UniProtKB/Swiss-Prot protein knowledgebase release 2016_06 statistics





1.  INTRODUCTION



Release 2016_06 of 08-Jun-16 of UniProtKB/Swiss-Prot contains 551385 sequence entries,

comprising 196948568 amino acids abstracted from 245011 references. 



197 sequences have been added since release 2016_05, the sequence data of

9 existing entries has been updated and the annotations of

114616 entries have been revised.



Number of fragments: 9156

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 39190





Protein existence (PE):           entries     %



1: Evidence at protein level        92717   16.8%

2: Evidence at transcript level     57784   10.5%

3: Inferred from homology          387581   70.3%

4: Predicted                        11351    2.1%

5: Uncertain                         1952    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: 13318



   The first twenty species represent 117649 sequences:  21.3 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5529

                            2x: 1911

                            3x: 1046

                            4x:  664

                            5x:  492

                            6x:  400

                            7x:  290

                            8x:  237

                            9x:  215

                           10x:  129

                       11- 20x:  713

                       21- 50x:  429

                       51-100x:  215

                         >100x: 1048





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20199  Homo sapiens (Human)

       2      16794  Mus musculus (Mouse)

       3      14697  Arabidopsis thaliana (Mouse-ear cress)

       4       7963  Rattus norvegicus (Rat)

       5       6721  Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

       6       5998  Bos taurus (Bovine)

       7       5120  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4434  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4131  Dictyostelium discoideum (Slime mold)

      11       3715  Caenorhabditis elegans

      12       3502  Oryza sativa subsp. japonica (Rice)

      13       3402  Xenopus laevis (African clawed frog)

      14       3306  Drosophila melanogaster (Fruit fly)

      15       2964  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2274  Gallus gallus (Chicken)

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

      18       2105  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2030  Escherichia coli O157:H7

      20       1890  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1787  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

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

      24       1703  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      25       1689  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      26       1680  Shigella flexneri

      27       1416  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1300  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       1059  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1027  Archaeoglobus fulgidus 

      34       1022  Yersinia pestis

      35        987  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      36        970  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

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

      38        929  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      39        927  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      40        926  Staphylococcus aureus (strain N315)

      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        890  Oryctolagus cuniculus (Rabbit)

      47        889  Staphylococcus aureus (strain MSSA476)

      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        848  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        826  Emericella nidulans  

      59        825  Escherichia coli (strain UTI89 / UPEC)

      60        822  Shigella dysenteriae serotype 1 (strain Sd197)

      61        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      62        812  Canis lupus familiaris (Dog) (Canis familiaris)

      63        791  Escherichia coli (strain SMS-3-5 / SECEC)

      64        790  Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) 

      65        789  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      66        784  Aquifex aeolicus (strain VF5)

      67        780  Oryza sativa subsp. indica (Rice)

      68        776  Pasteurella multocida (strain Pm70)

      69        774  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      70        771  Escherichia coli (strain K12 / DH10B)

      71        771  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      72        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      73        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      74        763  Zea mays (Maize)

      75        762  Escherichia coli (strain 55989 / EAEC)

      76        761  Escherichia coli O8 (strain IAI1)

      77        760  Shigella flexneri serotype 5b (strain 8401)

      78        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      79        758  Staphylococcus epidermidis (strain ATCC 12228)

      80        756  Escherichia coli (strain SE11)

      81        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      82        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      83        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      84        745  Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

      85        743  Staphylococcus aureus (strain NCTC 8325)

      86        741  Bacillus anthracis

      87        741  Bacillus halodurans 

      88        737  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      89        733  Vibrio vulnificus (strain CMCP6)

      90        731  Escherichia coli O81 (strain ED1a)

      91        722  Salmonella enteritidis PT4 (strain P125109)

      92        718  Vibrio vulnificus (strain YJ016)

      93        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      94        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      95        715  Enterobacter sp. (strain 638)

      96        714  Escherichia coli O1:K1 / APEC

      97        714  Salmonella paratyphi A (strain AKU_12601)

      98        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      99        713  Salmonella agona (strain SL483)

     100        713  Salmonella newport (strain SL254)

     101        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     102        712  Salmonella schwarzengrund (strain CVM19633)

     103        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     104        710  Salmonella heidelberg (strain SL476)

     105        705  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        693  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     112        692  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     113        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     114        684  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     115        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     116        678  Pseudomonas syringae pv. tomato (strain DC3000)

     117        670  Serratia proteamaculans (strain 568)

     118        670  Escherichia coli

     119        669  Mycobacterium leprae (strain TN)

     120        667  Yersinia pestis (strain Pestoides F)

     121        666  Staphylococcus aureus (strain USA300)

     122        665  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        645  Shewanella oneidensis (strain MR-1)

     128        645  Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens 

     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        620  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

     137        610  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     138        608  Xanthomonas campestris pv. campestris 

     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 (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        593  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     147        592  Listeria innocua serovar 6a (strain CLIP 11262)

     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        575  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  Vibrio fischeri (strain ATCC 700601 / ES114)

     160        567  Pseudomonas syringae pv. syringae (strain B728a)

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

     172        536  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     173        531  Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / 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        524  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     178        522  Xylella fastidiosa (strain 9a5c)

     179        518  Corynebacterium glutamicum 

     180        517  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     181        517  Chromobacterium violaceum 

     182        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     183        515  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     184        512  Pseudomonas aeruginosa (strain PA7)

     185        511  Deinococcus radiodurans 

     186        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     187        509  Geobacillus kaustophilus (strain HTA426)

     188        508  Staphylococcus aureus (strain Newman)

     189        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     190        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     191        506  Streptomyces avermitilis 

     192        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     193        500  Pseudomonas entomophila (strain L48)

     194        499  Brucella abortus biovar 1 (strain 9-941)

     195        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     196        496  Bacillus clausii (strain KSM-K16)

     197        495  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     198        495  Burkholderia pseudomallei (strain K96243)

     199        495  Haemophilus influenzae (strain 86-028NP)

     200        494  Proteus mirabilis (strain HI4320)

     201        494  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     202        492  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     203        492  Bacillus methylotrophicus (strain DSM 23117 / BGSC 10A6 / FZB42) 

     204        491  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     205        491  Xanthomonas campestris pv. campestris (strain 8004)

     206        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     207        487  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     208        487  Methanosarcina mazei  

     209        487  Shewanella sp. (strain MR-7)

     210        486  Mannheimia succiniciproducens (strain MBEL55E)

     211        484  Pseudomonas aeruginosa (strain LESB58)

     212        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     213        484  Thermosynechococcus elongatus (strain BP-1)

     214        484  Shewanella sp. (strain MR-4)

     215        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     216        482  Pyrococcus horikoshii 

     217        479  Brucella abortus (strain 2308)

     218        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     219        478  Pseudomonas putida (strain F1 / ATCC 700007)

     220        477  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     221        477  Pyrococcus abyssi (strain GE5 / Orsay)

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

     223        469  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     224        468  Clostridium perfringens (strain 13 / Type A)

     225        467  Nicotiana tabacum (Common tobacco)

     226        467  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     227        467  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     228        466  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     229        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     230        466  Shewanella frigidimarina (strain NCIMB 400)

     231        466  Pseudomonas putida (strain GB-1)

     232        466  Shewanella sp. (strain ANA-3)

     233        464  Aeromonas hydrophila subsp. hydrophila 

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

     235        462  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     236        462  Burkholderia mallei (strain ATCC 23344)

     237        462  Enterococcus faecalis (strain ATCC 700802 / V583)

     238        461  Campylobacter jejuni subsp. jejuni serotype O:2 

     239        459  Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Ralstonia eutropha 

     240        457  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     241        457  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     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  Aeromonas salmonicida (strain A449)

     247        452  Shewanella baltica (strain OS185)

     248        451  Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

     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           19385 (  4%)

    Bacteria         332583 ( 60%)

    Eukaryota        182787 ( 33%)

    Viruses           16630 (  3%)





   Within Eukaryota:



   



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

     Human                  20200 ( 11%)           (  4%)

     Other Mammalia         46309 ( 25%)           (  8%)

     Other Vertebrata       17904 ( 10%)           (  3%)

     Viridiplantae          37671 ( 21%)           (  7%)

     Fungi                  32015 ( 18%)           (  6%)

     Insecta                 8869 (  5%)           (  2%)

     Nematoda                4600 (  3%)           (  1%)

     Other                  15219 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9149             1001-1100     3889

                 51- 100   42098             1101-1200     2732

                101- 150   58495             1201-1300     2100

                151- 200   58461             1301-1400     1956

                201- 250   57299             1401-1500     1567

                251- 300   50926             1501-1600      762

                301- 350   51195             1601-1700      590

                351- 400   44366             1701-1800      502

                401- 450   36418             1801-1900      445

                451- 500   29329             1901-2000      365

                501- 550   20991             2001-2100      225

                551- 600   15009             2101-2200      306

                601- 650   12585             2201-2300      303

                651- 700    9081             2301-2400      188

                701- 750    7524             2401-2500      144

                751- 800    5409             >2500         1164

                801- 850    4683

                851- 900    5150

                901- 950    3978

                951-1000    2845



   





   The average sequence length in UniProtKB/Swiss-Prot is 357 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: 2583





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  835

                       2x:  348

                       3x:  159

                       4x:  127

                       5x:  109

                       6x:   85

                       7x:   56

                       8x:   56

                       9x:   27

                      10x:   41

                  11- 20x:  209

                  21- 50x:  203

                  51-100x:  114

                    >100x:  214





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



   Nb    Citations   Journal name

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

    1        23243   Journal of Biological Chemistry

    2        10602   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6287   Journal of Bacteriology

    4         5371   Biochemical and Biophysical Research Communications

    5         4980   Biochemistry

    6         4837   Nucleic Acids Research

    7         4750   Gene

    8         4655   FEBS Letters

    9         4513   The EMBO Journal

   10         4186   Molecular and Cellular Biology

   11         4155   Nature

   12         4020   Journal of Molecular Biology

   13         3471   Biochimica et Biophysica Acta

   14         3345   Cell

   15         3334   European Journal of Biochemistry

   16         2896   Journal of Virology

   17         2783   Science

   18         2718   Biochemical Journal

   19         2525   Genomics

   20         2346   Molecular Microbiology

   21         2276   Plant Physiology

   22         2054   Journal of Cell Biology

   23         1894   The American Journal of Human Genetics

   24         1781   Plant Molecular Biology

   25         1754   Genes and Development

   26         1746   The Plant Cell

   27         1655   Human Molecular Genetics

   28         1651   Nature Genetics

   29         1640   Virology

   30         1591   The Plant Journal

   31         1531   Development

   32         1525   Molecular Biology of the Cell

   33         1503   Oncogene

   34         1452   Human Mutation

   35         1378   Molecular and General Genetics

   36         1372   Molecular Cell

   37         1357   PLoS ONE

   38         1309   Journal of Immunology

   39         1294   Journal of Biochemistry

   40         1232   Genetics

   41         1223   Structure

   42         1116   Journal of Cell Science

   43         1088   Blood

   44         1068   Journal of General Virology

   45         1058   Infection and Immunity

   46         1005   Microbiology

   47          993   Archives of Biochemistry and Biophysics

   48          943   Developmental Biology

   49          942   Current Biology

   50          854   Cancer Research

   51          826   Yeast

   52          800   Acta Crystallographica, Section D

   53          799   FEMS Microbiology Letters

   54          796   Journal of Neuroscience

   55          767   Applied and Environmental Microbiology

   56          725   Toxicon

   57          722   Protein Science

   58          676   Journal of Clinical Investigation

   59          669   Neuron

   60          664   Human Genetics

   61          637   Nature Structural Biology

   62          634   Mechanisms of Development

   63          628   American Journal of Physiology

   64          594   Plant and Cell Physiology

   65          587   The Journal of Experimental Medicine

   66          569   Proteins

   67          562   Current Genetics

   68          526   Journal of Medical Genetics

   69          523   Molecular Endocrinology

   70          516   Nature Cell Biology

   71          512   Bioscience, Biotechnology, and Biochemistry

   72          508   Journal of Neurochemistry

   73          495   The Journal of Clinical Endocrinology and Metabolism

   74          487   Mammalian Genome

   75          478   Endocrinology

   76          462   Immunogenetics

   77          445   Molecular and Biochemical Parasitology

   78          437   Nature Structural and Molecular Biology

   79          430   The FEBS Journal

   80          425   Experimental Cell Research

   81          424   Developmental Cell

   82          419   Antimicrobial Agents and Chemotherapy

   83          406   Journal of Molecular Evolution

   84          403   Eukaryotic Cell

   85          403   PLoS Genetics

   86          388   Peptides

   87          386   Molecular Biology and Evolution

   88          383   DNA and Cell Biology

   89          373   RNA

   90          371   Planta

   91          370   DNA Sequence

   92          348   Journal of Investigative Dermatology

   93          347   Molecular Pharmacology

   94          337   Comparative Biochemistry and Physiology

   95          336   Neurology

   96          334   Brain Research. Molecular Brain Research

   97          325   Tissue Antigens

   98          324   EMBO Reports

   99          316   Biology of Reproduction

  100          308   Journal of the American Chemical Society

  101          305   The FASEB Journal

  102          297   Molecular Plant-Microbe Interactions

  103          295   Immunity

  104          294   Biological Chemistry Hoppe-Seyler

  105          294   Genes to Cells

  106          293   Developmental Dynamics

  107          292   The New England Journal of Medicine

  108          292   Biochimie

  109          290   Acta Crystallographica, Section F

  110          288   Virus Research

  111          281   Cytogenetics and Cell Genetics

  112          280   Genome Research

  113          279   European Journal of Human Genetics

  114          279   Journal of Experimental Botany

  115          266   Journal of General Microbiology

  116          256   Annals of Neurology

  117          252   European Journal of Immunology

  118          250   American Journal of Medical Genetics. Part A

  119          247   PLoS Pathogens

  120          245   Clinical Genetics

  121          244   BMC Genomics

  122          240   Investigative Ophthalmology and Visual Science

  123          238   Nature Immunology

  124          231   Journal of Human Genetics

  125          230   Archives of Microbiology

  126          221   DNA Research

  127          219   Journal of Medicinal Chemistry

  128          218   Applied Microbiology and Biotechnology

  129          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  130          217   Journal of Cellular Biochemistry

  131          210   Glycobiology

  132          203   Traffic

  133          202   Circulation Research

  134          200   Cell Cycle

  135          200   Molecular Genetics and Metabolism

  136          200   Archives of Virology

  137          199   Molecular and Cellular Endocrinology

  138          198   Molecular Immunology

  139          197   Diabetes

  140          194   PLoS Biology

  141          192   Journal of Lipid Research

  142          189   Protein Expression and Purification

  143          186   Phytochemistry

  144          178   Insect Biochemistry and Molecular Biology

  145          177   Molecular Genetics and Genomics

  146          174   International Journal of Cancer

  147          172   Molecular and Cellular Neuroscience

  148          172   Molecular Phylogenetics and Evolution

  149          171   Nature Medicine

  150          170   Hemoglobin





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)                      1148251                 2.08                                         

   Journal                            952443     440553      1.73       1                                 

   Submitted to EMBL/GenBank/DDBJ     185528     163487      0.34       2                                 

   Submitted to other databases         7171       6652      0.01       3                                 

   Book citation                        1492       1478     <0.01       4                                 

   Plant Gene Register                   600        588     <0.01       5                                 

   Thesis                                428        425     <0.01       6                                 

   Unpublished observations              386        382     <0.01       7                                 

   Patent                                197        193     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 376728



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2583502                 4.69                                         

   ALLERGEN                              707        707     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24548      24548      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        7040       7040      0.01      21                                 

   BIOTECHNOLOGY                         594        592     <0.01      28                                 

   CATALYTIC ACTIVITY                 257794     231420      0.47       5                                 

   CAUTION                             10386      10179      0.02      18                                 

   COFACTOR                           118873     108817      0.22       7                                 

   DEVELOPMENTAL STAGE                 10960      10960      0.02      17                                 

   DISEASE                              6214       4157      0.01      22                                 

   DISRUPTION PHENOTYPE                10285      10285      0.02      19                                 

   DOMAIN                              44247      38318      0.08       9                                 

   ENZYME REGULATION                   13484      13483      0.02      16                                 

   FUNCTION                           446828     428338      0.81       2                                 

   INDUCTION                           18244      18243      0.03      14                                 

   INTERACTION                         16037      16037      0.03      15                                 

   MASS SPECTROMETRY                    6103       4605      0.01      23                                 

   MISCELLANEOUS                       35147      32322      0.06      12                                 

   PATHWAY                            135508     122771      0.25       6                                 

   PHARMACEUTICAL                         99         99     <0.01      29                                 

   POLYMORPHISM                         1043        987     <0.01      24                                 

   PTM                                 50989      38838      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    43154      43154      0.08      10                                 

   SIMILARITY                         668122     526477      1.21       1                                 

   SUBCELLULAR LOCATION               340079     333352      0.62       3                                 

   SUBUNIT                            264806     264669      0.48       4                                 

   TISSUE SPECIFICITY                  42771      42771      0.08      11                                 

   TOXIC DOSE                            623        577     <0.01      27                                 

   WEB RESOURCE                         8190       6870      0.01      20                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        4165913                 7.56                                         

   ACT_SITE                           157245      96067      0.29      10                                 

   BINDING                            355107      94129      0.64       4                                 

   CA_BIND                              3987       1677      0.01      36                                 

   CARBOHYD                           112101      28746      0.20      15                                 

   CHAIN                              558965     544953      1.01       1                                 

   COILED                              21457      14796      0.04      26                                 

   COMPBIAS                            57579      30829      0.10      18                                 

   CONFLICT                           132116      46328      0.24      13                                 

   CROSSLNK                            11132       5584      0.02      32                                 

   DISULFID                           118117      32237      0.21      14                                 

   DNA_BIND                            11224      10198      0.02      31                                 

   DOMAIN                             179455     108862      0.33       8                                 

   HELIX                              220810      20762      0.40       6                                 

   INIT_MET                            18296      18296      0.03      27                                 

   INTRAMEM                             2430       1061     <0.01      37                                 

   LIPID                               12567       8072      0.02      29                                 

   METAL                              357263      88654      0.65       3                                 

   MOD_RES                            215957      68427      0.39       7                                 

   MOTIF                               40097      25913      0.07      24                                 

   MUTAGEN                             57391      12979      0.10      19                                 

   NON_CONS                             2238        777     <0.01      38                                 

   NON_STD                               359        284     <0.01      39                                 

   NON_TER                             12290       9404      0.02      30                                 

   NP_BIND                            139586      79964      0.25      11                                 

   PEPTIDE                             10740       7294      0.02      33                                 

   PROPEP                              13461      11543      0.02      28                                 

   REGION                             178526      84992      0.32       9                                 

   REPEAT                             100646      14344      0.18      16                                 

   SIGNAL                              40330      40320      0.07      23                                 

   SITE                                52526      29304      0.10      21                                 

   STRAND                             230099      19577      0.42       5                                 

   TOPO_DOM                           136065      28033      0.25      12                                 

   TRANSIT                              9094       8981      0.02      34                                 

   TRANSMEM                           365575      75826      0.66       2                                 

   TURN                                53124      16827      0.10      20                                 

   UNSURE                               4273        755      0.01      35                                 

   VAR_SEQ                             51037      21472      0.09      22                                 

   VARIANT                             92574      17035      0.17      17                                 

   ZN_FING                             30074      13347      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)               17800274                32.28                                                           

   Allergome                            1696       1111     <0.01     111      Protein family/group databases               

   ArachnoServer                        1145       1135     <0.01     117      Organism-specific databases                  

   Bgee                                38881      38881      0.07      51      Gene expression databases                    

   BindingDB                            4610       4610      0.01      96      Chemistry                                    

   BioCyc                             325557     308260      0.59      20      Enzyme and pathway databases                 

   BioGrid                             48283      47827      0.09      46      Protein-protein interaction databases        

   BioMuta                             17246      17242      0.03      71      Polymorphism and mutation databases          

   BRENDA                              12759      11989      0.02      80      Enzyme and pathway databases                 

   CAZy                                 7889       7098      0.01      83      Protein family/group databases               

   CCDS                                46595      33600      0.08      47      Sequence databases                           

   CGD                                  1708       1692     <0.01     110      Organism-specific databases                  

   ChEMBL                               6391       6391      0.01      86      Chemistry                                    

   ChiTaRS                             16471      16461      0.03      75      Other                                        

   CleanEx                             30043      29403      0.05      57      Gene expression databases                    

   CollecTF                              133        133     <0.01     136      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     137      2D gel databases                             

   ConoServer                            949        866     <0.01     119      Organism-specific databases                  

   CTD                                 73510      72757      0.13      42      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     134      PTM databases                                

   dictyBase                            4207       4092      0.01      99      Organism-specific databases                  

   DIP                                 16829      16772      0.03      72      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     125      3D structure databases                       

   DMDM                                16376      16373      0.03      76      Polymorphism and mutation databases          

   DNASU                               18876      18805      0.03      67      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     146        146     <0.01     135      2D gel databases                             

   DrugBank                            11784       1909      0.02      81      Chemistry                                    

   EchoBASE                             4161       4161      0.01     100      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      98      Organism-specific databases                  

   eggNOG                             657125     327981      1.19       5      Phylogenomic databases                       

   EMBL                               977612     540038      1.77       3      Sequence databases                           

   Ensembl                             84506      48463      0.15      40      Genome annotation databases                  

   EnsemblBacteria                    354766     335757      0.64      17      Genome annotation databases                  

   EnsemblFungi                        30234      27797      0.05      56      Genome annotation databases                  

   EnsemblMetazoa                      13145       9822      0.02      78      Genome annotation databases                  

   EnsemblPlants                       22068      18793      0.04      61      Genome annotation databases                  

   EnsemblProtists                      4881       4718      0.01      95      Genome annotation databases                  

   EPD                                 23382      23382      0.04      60      Proteomic databases                          

   ESTHER                               2438       2436     <0.01     107      Protein family/group databases               

   euHCVdb                                55         44     <0.01     139      Organism-specific databases                  

   EuPathDB                            18009      18008      0.03      70      Organism-specific databases                  

   EvolutionaryTrace                   16552      16550      0.03      74      Other                                        

   ExpressionAtlas                     33111      33111      0.06      53      Gene expression databases                    

   FlyBase                              5995       5633      0.01      89      Organism-specific databases                  

   Gene3D                             472178     348023      0.86       9      Family and domain databases                  

   GeneCards                           20021      19847      0.04      64      Organism-specific databases                  

   GeneDB                                389        350     <0.01     131      Genome annotation databases                  

   GeneID                             273620     264846      0.50      23      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     116      Organism-specific databases                  

   GeneTree                            55449      55406      0.10      43      Phylogenomic databases                       

   Genevisible                         55140      55140      0.10      44      Gene expression databases                    

   GeneWiki                            10368      10282      0.02      82      Other                                        

   GenomeRNAi                          21790      21790      0.04      62      Other                                        

   GO                                2721189     523206      4.94       1      Ontologies                                   

   Gramene                             18232      15843      0.03      69      Genome annotation databases                  

   GuidetoPHARMACOLOGY                  1889       1889     <0.01     109      Chemistry                                    

   H-InvDB                              5589       4768      0.01      91      Organism-specific databases                  

   HAMAP                              325973     322901      0.59      19      Family and domain databases                  

   HGNC                                20010      19862      0.04      65      Organism-specific databases                  

   HOGENOM                            388758     388758      0.71      16      Phylogenomic databases                       

   HOVERGEN                            75777      75777      0.14      41      Phylogenomic databases                       

   HPA                                 24700      16208      0.04      59      Organism-specific databases                  

   InParanoid                         135979     135979      0.25      27      Phylogenomic databases                       

   IntAct                              46065      46065      0.08      48      Protein-protein interaction databases        

   InterPro                          1938764     531681      3.52       2      Family and domain databases                  

   iPTMnet                             45878      45878      0.08      49      PTM databases                                

   KEGG                               500150     466416      0.91       7      Genome annotation databases                  

   KO                                 390035     389593      0.71      15      Phylogenomic databases                       

   LegioList                             765        763     <0.01     122      Organism-specific databases                  

   Leproma                               672        669     <0.01     123      Organism-specific databases                  

   MaizeGDB                              506        501     <0.01     128      Organism-specific databases                  

   MalaCards                            3773       3771      0.01     101      Organism-specific databases                  

   MaxQB                               32301      32301      0.06      54      Proteomic databases                          

   MEROPS                              12941      12941      0.02      79      Protein family/group databases               

   MGI                                 16709      16665      0.03      73      Organism-specific databases                  

   MIM                                 19772      14503      0.04      66      Organism-specific databases                  

   MINT                                31711      31711      0.06      55      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     138      Protein family/group databases               

   mycoCLAP                              348        344     <0.01     133      Protein family/group databases               

   neXtProt                            20041      20040      0.04      63      Organism-specific databases                  

   OGP                                   375        375     <0.01     132      2D gel databases                             

   OMA                                407319     407319      0.74      13      Phylogenomic databases                       

   Orphanet                             6148       3289      0.01      87      Organism-specific databases                  

   OrthoDB                            391069     391069      0.71      14      Phylogenomic databases                       

   PANTHER                            172482     165641      0.31      26      Family and domain databases                  

   PATRIC                             308217     308182      0.56      21      Genome annotation databases                  

   PaxDb                              110748     110619      0.20      34      Proteomic databases                          

   PDB                                129685      23482      0.24      31      3D structure databases                       

   PDBsum                             129685      23482      0.24      30      3D structure databases                       

   PeptideAtlas                         5159       5159      0.01      93      Proteomic databases                          

   PeroxiBase                            771        755     <0.01     121      Protein family/group databases               

   Pfam                               744774     510015      1.35       4      Family and domain databases                  

   PharmGKB                            18379      18338      0.03      68      Organism-specific databases                  

   PhosphoSite                         33546      33546      0.06      52      PTM databases                                

   PhylomeDB                           94782      94782      0.17      38      Phylogenomic databases                       

   PIR                                123019     112721      0.22      33      Sequence databases                           

   PIRSF                              104402     103364      0.19      36      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     112      Other                                        

   PomBase                              5140       5121      0.01      94      Organism-specific databases                  

   PRIDE                              123931     123931      0.22      32      Proteomic databases                          

   PRINTS                             133775     117996      0.24      29      Family and domain databases                  

   PRO                                 90090      90090      0.16      39      Other                                        

   ProDom                              29139      28958      0.05      58      Family and domain databases                  

   ProMEX                                436        436     <0.01     129      Proteomic databases                          

   PROSITE                            452975     291227      0.82      11      Family and domain databases                  

   ProteinModelPortal                 443936     443936      0.81      12      3D structure databases                       

   Proteomes                          469317     448462      0.85      10      Other                                        

   PseudoCAP                            1308       1299     <0.01     113      Organism-specific databases                  

   Reactome                           101116      30603      0.18      37      Enzyme and pathway databases                 

   REBASE                                405        405     <0.01     130      Protein family/group databases               

   RefSeq                             599575     462342      1.09       6      Sequence databases                           

   REPRODUCTION-2DPAGE                  1259       1038     <0.01     114      2D gel databases                             

   RGD                                  7889       7886      0.01      84      Organism-specific databases                  

   SABIO-RK                             3329       3329      0.01     102      Enzyme and pathway databases                 

   SGD                                  6739       6734      0.01      85      Organism-specific databases                  

   SignaLink                            3000       3000      0.01     104      Enzyme and pathway databases                 

   SIGNOR                               2940       2940      0.01     105      Enzyme and pathway databases                 

   SMART                              189217     139696      0.34      25      Family and domain databases                  

   SMR                                226015     226015      0.41      24      3D structure databases                       

   STRING                             326041     326041      0.59      18      Protein-protein interaction databases        

   SUPFAM                             479693     363776      0.87       8      Family and domain databases                  

   SWISS-2DPAGE                         1180       1180     <0.01     115      2D gel databases                             

   SwissLipids                          1004        926     <0.01     118      Chemistry                                    

   SwissPalm                            5944       5944      0.01      90      PTM databases                                

   TAIR                                14681      14625      0.03      77      Organism-specific databases                  

   TCDB                                 6017       5986      0.01      88      Protein family/group databases               

   TIGRFAMs                           292183     272032      0.53      22      Family and domain databases                  

   TopDownProteomics                    3134       2858      0.01     103      Proteomic databases                          

   TreeFam                             44962      44956      0.08      50      Phylogenomic databases                       

   TubercuList                          2123       2087     <0.01     108      Organism-specific databases                  

   UCD-2DPAGE                            508        499     <0.01     127      2D gel databases                             

   UCSC                                48730      44719      0.09      45      Genome annotation databases                  

   UniCarbKB                             584        584     <0.01     126      PTM databases                                

   UniGene                            106330      94449      0.19      35      Sequence databases                           

   UniPathway                         135206     122480      0.25      28      Enzyme and pathway databases                 

   VectorBase                            618        600     <0.01     124      Genome annotation databases                  

   WBParaSite                             29         29     <0.01     140      Genome annotation databases                  

   World-2DPAGE                          925        914     <0.01     120      2D gel databases                             

   WormBase                             5515       4255      0.01      92      Organism-specific databases                  

   Xenbase                              4450       4444      0.01      97      Organism-specific databases                  

   ZFIN                                 2803       2803      0.01     106      Organism-specific databases                  



Total number of cross-referenced databases: 140



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.26   Gln (Q) 3.93   Leu (L) 9.65   Ser (S) 6.59

   Arg (R) 5.53   Glu (E) 6.74   Lys (K) 5.82   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) 5.93   Pro (P) 4.72   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



4463 entries are encoded on a mitochondrion, and 3843 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: 77639