96        714  Salmonella paratyphi A (strain AKU_12601)

      97        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      98        713  Salmonella agona (strain SL483)

      99        713  Salmonella newport (strain SL254)

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

     101        712  Oryza sativa subsp. indica (Rice)

     102        712  Salmonella schwarzengrund (strain CVM19633)

     103        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     104        710  Salmonella heidelberg (strain SL476)

     105        704  Pseudomonas putida (strain KT2440)

     106        702  Salmonella dublin (strain CT_02021853)

     107        698  Klebsiella pneumoniae (strain 342)

     108        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     109        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     110        693  Pan troglodytes (Chimpanzee)

     111        691  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     112        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     113        684  Salmonella gallinarum (strain 287/91 / NCTC 13346)

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

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

     116        675  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     117        670  Serratia proteamaculans (strain 568)

     118        668  Escherichia coli

     119        668  Mycobacterium leprae (strain TN)

     120        667  Yersinia pestis (strain Pestoides F)

     121        666  Staphylococcus aureus (strain USA300)

     122        664  Bacillus cereus 

     123        661  Bradyrhizobium diazoefficiens 

     124        658  Rhizobium sp. (strain NGR234)

     125        653  Debaryomyces hansenii   

     126        650  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     127        644  Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens 

     128        643  Shewanella oneidensis (strain MR-1)

     129        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     130        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     131        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

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

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

     134        620  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

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

     138        607  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     139        607  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     140        603  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        593  Bacillus cereus (strain ATCC 10987 / NRS 248)

     146        592  Listeria innocua serovar 6a (strain CLIP 11262)

     147        591  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     148        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     149        589  Pseudomonas aeruginosa (strain UCBPP-PA14)

     150        586  Rickettsia prowazekii (strain Madrid E)

     151        579  Neisseria meningitidis serogroup B (strain MC58)

     152        576  Brucella suis biovar 1 (strain 1330)

     153        574  Caenorhabditis briggsae

     154        573  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     155        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     156        569  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     157        568  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        568  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     159        567  Pseudomonas syringae pv. syringae (strain B728a)

     160        566  Vibrio fischeri (strain ATCC 700601 / ES114)

     161        564  Bacillus licheniformis 

     162        562  Bacillus cereus (strain ZK / E33L)

     163        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

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

     170        545  Pseudomonas savastanoi pv. phaseolicola  (Pseudomonas syringae pv. phaseolicola 

     171        541  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        518  Corynebacterium glutamicum 

     179        516  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     180        516  Chromobacterium violaceum 

     181        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     182        515  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        512  Pseudomonas aeruginosa (strain PA7)

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

     185        509  Deinococcus radiodurans 

     186        508  Staphylococcus aureus (strain Newman)

     187        508  Geobacillus kaustophilus (strain HTA426)

     188        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     189        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     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        494  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     201        493  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     202        492  Bacillus amyloliquefaciens subsp. plantarum 

     203        491  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     204        491  Xanthomonas campestris pv. campestris (strain 8004)

     205        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     206        487  Methanosarcina mazei  

     207        487  Shewanella sp. (strain MR-7)

     208        486  Mannheimia succiniciproducens (strain MBEL55E)

     209        484  Pseudomonas aeruginosa (strain LESB58)

     210        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     211        484  Thermosynechococcus elongatus (strain BP-1)

     212        484  Shewanella sp. (strain MR-4)

     213        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     214        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     215        482  Pyrococcus horikoshii 

     216        479  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     217        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     218        478  Pseudomonas putida (strain F1 / ATCC 700007)

     219        477  Pyrococcus abyssi (strain GE5 / Orsay)

     220        477  Brucella abortus (strain 2308)

     221        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     222        474  Burkholderia lata (strain ATCC 17760 / LMG 22485 / NCIMB 9086 / R18194 / 383)

     223        468  Clostridium perfringens (strain 13 / Type A)

     224        467  Nicotiana tabacum (Common tobacco)

     225        467  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     226        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     227        466  Shewanella frigidimarina (strain NCIMB 400)

     228        466  Pseudomonas putida (strain GB-1)

     229        466  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     230        466  Shewanella sp. (strain ANA-3)

     231        464  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     232        464  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     233        464  Aeromonas hydrophila subsp. hydrophila 

     234        464  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

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

     241        456  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     242        455  Staphylococcus aureus (strain JH1)

     243        455  Ovis aries (Sheep)

     244        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     245        453  Pseudomonas putida (strain W619)

     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           19348 (  4%)

    Bacteria         332160 ( 61%)

    Eukaryota        180762 ( 33%)

    Viruses           16602 (  3%)





   Within Eukaryota:



   



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

     Human                  20208 ( 11%)           (  4%)

     Other Mammalia         46163 ( 26%)           (  8%)

     Other Vertebrata       17843 ( 10%)           (  3%)

     Viridiplantae          36663 ( 20%)           (  7%)

     Fungi                  31582 ( 17%)           (  6%)

     Insecta                 8782 (  5%)           (  2%)

     Nematoda                4465 (  2%)           (  1%)

     Other                  15056 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9129             1001-1100     3835

                 51- 100   41936             1101-1200     2696

                101- 150   58407             1201-1300     2074

                151- 200   58311             1301-1400     1937

                201- 250   57158             1401-1500     1558

                251- 300   50764             1501-1600      758

                301- 350   51020             1601-1700      583

                351- 400   44167             1701-1800      489

                401- 450   36233             1801-1900      444

                451- 500   29106             1901-2000      363

                501- 550   20796             2001-2100      221

                551- 600   14903             2101-2200      299

                601- 650   12474             2201-2300      303

                651- 700    9012             2301-2400      187

                701- 750    7457             2401-2500      142

                751- 800    5340             >2500         1132

                801- 850    4643

                851- 900    5113

                901- 950    3946

                951-1000    2815



   





   The average sequence length in UniProtKB/Swiss-Prot is 356 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: 2505





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  812

                       2x:  327

                       3x:  175

                       4x:  119

                       5x:  100

                       6x:   79

                       7x:   51

                       8x:   48

                       9x:   32

                      10x:   40

                  11- 20x:  204

                  21- 50x:  201

                  51-100x:  114

                    >100x:  203





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



   Nb    Citations   Journal name

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

    1        22677   Journal of Biological Chemistry

    2        10320   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6174   Journal of Bacteriology

    4         5283   Biochemical and Biophysical Research Communications

    5         4858   Biochemistry

    6         4763   Nucleic Acids Research

    7         4707   Gene

    8         4583   FEBS Letters

    9         4437   The EMBO Journal

   10         4112   Molecular and Cellular Biology

   11         4030   Nature

   12         3919   Journal of Molecular Biology

   13         3389   Biochimica et Biophysica Acta

   14         3313   European Journal of Biochemistry

   15         3249   Cell

   16         2807   Journal of Virology

   17         2701   Science

   18         2661   Biochemical Journal

   19         2517   Genomics

   20         2262   Molecular Microbiology

   21         2149   Plant Physiology

   22         2008   Journal of Cell Biology

   23         1827   The American Journal of Human Genetics

   24         1741   Plant Molecular Biology

   25         1713   Genes and Development

   26         1619   Nature Genetics

   27         1614   The Plant Cell

   28         1608   Human Molecular Genetics

   29         1607   Virology

   30         1483   Oncogene

   31         1480   Molecular Biology of the Cell

   32         1467   The Plant Journal

   33         1466   Development

   34         1418   Human Mutation

   35         1369   Molecular and General Genetics

   36         1327   Molecular Cell

   37         1283   Journal of Biochemistry

   38         1237   Journal of Immunology

   39         1192   Structure

   40         1186   Genetics

   41         1082   PLoS ONE

   42         1058   Journal of Cell Science

   43         1052   Journal of General Virology

   44         1049   Blood

   45         1030   Infection and Immunity

   46          977   Microbiology

   47          976   Archives of Biochemistry and Biophysics

   48          897   Developmental Biology

   49          891   Current Biology

   50          836   Cancer Research

   51          824   Yeast

   52          785   FEMS Microbiology Letters

   53          772   Acta Crystallographica, Section D

   54          762   Journal of Neuroscience

   55          736   Applied and Environmental Microbiology

   56          713   Protein Science

   57          713   Toxicon

   58          654   Human Genetics

   59          650   Neuron

   60          637   Nature Structural Biology

   61          635   Journal of Clinical Investigation

   62          632   Mechanisms of Development

   63          611   American Journal of Physiology

   64          561   The Journal of Experimental Medicine

   65          559   Plant and Cell Physiology

   66          555   Current Genetics

   67          552   Proteins

   68          508   Molecular Endocrinology

   69          500   Journal of Medical Genetics

   70          499   Journal of Neurochemistry

   71          494   Nature Cell Biology

   72          489   Bioscience, Biotechnology, and Biochemistry

   73          484   Mammalian Genome

   74          476   The Journal of Clinical Endocrinology and Metabolism

   75          465   Endocrinology

   76          461   Immunogenetics

   77          443   Molecular and Biochemical Parasitology

   78          411   Experimental Cell Research

   79          409   Nature Structural and Molecular Biology

   80          403   Journal of Molecular Evolution

   81          392   Antimicrobial Agents and Chemotherapy

   82          391   The FEBS Journal

   83          386   Developmental Cell

   84          385   Molecular Biology and Evolution

   85          383   Peptides

   86          379   DNA and Cell Biology

   87          374   Eukaryotic Cell

   88          369   DNA Sequence

   89          368   RNA

   90          351   Planta

   91          345   Journal of Investigative Dermatology

   92          336   Molecular Pharmacology

   93          333   Brain Research. Molecular Brain Research

   94          329   Comparative Biochemistry and Physiology

   95          325   Tissue Antigens

   96          316   PLoS Genetics

   97          314   Neurology

   98          300   Biology of Reproduction

   99          298   EMBO Reports

  100          294   Biological Chemistry Hoppe-Seyler

  101          289   The FASEB Journal

  102          287   Developmental Dynamics

  103          286   Genes to Cells

  104          283   Biochimie

  105          283   Journal of the American Chemical Society

  106          282   Immunity

  107          281   The New England Journal of Medicine

  108          281   Cytogenetics and Cell Genetics

  109          277   Molecular Plant-Microbe Interactions

  110          277   Genome Research

  111          276   Virus Research

  112          267   Acta Crystallographica, Section F

  113          264   Journal of General Microbiology

  114          263   European Journal of Human Genetics

  115          253   Journal of Experimental Botany

  116          248   Annals of Neurology

  117          241   European Journal of Immunology

  118          232   Investigative Ophthalmology and Visual Science

  119          227   BMC Genomics

  120          224   Journal of Human Genetics

  121          221   American Journal of Medical Genetics. Part A

  122          220   DNA Research

  123          219   Archives of Microbiology

  124          219   Nature Immunology

  125          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  126          213   Clinical Genetics

  127          212   PLoS Pathogens

  128          211   Journal of Medicinal Chemistry

  129          209   Journal of Cellular Biochemistry

  130          205   Glycobiology

  131          199   Molecular and Cellular Endocrinology

  132          196   Traffic

  133          195   Circulation Research

  134          195   Archives of Virology

  135          194   Molecular Immunology

  136          192   Diabetes

  137          190   Applied Microbiology and Biotechnology

  138          189   Cell Cycle

  139          185   Molecular Genetics and Metabolism

  140          179   PLoS Biology

  141          179   Phytochemistry

  142          178   Protein Expression and Purification

  143          176   Insect Biochemistry and Molecular Biology

  144          173   International Journal of Cancer

  145          171   Molecular Phylogenetics and Evolution

  146          168   American Journal of Medical Genetics

  147          167   Journal of Lipid Research

  148          166   Proteomics

  149          164   Biological Chemistry

  150          163   Molecular Genetics and Genomics





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)                      1108232                 2.02                                         

   Journal                            913615     437144      1.66       1                                 

   Submitted to EMBL/GenBank/DDBJ     184452     162818      0.34       2                                 

   Submitted to other databases         7114       6599      0.01       3                                 

   Book citation                        1485       1471     <0.01       4                                 

   Plant Gene Register                   598        586     <0.01       5                                 

   Thesis                                426        423     <0.01       6                                 

   Unpublished observations              344        340     <0.01       7                                 

   Patent                                192        189     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 364954



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2548825                 4.64                                         

   ALLERGEN                              666        666     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24282      24282      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6551       6551      0.01      21                                 

   BIOTECHNOLOGY                         446        444     <0.01      28                                 

   CATALYTIC ACTIVITY                 254263     229123      0.46       5                                 

   CAUTION                             10179       9987      0.02      18                                 

   COFACTOR                           117473     107559      0.21       7                                 

   DEVELOPMENTAL STAGE                 10611      10611      0.02      17                                 

   DISEASE                              6030       4051      0.01      22                                 

   DISRUPTION PHENOTYPE                 8839       8839      0.02      19                                 

   DOMAIN                              43163      37409      0.08       9                                 

   ENZYME REGULATION                   13165      13165      0.02      16                                 

   FUNCTION                           441715     423677      0.80       2                                 

   INDUCTION                           17417      17417      0.03      14                                 

   INTERACTION                         15548      15548      0.03      15                                 

   MASS SPECTROMETRY                    5933       4499      0.01      23                                 

   MISCELLANEOUS                       34592      31790      0.06      12                                 

   PATHWAY                            134772     122146      0.25       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1045        989     <0.01      24                                 

   PTM                                 48948      37366      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42589      42589      0.08      10                                 

   SIMILARITY                         662491     523963      1.21       1                                 

   SUBCELLULAR LOCATION               336809     330232      0.61       3                                 

   SUBUNIT                            260102     260102      0.47       4                                 

   TISSUE SPECIFICITY                  41629      41629      0.08      11                                 

   TOXIC DOSE                            610        564     <0.01      27                                 

   WEB RESOURCE                         8232       6886      0.01      20                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        4038599                 7.36                                         

   ACT_SITE                           153160      93723      0.28      10                                 

   BINDING                            344122      91287      0.63       4                                 

   CA_BIND                              3985       1678      0.01      35                                 

   CARBOHYD                           110583      28333      0.20      15                                 

   CHAIN                              556356     542499      1.01       1                                 

   COILED                              21212      14645      0.04      26                                 

   COMPBIAS                            56809      30353      0.10      18                                 

   CONFLICT                           131236      45970      0.24      13                                 

   CROSSLNK                             7618       4182      0.01      34                                 

   DISULFID                           116004      31667      0.21      14                                 

   DNA_BIND                            11111      10102      0.02      31                                 

   DOMAIN                             175925     106616      0.32       8                                 

   HELIX                              208520      19753      0.38       6                                 

   INIT_MET                            17977      17977      0.03      27                                 

   INTRAMEM                             2360       1028     <0.01      37                                 

   LIPID                               12331       7931      0.02      29                                 

   METAL                              348020      86321      0.63       3                                 

   MOD_RES                            185405      64114      0.34       7                                 

   MOTIF                               38820      25112      0.07      24                                 

   MUTAGEN                             53009      12101      0.10      19                                 

   NON_CONS                             2050        756     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12273       9386      0.02      30                                 

   NP_BIND                            134994      78867      0.25      11                                 

   PEPTIDE                             10580       7215      0.02      32                                 

   PROPEP                              13086      11275      0.02      28                                 

   REGION                             171573      81625      0.31       9                                 

   REPEAT                              99734      14407      0.18      16                                 

   SIGNAL                              39724      39714      0.07      23                                 

   SITE                                50589      28105      0.09      21                                 

   STRAND                             217664      18636      0.40       5                                 

   TOPO_DOM                           134603      27673      0.25      12                                 

   TRANSIT                              8943       8830      0.02      33                                 

   TRANSMEM                           363223      75277      0.66       2                                 

   TURN                                50413      16046      0.09      22                                 

   UNSURE                               3645        736      0.01      36                                 

   VAR_SEQ                             50607      21261      0.09      20                                 

   VARIANT                             90135      16989      0.16      17                                 

   ZN_FING                             29842      13187      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)               17525396                31.93                                                           

   Allergome                            1648       1071     <0.01     108      Protein family/group databases               

   ArachnoServer                        1120       1110     <0.01     114      Organism-specific databases                  

   Bgee                                38840      38840      0.07      51      Gene expression databases                    

   BindingDB                            5566       5566      0.01      91      Chemistry                                    

   BioCyc                             325005     307753      0.59      19      Enzyme and pathway databases                 

   BioGrid                             42117      41730      0.08      50      Protein-protein interaction databases        

   BioMuta                             17254      17253      0.03      68      Polymorphism and mutation databases          

   BRENDA                              12681      11914      0.02      78      Enzyme and pathway databases                 

   CAZy                                 7816       7033      0.01      82      Protein family/group databases               

   CCDS                                45692      33440      0.08      46      Sequence databases                           

   CGD                                   967        936     <0.01     115      Organism-specific databases                  

   ChEMBL                               6161       6161      0.01      86      Chemistry                                    

   ChiTaRS                             16455      16445      0.03      72      Other                                        

   CleanEx                             30059      29419      0.05      56      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     132      2D gel databases                             

   ConoServer                            949        866     <0.01     116      Organism-specific databases                  

   CTD                                 72857      72155      0.13      41      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      89      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     130      PTM databases                                

   dictyBase                            4207       4091      0.01      99      Organism-specific databases                  

   DIP                                 16261      16202      0.03      74      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     122      3D structure databases                       

   DMDM                                16396      16395      0.03      73      Polymorphism and mutation databases          

   DNASU                               18825      18754      0.03      65      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     148        146     <0.01     131      2D gel databases                             

   DrugBank                            11228       1777      0.02      79      Chemistry                                    

   EchoBASE                             4161       4161      0.01     100      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      98      Organism-specific databases                  

   eggNOG                             431796     431796      0.79      12      Phylogenomic databases                       

   EMBL                               965969     537622      1.76       3      Sequence databases                           

   Ensembl                             83463      48419      0.15      39      Genome annotation databases                  

   EnsemblBacteria                    353689     334771      0.64      17      Genome annotation databases                  

   EnsemblFungi                        18799      18524      0.03      66      Genome annotation databases                  

   EnsemblMetazoa                      12788       9546      0.02      77      Genome annotation databases                  

   EnsemblPlants                       20684      17697      0.04      61      Genome annotation databases                  

   EnsemblProtists                      4458       4333      0.01      97      Genome annotation databases                  

   ESTHER                               2413       2413     <0.01     105      Protein family/group databases               

   euHCVdb                                55         44     <0.01     134      Organism-specific databases                  

   EuPathDB                            16762      16762      0.03      69      Organism-specific databases                  

   EvolutionaryTrace                   16520      16519      0.03      71      Other                                        

   ExpressionAtlas                     32014      32014      0.06      53      Gene expression databases                    

   FlyBase                              5950       5576      0.01      88      Organism-specific databases                  

   Gene3D                             464269     342249      0.85       7      Family and domain databases                  

   GeneCards                           20871      19783      0.04      60      Organism-specific databases                  

   GeneFarm                             3373       3361      0.01     101      Organism-specific databases                  

   GeneID                             278954     269631      0.51      23      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     113      Organism-specific databases                  

   GeneTree                            55341      55317      0.10      45      Phylogenomic databases                       

   Genevisible                         42504      42504      0.08      49      Gene expression databases                    

   GeneWiki                            10368      10282      0.02      80      Other                                        

   GenoList                             7075       7063      0.01      83      Organism-specific databases                  

   GenomeRNAi                          21696      21696      0.04      59      Other                                        

   GO                                2670600     520206      4.87       1      Ontologies                                   

   Gramene                              6297       6297      0.01      85      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2121       2121     <0.01     106      Chemistry                                    

   H-InvDB                              5592       4769      0.01      90      Organism-specific databases                  

   HAMAP                              324526     321564      0.59      20      Family and domain databases                  

   HGNC                                20015      19859      0.04      63      Organism-specific databases                  

   HOGENOM                            387634     387634      0.71      15      Phylogenomic databases                       

   HOVERGEN                            75706      75706      0.14      40      Phylogenomic databases                       

   HPA                                 24716      16223      0.05      58      Organism-specific databases                  

   InParanoid                         135431     135431      0.25      27      Phylogenomic databases                       

   IntAct                              44249      44249      0.08      48      Protein-protein interaction databases        

   InterPro                          1920662     527920      3.50       2      Family and domain databases                  

   KEGG                               486830     458962      0.89       6      Genome annotation databases                  

   KO                                 381910     381418      0.70      16      Phylogenomic databases                       

   LegioList                             765        763     <0.01     119      Organism-specific databases                  

   Leproma                               671        668     <0.01     120      Organism-specific databases                  

   MaizeGDB                              505        500     <0.01     124      Organism-specific databases                  

   MaxQB                               31465      31465      0.06      55      Proteomic databases                          

   MEROPS                              12882      12882      0.02      76      Protein family/group databases               

   MGI                                 16632      16588      0.03      70      Organism-specific databases                  

   MIM                                 19343      14246      0.04      64      Organism-specific databases                  

   MINT                                31646      31646      0.06      54      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     133      Protein family/group databases               

   mycoCLAP                              346        342     <0.01     128      Protein family/group databases               

   NextBio                             71369      71369      0.13      42      Other                                        

   neXtProt                            20049      20049      0.04      62      Organism-specific databases                  

   OGP                                   375        375     <0.01     127      2D gel databases                             

   OMA                                408764     408764      0.74      13      Phylogenomic databases                       

   Orphanet                             6148       3289      0.01      87      Organism-specific databases                  

   OrthoDB                            390249     390249      0.71      14      Phylogenomic databases                       

   PANTHER                            182821     175496      0.33      25      Family and domain databases                  

   PATRIC                             307974     307939      0.56      21      Genome annotation databases                  

   PaxDb                               66771      66770      0.12      43      Proteomic databases                          

   PDB                                116593      22237      0.21      33      3D structure databases                       

   PDBsum                             116593      22237      0.21      32      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      94      Proteomic databases                          

   PeroxiBase                            771        755     <0.01     118      Protein family/group databases               

   Pfam                               737376     508606      1.34       5      Family and domain databases                  

   PharmGKB                            18391      18358      0.03      67      Organism-specific databases                  

   PhosphoSite                         33550      33550      0.06      52      PTM databases                                

   PhylomeDB                           94404      94404      0.17      36      Phylogenomic databases                       

   PIR                                122391     112133      0.22      31      Sequence databases                           

   PIRSF                              104287     103250      0.19      34      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     109      Other                                        

   PomBase                              5139       5119      0.01      95      Organism-specific databases                  

   PRIDE                              123548     123548      0.23      30      Proteomic databases                          

   PRINTS                             135236     119282      0.25      28      Family and domain databases                  

   PRO                                 89312      89312      0.16      38      Other                                        

   ProDom                              29274      29095      0.05      57      Family and domain databases                  

   ProMEX                                407        407     <0.01     126      Proteomic databases                          

   PROSITE                            448842     289016      0.82       8      Family and domain databases                  

   ProteinModelPortal                 442546     442546      0.81       9      3D structure databases                       

   Proteomes                          438451     424782      0.80      11      Other                                        

   PseudoCAP                            1300       1291     <0.01     110      Organism-specific databases                  

   Reactome                            94269      28128      0.17      37      Enzyme and pathway databases                 

   REBASE                                408        408     <0.01     125      Protein family/group databases               

   RefSeq                             855245     479394      1.56       4      Sequence databases                           

   REPRODUCTION-2DPAGE                  1259       1038     <0.01     111      2D gel databases                             

   RGD                                  7848       7845      0.01      81      Organism-specific databases                  

   SABIO-RK                             3075       3075      0.01     102      Enzyme and pathway databases                 

   SGD                                  6737       6732      0.01      84      Organism-specific databases                  

   SignaLink                            3019       2983      0.01     103      Enzyme and pathway databases                 

   SMART                              170602     127809      0.31      26      Family and domain databases                  

   SMR                                225047     225047      0.41      24      3D structure databases                       

   STRING                             344466     344466      0.63      18      Protein-protein interaction databases        

   SUPFAM                             442508     341303      0.81      10      Family and domain databases                  

   SWISS-2DPAGE                         1181       1180     <0.01     112      2D gel databases                             

   TAIR                                14024      13968      0.03      75      Organism-specific databases                  

   TCDB                                 5400       5379      0.01      92      Protein family/group databases               

   TIGRFAMs                           292025     271788      0.53      22      Family and domain databases                  

   TreeFam                             44837      44832      0.08      47      Phylogenomic databases                       

   TubercuList                          2104       2068     <0.01     107      Organism-specific databases                  

   UCD-2DPAGE                            508        499     <0.01     123      2D gel databases                             

   UCSC                                59862      44874      0.11      44      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     129      PTM databases                                

   UniGene                            103406      92902      0.19      35      Sequence databases                           

   UniPathway                         134561     121944      0.25      29      Enzyme and pathway databases                 

   VectorBase                            615        597     <0.01     121      Genome annotation databases                  

   World-2DPAGE                          923        912     <0.01     117      2D gel databases                             

   WormBase                             5268       4117      0.01      93      Organism-specific databases                  

   Xenbase                              4770       4764      0.01      96      Organism-specific databases                  

   ZFIN                                 2785       2785      0.01     104      Organism-specific databases                  



Total number of cross-referenced databases: 134



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) 6.58

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

   Asn (N) 4.06   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) 5.94   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



4464 entries are encoded on a mitochondrion, and 3819 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: 76878