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         UniProtKB/Swiss-Prot protein knowledgebase release 2019_01 statistics





1.  INTRODUCTION



Release 2019_01 of 16-Jan-19 of UniProtKB/Swiss-Prot contains 559077 sequence entries,

comprising 200828568 amino acids abstracted from 264040 references. 



199 sequences have been added since release 2018_11, the sequence data of

22 existing entries has been updated and the annotations of

362788 entries have been revised.



Number of fragments: 9159

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40019





Protein existence (PE):           entries     %



1: Evidence at protein level        99969   17.9%

2: Evidence at transcript level     57170   10.2%

3: Inferred from homology          386615   69.2%

4: Predicted                        13489    2.4%

5: Uncertain                         1834    0.3%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 13709



   The first twenty species represent 120750 sequences:  21.6 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5663

                            2x: 1963

                            3x: 1071

                            4x:  694

                            5x:  515

                            6x:  410

                            7x:  298

                            8x:  249

                            9x:  228

                           10x:  142

                       11- 20x:  749

                       21- 50x:  457

                       51-100x:  220

                         >100x: 1050





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20413  Homo sapiens (Human)

       2      17006  Mus musculus (Mouse)

       3      15828  Arabidopsis thaliana (Mouse-ear cress)

       4       8054  Rattus norvegicus (Rat)

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

       6       6004  Bos taurus (Bovine)

       7       5141  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4475  Escherichia coli (strain K12)

       9       4188  Bacillus subtilis (strain 168)

      10       4146  Dictyostelium discoideum (Slime mold)

      11       4038  Caenorhabditis elegans

      12       4034  Oryza sativa subsp. japonica (Rice)

      13       3551  Drosophila melanogaster (Fruit fly)

      14       3444  Xenopus laevis (African clawed frog)

      15       3090  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2291  Gallus gallus (Chicken)

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

      18       2173  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2037  Escherichia coli O157:H7

      20       1898  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1796  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

      22       1787  Methanocaldococcus jannaschii  

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

      24       1706  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      25       1694  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      26       1683  Shigella flexneri

      27       1428  Sus scrofa (Pig)

      28       1347  Salmonella typhi

      29       1326  Pseudomonas aeruginosa 

      30       1244  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

      31       1173  Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)

      32       1064  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1034  Archaeoglobus fulgidus 

      34       1022  Yersinia pestis

      35       1009  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      36        975  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

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

      38        930  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        925  Emericella nidulans  

      42        919  Kluyveromyces lactis   

      43        909  Acanthamoeba polyphaga mimivirus (APMV)

      44        899  Staphylococcus aureus (strain COL)

      45        895  Staphylococcus aureus (strain MW2)

      46        893  Oryctolagus cuniculus (Rabbit)

      47        892  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      48        889  Staphylococcus aureus (strain MSSA476)

      49        888  Staphylococcus aureus (strain MRSA252)

      50        883  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      51        882  Salmonella choleraesuis (strain SC-B67)

      52        879  Shigella sonnei (strain Ss046)

      53        878  Candida glabrata   

      54        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      55        856  Neurospora crassa 

      56        841  Escherichia coli O9:H4 (strain HS)

      57        839  Oryza sativa subsp. indica (Rice)

      58        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      59        829  Shigella boydii serotype 4 (strain Sb227)

      60        825  Escherichia coli (strain UTI89 / UPEC)

      61        822  Canis lupus familiaris (Dog) (Canis familiaris)

      62        822  Shigella dysenteriae serotype 1 (strain Sd197)

      63        821  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

      64        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      65        810  Zea mays (Maize)

      66        803  Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) 

      67        793  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      68        792  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      69        791  Escherichia coli (strain SMS-3-5 / SECEC)

      70        784  Aquifex aeolicus (strain VF5)

      71        776  Pasteurella multocida (strain Pm70)

      72        771  Escherichia coli (strain K12 / DH10B)

      73        771  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      74        766  Staphylococcus aureus (strain NCTC 8325)

      75        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      76        765  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      77        762  Escherichia coli (strain 55989 / EAEC)

      78        761  Escherichia coli O8 (strain IAI1)

      79        760  Shigella flexneri serotype 5b (strain 8401)

      80        760  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      81        759  Staphylococcus epidermidis (strain ATCC 12228)

      82        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      83        756  Escherichia coli (strain SE11)

      84        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      85        751  Bacillus anthracis

      86        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      87        746  Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)

      88        741  Bacillus halodurans 

      89        737  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      90        733  Vibrio vulnificus (strain CMCP6)

      91        731  Escherichia coli O81 (strain ED1a)

      92        722  Salmonella enteritidis PT4 (strain P125109)

      93        718  Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

      94        718  Vibrio vulnificus (strain YJ016)

      95        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      96        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      97        715  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      98        715  Enterobacter sp. (strain 638)

      99        714  Escherichia coli O1:K1 / APEC

     100        714  Salmonella paratyphi A (strain AKU_12601)

     101        713  Salmonella agona (strain SL483)

     102        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     103        713  Salmonella newport (strain SL254)

     104        712  Salmonella schwarzengrund (strain CVM19633)

     105        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     106        710  Salmonella heidelberg (strain SL476)

     107        702  Salmonella dublin (strain CT_02021853)

     108        698  Klebsiella pneumoniae (strain 342)

     109        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     110        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     111        693  Pan troglodytes (Chimpanzee)

     112        692  Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)

     113        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

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

     115        680  Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)

     116        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     117        674  Escherichia coli

     118        673  Staphylococcus aureus (strain USA300)

     119        670  Serratia proteamaculans (strain 568)

     120        669  Mycobacterium leprae (strain TN)

     121        667  Yersinia pestis (strain Pestoides F)

     122        665  Bacillus cereus 

     123        664  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     124        664  Bradyrhizobium diazoefficiens 

     125        658  Sinorhizobium fredii (strain NBRC 101917 / NGR234)

     126        653  Debaryomyces hansenii   

     127        646  Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens 

     128        645  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        622  Treponema pallidum (strain Nichols)

     135        620  Methanothermobacter thermautotrophicus  

     136        615  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     137        614  Staphylococcus haemolyticus (strain JCSC1435)

     138        611  Mesorhizobium japonicum  (Mesorhizobium loti 

     139        610  Xanthomonas campestris pv. campestris 

     140        603  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

     141        603  Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)

     142        602  Photobacterium profundum (strain SS9)

     143        602  Staphylococcus saprophyticus subsp. saprophyticus 

     144        601  Salmonella paratyphi C (strain RKS4594)

     145        600  Yersinia pestis bv. Antiqua (strain Angola)

     146        594  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     147        594  Bacillus cereus (strain ATCC 10987 / NRS 248)

     148        594  Pseudomonas aeruginosa (strain UCBPP-PA14)

     149        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     150        586  Rickettsia prowazekii (strain Madrid E)

     151        582  Neisseria meningitidis serogroup B (strain MC58)

     152        580  Caenorhabditis briggsae

     153        579  Brucella suis biovar 1 (strain 1330)

     154        574  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     155        573  Aliivibrio fischeri (strain ATCC 700601 / ES114) (Vibrio fischeri)

     156        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     157        571  Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus)

     158        569  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     159        568  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     160        567  Pseudomonas syringae pv. syringae (strain B728a)

     161        564  Bacillus licheniformis 

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

     163        562  Bacillus cereus (strain ZK / E33L)

     164        559  Clostridium acetobutylicum 

     165        557  Xanthomonas axonopodis pv. citri (strain 306)

     166        555  Pseudomonas fluorescens (strain Pf0-1)

     167        555  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     168        554  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     169        553  Oceanobacillus iheyensis 

     170        551  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     171        550  Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)

     172        547  Pseudomonas savastanoi pv. phaseolicola  (Pseudomonas syringae pv. phaseolicola 

     173        537  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     174        531  Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99)

     175        529  Corynebacterium glutamicum 

     176        529  Listeria monocytogenes serotype 4b (strain F2365)

     177        529  Sodalis glossinidius (strain morsitans)

     178        527  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     179        522  Xylella fastidiosa (strain 9a5c)

     180        520  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     181        517  Chromobacterium violaceum 

     182        516  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     183        515  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     184        514  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     185        513  Staphylococcus aureus (strain Newman)

     186        513  Deinococcus radiodurans 

     187        512  Pseudomonas aeruginosa (strain PA7)

     188        511  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     189        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     190        510  Geobacillus kaustophilus (strain HTA426)

     191        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     192        508  Streptomyces avermitilis 

     193        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     194        502  Pseudomonas entomophila (strain L48)

     195        501  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     196        501  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     197        499  Brucella abortus biovar 1 (strain 9-941)

     198        498  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     199        497  Haemophilus influenzae (strain 86-028NP)

     200        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     201        496  Bacillus clausii (strain KSM-K16)

     202        496  Burkholderia pseudomallei (strain K96243)

     203        494  Proteus mirabilis (strain HI4320)

     204        493  Xanthomonas campestris pv. campestris (strain 8004)

     205        492  Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / FZB42) 

     206        491  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     207        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     208        488  Methanosarcina mazei  

     209        487  Shewanella sp. (strain MR-7)

     210        487  Pyrococcus horikoshii 

     211        486  Mannheimia succiniciproducens (strain MBEL55E)

     212        485  Thermosynechococcus elongatus (strain BP-1)

     213        484  Pseudomonas aeruginosa (strain LESB58)

     214        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     215        484  Shewanella sp. (strain MR-4)

     216        483  Brucella abortus (strain 2308)

     217        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     218        480  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     219        479  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     220        479  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     221        478  Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)

     222        477  Pyrococcus abyssi (strain GE5 / Orsay)

     223        477  Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) 

     224        475  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     225        475  Nicotiana tabacum (Common tobacco)

     226        474  Burkholderia lata 

     227        472  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     228        468  Clostridium perfringens (strain 13 / Type A)

     229        467  Shewanella frigidimarina (strain NCIMB 400)

     230        467  Campylobacter jejuni subsp. jejuni serotype O:2 

     231        466  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     232        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     233        466  Pseudomonas putida (strain GB-1)

     234        466  Shewanella sp. (strain ANA-3)

     235        465  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     236        464  Aeromonas hydrophila subsp. hydrophila 

     237        463  Enterococcus faecalis (strain ATCC 700802 / V583)

     238        462  Burkholderia mallei (strain ATCC 23344)

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

     240        458  Solanum lycopersicum (Tomato) (Lycopersicon esculentum)

     241        458  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     242        457  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     243        457  Ovis aries (Sheep)

     244        455  Staphylococcus aureus (strain JH1)

     245        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     246        453  Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

     247        453  Pseudomonas putida (strain W619)

     248        452  Shewanella baltica (strain OS185)

     249        452  Aeromonas salmonicida (strain A449)

     250        450  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19549 (  3%)

    Bacteria         333792 ( 60%)

    Eukaryota        188892 ( 34%)

    Viruses           16844 (  3%)





   Within Eukaryota:



   



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

     Human                  20414 ( 11%)           (  4%)

     Other Mammalia         46697 ( 25%)           (  8%)

     Other Vertebrata       18356 ( 10%)           (  3%)

     Viridiplantae          39787 ( 21%)           (  7%)

     Fungi                  33866 ( 18%)           (  6%)

     Insecta                 9229 (  5%)           (  2%)

     Nematoda                4944 (  3%)           (  1%)

     Other                  15599 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9586             1001-1100     3992

                 51- 100   42554             1101-1200     2801

                101- 150   59023             1201-1300     2144

                151- 200   58896             1301-1400     2003

                201- 250   57741             1401-1500     1622

                251- 300   51475             1501-1600      791

                301- 350   51851             1601-1700      616

                351- 400   44994             1701-1800      558

                401- 450   36975             1801-1900      474

                451- 500   29809             1901-2000      378

                501- 550   21523             2001-2100      248

                551- 600   15354             2101-2200      340

                601- 650   12829             2201-2300      315

                651- 700    9224             2301-2400      212

                701- 750    7651             2401-2500      161

                751- 800    5534             >2500         1284

                801- 850    4776

                851- 900    5209

                901- 950    4049

                951-1000    2926



   





   The average sequence length in UniProtKB/Swiss-Prot is 359 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: 2764





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  869

                       2x:  395

                       3x:  166

                       4x:  133

                       5x:  109

                       6x:   94

                       7x:   73

                       8x:   54

                       9x:   39

                      10x:   35

                  11- 20x:  219

                  21- 50x:  226

                  51-100x:  121

                    >100x:  231





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



   Nb    Citations   Journal name

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

    1        24531   Journal of Biological Chemistry

    2        11390   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6617   Journal of Bacteriology

    4         5628   Biochemical and Biophysical Research Communications

    5         5324   Biochemistry

    6         4991   Nucleic Acids Research

    7         4826   FEBS Letters

    8         4806   Gene

    9         4689   The EMBO Journal

   10         4520   Nature

   11         4338   Molecular and Cellular Biology

   12         4261   Journal of Molecular Biology

   13         3627   Biochimica et Biophysica Acta

   14         3565   Cell

   15         3395   European Journal of Biochemistry

   16         3245   Journal of Virology

   17         3004   Science

   18         2856   Biochemical Journal

   19         2559   Plant Physiology

   20         2534   Genomics

   21         2529   Molecular Microbiology

   22         2191   Journal of Cell Biology

   23         2147   The American Journal of Human Genetics

   24         1991   The Plant Cell

   25         1895   PLoS ONE

   26         1859   Plant Molecular Biology

   27         1834   Genes and Development

   28         1833   The Plant Journal

   29         1803   Human Molecular Genetics

   30         1799   Virology

   31         1750   Nature Genetics

   32         1667   Development

   33         1661   Molecular Biology of the Cell

   34         1571   Human Mutation

   35         1541   Molecular Cell

   36         1540   Oncogene

   37         1449   Journal of Immunology

   38         1394   Molecular and General Genetics

   39         1339   Journal of Biochemistry

   40         1335   Structure

   41         1312   Genetics

   42         1248   Journal of Cell Science

   43         1155   Blood

   44         1144   Journal of General Virology

   45         1111   Infection and Immunity

   46         1055   Microbiology

   47         1048   Developmental Biology

   48         1047   Current Biology

   49         1044   Archives of Biochemistry and Biophysics

   50          902   Applied and Environmental Microbiology

   51          896   Journal of Neuroscience

   52          882   Cancer Research

   53          881   Acta Crystallographica, Section D

   54          838   Yeast

   55          836   FEMS Microbiology Letters

   56          771   Protein Science

   57          770   Toxicon

   58          743   Neuron

   59          724   Journal of Clinical Investigation

   60          691   Human Genetics

   61          675   Plant and Cell Physiology

   62          673   American Journal of Physiology

   63          648   Mechanisms of Development

   64          645   Nature Structural Biology

   65          640   PLoS Genetics

   66          637   The Journal of Experimental Medicine

   67          620   Proteins

   68          601   Journal of Medical Genetics

   69          574   Current Genetics

   70          571   Nature Cell Biology

   71          551   Bioscience, Biotechnology, and Biochemistry

   72          533   Nature Structural and Molecular Biology

   73          532   Molecular Endocrinology

   74          532   Journal of Neurochemistry

   75          519   The Journal of Clinical Endocrinology and Metabolism

   76          511   Developmental Cell

   77          507   The FEBS Journal

   78          503   Endocrinology

   79          489   Mammalian Genome

   80          472   Immunogenetics

   81          466   Antimicrobial Agents and Chemotherapy

   82          457   Experimental Cell Research

   83          448   Molecular and Biochemical Parasitology

   84          431   Eukaryotic Cell

   85          425   Planta

   86          418   Nature Communications

   87          417   RNA

   88          412   Peptides

   89          407   Journal of Molecular Evolution

   90          397   Molecular Biology and Evolution

   91          388   DNA and Cell Biology

   92          384   Journal of Experimental Botany

   93          377   Journal of the American Chemical Society

   94          375   Molecular Pharmacology

   95          374   DNA Sequence

   96          367   PLoS Pathogens

   97          362   EMBO Reports

   98          360   Neurology

   99          359   Journal of Investigative Dermatology

  100          355   The FASEB Journal

  101          350   Comparative Biochemistry and Physiology

  102          347   Biology of Reproduction

  103          347   Acta Crystallographica, Section F

  104          346   Scientific Reports

  105          342   Molecular Plant-Microbe Interactions

  106          339   Brain Research. Molecular Brain Research

  107          339   American Journal of Medical Genetics. Part A

  108          336   European Journal of Human Genetics

  109          331   Immunity

  110          326   Tissue Antigens

  111          322   Virus Research

  112          318   Biochimie

  113          318   The New England Journal of Medicine

  114          317   Genes to Cells

  115          313   Developmental Dynamics

  116          296   Biological Chemistry Hoppe-Seyler

  117          296   Clinical Genetics

  118          296   Genome Research

  119          288   Annals of Neurology

  120          282   Cytogenetics and Cell Genetics

  121          277   European Journal of Immunology

  122          271   Journal of General Microbiology

  123          271   Nature Immunology

  124          269   BMC Genomics

  125          266   Investigative Ophthalmology and Visual Science

  126          260   Applied Microbiology and Biotechnology

  127          254   Journal of Human Genetics

  128          250   Journal of Medicinal Chemistry

  129          245   PLoS Biology

  130          241   Archives of Microbiology

  131          235   Glycobiology

  132          231   DNA Research

  133          230   Journal of Lipid Research

  134          229   Journal of Cellular Biochemistry

  135          224   Traffic

  136          220   Molecular Genetics and Metabolism

  137          220   Cell Cycle

  138          219   Molecular Immunology

  139          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  140          215   Circulation Research

  141          213   Archives of Virology

  142          208   Diabetes

  143          207   Molecular and Cellular Endocrinology

  144          204   Protein Expression and Purification

  145          204   Phytochemistry

  146          203   Fungal Genetics and Biology

  147          202   Cell Reports

  148          199   Nature Medicine

  149          196   Molecular Genetics and Genomics

  150          186   Chemistry and Biology





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)                      1220237                 2.18                                         

   Journal                           1042774     454852      1.87       1                                 

   Submitted to EMBL/GenBank/DDBJ     166641     150996      0.30       2                                 

   Submitted to other databases         7382       6817      0.01       3                                 

   Book citation                        1772       1749     <0.01       4                                 

   Plant Gene Register                   612        599     <0.01       5                                 

   Thesis                                434        431     <0.01       6                                 

   Unpublished observations              407        403     <0.01       7                                 

   Patent                                209        203     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 408124



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2532318                 4.53                                         

   ACTIVITY REGULATION                 14807      14807      0.03      16                                 

   ALLERGEN                              764        764     <0.01      26                                 

   ALTERNATIVE PRODUCTS                25265      25265      0.05      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        8251       8251      0.01      20                                 

   BIOTECHNOLOGY                         974        960     <0.01      25                                 

   CATALYTIC ACTIVITY                 282182     237510      0.50       4                                 

   CAUTION                             12858      12612      0.02      18                                 

   COFACTOR                           123171     112770      0.22       7                                 

   DEVELOPMENTAL STAGE                 12154      12153      0.02      19                                 

   DISEASE                              7031       4716      0.01      21                                 

   DISRUPTION PHENOTYPE                14316      14314      0.03      17                                 

   DOMAIN                              48832      42035      0.09       9                                 

   FUNCTION                           466212     445565      0.83       2                                 

   INDUCTION                           20976      20964      0.04      14                                 

   INTERACTION                         19170      19170      0.03      15                                 

   MASS SPECTROMETRY                    6938       5229      0.01      22                                 

   MISCELLANEOUS                       38582      35515      0.07      12                                 

   PATHWAY                            138188     125357      0.25       6                                 

   PHARMACEUTICAL                        117        113     <0.01      29                                 

   POLYMORPHISM                         1324       1268     <0.01      24                                 

   PTM                                 56591      41747      0.10       8                                 

   RNA EDITING                           627        627     <0.01      28                                 

   SEQUENCE CAUTION                    44055      44055      0.08      11                                 

   SIMILARITY                         507948     503800      0.91       1                                 

   SUBCELLULAR LOCATION               349160     341774      0.62       3                                 

   SUBUNIT                            278602     277779      0.50       5                                 

   TISSUE SPECIFICITY                  45806      45805      0.08      10                                 

   TOXIC DOSE                            668        610     <0.01      27                                 

   WEB RESOURCE                         6749       5589      0.01      23                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        4492023                 8.03                                         

   ACT_SITE                           163831      99371      0.29      10                                 

   BINDING                            405195     107285      0.72       2                                 

   CA_BIND                              4177       1730      0.01      36                                 

   CARBOHYD                           115929      29801      0.21      15                                 

   CHAIN                              567012     552004      1.01       1                                 

   COILED                              22034      15227      0.04      27                                 

   COMPBIAS                            59057      31773      0.11      20                                 

   CONFLICT                           135285      47370      0.24      13                                 

   CROSSLNK                            23621       8468      0.04      26                                 

   DISULFID                           125136      33714      0.22      14                                 

   DNA_BIND                            11671      10549      0.02      32                                 

   DOMAIN                             194557     119928      0.35       9                                 

   HELIX                              255508      23605      0.46       6                                 

   INIT_MET                            17164      17164      0.03      28                                 

   INTRAMEM                             2668       1196     <0.01      37                                 

   LIPID                               13037       8422      0.02      30                                 

   METAL                              381033      94213      0.68       3                                 

   MOD_RES                            248764      71878      0.44       7                                 

   MOTIF                               43131      28126      0.08      23                                 

   MUTAGEN                             70268      15377      0.13      18                                 

   NON_CONS                             2258        788     <0.01      38                                 

   NON_STD                               357        282     <0.01      39                                 

   NON_TER                             12403       9517      0.02      31                                 

   NP_BIND                            157134      85388      0.28      11                                 

   PEPTIDE                             11579       7969      0.02      33                                 

   PROPEP                              14220      12130      0.03      29                                 

   REGION                             198127      93754      0.35       8                                 

   REPEAT                             105511      14752      0.19      16                                 

   SIGNAL                              41698      41697      0.07      24                                 

   SITE                                57940      31788      0.10      21                                 

   STRAND                             266064      22221      0.48       5                                 

   TOPO_DOM                           140348      28757      0.25      12                                 

   TRANSIT                              9098       8982      0.02      34                                 

   TRANSMEM                           370742      77378      0.66       4                                 

   TURN                                61535      19133      0.11      19                                 

   UNSURE                               4455        797      0.01      35                                 

   VAR_SEQ                             52010      22029      0.09      22                                 

   VARIANT                             96908      17092      0.17      17                                 

   ZN_FING                             30558      13417      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)               18992526                33.97                                                           

   Allergome                            1789       1169     <0.01     122      Protein family/group databases               

   ArachnoServer                        1145       1136     <0.01     131      Organism-specific databases                  

   Araport                             15849      15753      0.03      84      Organism-specific databases                  

   Bgee                                56497      56497      0.10      45      Gene expression databases                    

   BindingDB                            5001       5001      0.01     105      Chemistry                                    

   BioCyc                             237386     232881      0.42      24      Enzyme and pathway databases                 

   BioGrid                             51078      50576      0.09      50      Protein-protein interaction databases        

   BioMuta                             20371      20359      0.04      71      Polymorphism and mutation databases          

   BRENDA                              12912      12138      0.02      87      Enzyme and pathway databases                 

   CarbonylDB                           1157       1157     <0.01     130      PTM databases                                

   CAZy                                 9492       8557      0.02      90      Protein family/group databases               

   CCDS                                48188      34164      0.09      52      Sequence databases                           

   CDD                                185221     169237      0.33      27      Family and domain databases                  

   CGD                                  1997       1980     <0.01     119      Organism-specific databases                  

   ChEMBL                               6869       6869      0.01      97      Chemistry                                    

   ChiTaRS                             20479      20468      0.04      70      Other                                        

   CleanEx                             30009      29378      0.05      58      Gene expression databases                    

   CollecTF                              133        133     <0.01     153      Gene expression databases                    

   ComplexPortal                        8554       4502      0.02      91      Protein-protein interaction databases        

   COMPLUYEAST-2DPAGE                     97         97     <0.01     154      2D gel databases                             

   ConoServer                            951        868     <0.01     132      Organism-specific databases                  

   CORUM                                5802       5802      0.01     101      Protein-protein interaction databases        

   CTD                                 75010      74108      0.13      43      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     150      PTM databases                                

   dictyBase                            4221       4106      0.01     109      Organism-specific databases                  

   DIP                                 17361      17329      0.03      80      Protein-protein interaction databases        

   DisGeNET                            14838      14604      0.03      85      Organism-specific databases                  

   DisProt                               708        703     <0.01     136      3D structure databases                       

   DMDM                                16275      16274      0.03      83      Polymorphism and mutation databases          

   DNASU                               18999      18932      0.03      75      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     145        145     <0.01     152      2D gel databases                             

   DrugBank                            18747       3637      0.03      76      Chemistry                                    

   EchoBASE                             4159       4159      0.01     110      Organism-specific databases                  

   EcoGene                              4293       4293      0.01     108      Organism-specific databases                  

   eggNOG                             665065     331818      1.19       5      Phylogenomic databases                       

   ELM                                  1811       1811     <0.01     121      Protein-protein interaction databases        

   EMBL                               984948     547340      1.76       3      Sequence databases                           

   Ensembl                             90926      50625      0.16      41      Genome annotation databases                  

   EnsemblBacteria                    355463     336333      0.64      17      Genome annotation databases                  

   EnsemblFungi                        29339      27837      0.05      60      Genome annotation databases                  

   EnsemblMetazoa                      17369      10159      0.03      79      Genome annotation databases                  

   EnsemblPlants                       27564      20586      0.05      63      Genome annotation databases                  

   EnsemblProtists                      5017       4831      0.01     104      Genome annotation databases                  

   EPD                                 21825      21825      0.04      68      Proteomic databases                          

   ESTHER                               2518       2518     <0.01     117      Protein family/group databases               

   euHCVdb                                55         44     <0.01     155      Organism-specific databases                  

   EuPathDB                            31173      30982      0.06      57      Organism-specific databases                  

   EvolutionaryTrace                   16628      16628      0.03      82      Other                                        

   ExpressionAtlas                     51782      51782      0.09      48      Gene expression databases                    

   FlyBase                              6179       5883      0.01      99      Organism-specific databases                  

   Gene3D                             368040     293716      0.66      16      Family and domain databases                  

   GeneCards                           20367      20196      0.04      72      Organism-specific databases                  

   GeneDB                                575        519     <0.01     140      Genome annotation databases                  

   GeneID                             290097     280132      0.52      22      Genome annotation databases                  

   GeneReviews                          1479       1475     <0.01     123      Organism-specific databases                  

   GeneTree                            59122      59047      0.11      44      Phylogenomic databases                       

   Genevisible                         55240      55240      0.10      46      Gene expression databases                    

   GeneWiki                            10355      10272      0.02      89      Other                                        

   GenomeRNAi                          22107      22107      0.04      66      Other                                        

   GlyConnect                           1435       1367     <0.01     124      PTM databases                                

   GO                                2939518     532857      5.26       1      Ontologies                                   

   Gramene                             27564      20586      0.05      62      Genome annotation databases                  

   GuidetoPHARMACOLOGY                  1957       1957     <0.01     120      Chemistry                                    

   H-InvDB                              5626       4800      0.01     102      Organism-specific databases                  

   HAMAP                              329844     326968      0.59      19      Family and domain databases                  

   HGNC                                20352      20213      0.04      74      Organism-specific databases                  

   HOGENOM                            391804     391804      0.70      15      Phylogenomic databases                       

   HOVERGEN                            76128      76128      0.14      42      Phylogenomic databases                       

   HPA                                 27390      16823      0.05      64      Organism-specific databases                  

   IMGT_GENE-DB                          253        253     <0.01     149      Protein family/group databases               

   InParanoid                         139601     139601      0.25      30      Phylogenomic databases                       

   IntAct                              52814      52814      0.09      47      Protein-protein interaction databases        

   InterPro                          2248370     540803      4.02       2      Family and domain databases                  

   iPTMnet                             51310      51310      0.09      49      PTM databases                                

   jPOST                               26838      26838      0.05      65      Proteomic databases                          

   KEGG                               502324     474870      0.90       7      Genome annotation databases                  

   KO                                 405210     404765      0.72      14      Phylogenomic databases                       

   LegioList                             765        763     <0.01     135      Organism-specific databases                  

   Leproma                               672        669     <0.01     137      Organism-specific databases                  

   MaizeGDB                              510        506     <0.01     141      Organism-specific databases                  

   MalaCards                            4499       4496      0.01     107      Organism-specific databases                  

   MaxQB                               29713      29713      0.05      59      Proteomic databases                          

   MEROPS                              11401      11401      0.02      88      Protein family/group databases               

   MGI                                 16916      16876      0.03      81      Organism-specific databases                  

   MIM                                 21094      15095      0.04      69      Organism-specific databases                  

   MINT                                21868      21868      0.04      67      Protein-protein interaction databases        

   MoonDB                                348        348     <0.01     147      Protein family/group databases               

   MoonProt                              279        279     <0.01     148      Protein family/group databases               

   mycoCLAP                              355        352     <0.01     146      Protein family/group databases               

   neXtProt                            20361      20361      0.04      73      Organism-specific databases                  

   OGP                                   373        373     <0.01     145      2D gel databases                             

   OMA                                408786     408786      0.73      13      Phylogenomic databases                       

   OpenTargets                         18387      18228      0.03      77      Organism-specific databases                  

   Orphanet                             7456       3933      0.01      94      Organism-specific databases                  

   OrthoDB                            256521     256521      0.46      23      Phylogenomic databases                       

   PANTHER                            295544     281577      0.53      20      Family and domain databases                  

   PATRIC                              91909      91909      0.16      40      Genome annotation databases                  

   PaxDb                              124707     124707      0.22      33      Proteomic databases                          

   PDB                                170989      27117      0.31      28      3D structure databases                       

   PDBsum                             170989      27117      0.31      29      3D structure databases                       

   PeptideAtlas                        32145      32145      0.06      56      Proteomic databases                          

   PeroxiBase                            780        758     <0.01     134      Protein family/group databases               

   Pfam                               760851     518484      1.36       4      Family and domain databases                  

   PharmGKB                            18357      18315      0.03      78      Organism-specific databases                  

   PhosphoSitePlus                     39019      39019      0.07      54      PTM databases                                

   PhylomeDB                           96355      96355      0.17      38      Phylogenomic databases                       

   PIR                                124207     113756      0.22      34      Sequence databases                           

   PIRSF                              108931     107902      0.19      37      Family and domain databases                  

   PMAP-CutDB                           1401       1401     <0.01     125      Other                                        

   PomBase                              5133       5129      0.01     103      Organism-specific databases                  

   PRIDE                              230711     230711      0.41      25      Proteomic databases                          

   PRINTS                             132712     117169      0.24      32      Family and domain databases                  

   PRO                                 95976      95976      0.17      39      Other                                        

   ProDom                              29154      28971      0.05      61      Family and domain databases                  

   ProMEX                                457        457     <0.01     143      Proteomic databases                          

   PROSITE                            467832     299082      0.84      10      Family and domain databases                  

   ProteinModelPortal                 449218     449218      0.80      11      3D structure databases                       

   Proteomes                          480005     455928      0.86       9      Other                                        

   ProteomicsDB                        36368      19824      0.07      55      Proteomic databases                          

   PseudoCAP                            1334       1325     <0.01     127      Organism-specific databases                  

   Reactome                           123274      36353      0.22      35      Enzyme and pathway databases                 

   REBASE                                409        409     <0.01     144      Protein family/group databases               

   RefSeq                             608842     463703      1.09       6      Sequence databases                           

   REPRODUCTION-2DPAGE                  1259       1038     <0.01     128      2D gel databases                             

   RGD                                  7978       7977      0.01      93      Organism-specific databases                  

   SABIO-RK                             4098       4098      0.01     111      Enzyme and pathway databases                 

   SFLD                                 8065       5979      0.01      92      Family and domain databases                  

   SGD                                  6740       6735      0.01      98      Organism-specific databases                  

   SignaLink                            3065       3065      0.01     116      Enzyme and pathway databases                 

   SIGNOR                               4083       4083      0.01     112      Enzyme and pathway databases                 

   SMART                              192454     141955      0.34      26      Family and domain databases                  

   SMR                                444726     444726      0.80      12      3D structure databases                       

   STRING                             332842     332842      0.60      18      Protein-protein interaction databases        

   SUPFAM                             498424     377960      0.89       8      Family and domain databases                  

   SWISS-2DPAGE                         1177       1177     <0.01     129      2D gel databases                             

   SwissLipids                          1361       1274     <0.01     126      Chemistry                                    

   SwissPalm                            7372       7372      0.01      95      PTM databases                                

   TAIR                                14636      14580      0.03      86      Organism-specific databases                  

   TCDB                                 6950       6899      0.01      96      Protein family/group databases               

   TIGRFAMs                           292404     272415      0.52      21      Family and domain databases                  

   TopDownProteomics                    3241       2964      0.01     114      Proteomic databases                          

   TreeFam                             45501      45491      0.08      53      Phylogenomic databases                       

   TubercuList                          2191       2155     <0.01     118      Organism-specific databases                  

   UCD-2DPAGE                            496        496     <0.01     142      2D gel databases                             

   UCSC                                49950      45629      0.09      51      Genome annotation databases                  

   UniCarbKB                             584        584     <0.01     139      PTM databases                                

   UniGene                            109919      96322      0.20      36      Sequence databases                           

   UniLectin                             238        238     <0.01     151      Protein family/group databases               

   UniPathway                         136363     123572      0.24      31      Enzyme and pathway databases                 

   VectorBase                            597        517     <0.01     138      Genome annotation databases                  

   VGNC                                 3919       3919      0.01     113      Organism-specific databases                  

   WBParaSite                             34         34     <0.01     156      Genome annotation databases                  

   World-2DPAGE                          930        919     <0.01     133      2D gel databases                             

   WormBase                             6027       4597      0.01     100      Organism-specific databases                  

   Xenbase                              4565       4556      0.01     106      Organism-specific databases                  

   ZFIN                                 3070       3065      0.01     115      Organism-specific databases                  



Total number of cross-referenced databases: 156



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.25   Gln (Q) 3.93   Leu (L) 9.65   Ser (S) 6.62

   Arg (R) 5.53   Glu (E) 6.73   Lys (K) 5.81   Thr (T) 5.35

   Asn (N) 4.05   Gly (G) 7.07   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) 1.38   Ile (I) 5.92   Pro (P) 4.73   Val (V) 6.86



   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 3887 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: 79317