UniProtKB/Swiss-Prot protein knowledgebase release 2016_05 statistics





1.  INTRODUCTION



Release 2016_05 of 11-May-16 of UniProtKB/Swiss-Prot contains 551193 sequence entries,

comprising 196822649 amino acids abstracted from 244578 references. 



242 sequences have been added since release 2016_04, the sequence data of

22 existing entries has been updated and the annotations of

120967 entries have been revised.



Number of fragments: 9153

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 39167





Protein existence (PE):           entries     %



1: Evidence at protein level        92536   16.8%

2: Evidence at transcript level     57757   10.5%

3: Inferred from homology          387589   70.3%

4: Predicted                        11358    2.1%

5: Uncertain                         1953    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 117546 sequences:  21.3 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5532

                            2x: 1908

                            3x: 1047

                            4x:  664

                            5x:  492

                            6x:  402

                            7x:  290

                            8x:  236

                            9x:  215

                           10x:  129

                       11- 20x:  712

                       21- 50x:  428

                       51-100x:  215

                         >100x: 1048





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20201  Homo sapiens (Human)

       2      16785  Mus musculus (Mouse)

       3      14639  Arabidopsis thaliana (Mouse-ear cress)

       4       7959  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       3707  Caenorhabditis elegans

      12       3485  Oryza sativa subsp. japonica (Rice)

      13       3402  Xenopus laevis (African clawed frog)

      14       3298  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       2104  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       1786  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       1171  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        825  Escherichia coli (strain UTI89 / UPEC)

      59        822  Shigella dysenteriae serotype 1 (strain Sd197)

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

      61        812  Canis lupus familiaris (Dog) (Canis familiaris)

      62        800  Emericella nidulans  

      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        778  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 halodurans 

      87        739  Bacillus anthracis

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

     112        689  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     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         332567 ( 60%)

    Eukaryota        182612 ( 33%)

    Viruses           16629 (  3%)





   Within Eukaryota:



   



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

     Human                  20202 ( 11%)           (  4%)

     Other Mammalia         46297 ( 25%)           (  8%)

     Other Vertebrata       17899 ( 10%)           (  3%)

     Viridiplantae          37575 ( 21%)           (  7%)

     Fungi                  31967 ( 18%)           (  6%)

     Insecta                 8861 (  5%)           (  2%)

     Nematoda                4592 (  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    9141             1001-1100     3883

                 51- 100   42092             1101-1200     2731

                101- 150   58491             1201-1300     2099

                151- 200   58448             1301-1400     1952

                201- 250   57290             1401-1500     1566

                251- 300   50914             1501-1600      761

                301- 350   51182             1601-1700      590

                351- 400   44354             1701-1800      500

                401- 450   36403             1801-1900      445

                451- 500   29308             1901-2000      365

                501- 550   20979             2001-2100      224

                551- 600   14999             2101-2200      306

                601- 650   12579             2201-2300      303

                651- 700    9073             2301-2400      187

                701- 750    7519             2401-2500      143

                751- 800    5409             >2500         1156

                801- 850    4681

                851- 900    5148

                901- 950    3977

                951-1000    2842



   





   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: 2578





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  833

                       2x:  345

                       3x:  161

                       4x:  126

                       5x:  110

                       6x:   84

                       7x:   55

                       8x:   56

                       9x:   28

                      10x:   40

                  11- 20x:  212

                  21- 50x:  202

                  51-100x:  113

                    >100x:  213





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



   Nb    Citations   Journal name

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

    1        23204   Journal of Biological Chemistry

    2        10589   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6281   Journal of Bacteriology

    4         5367   Biochemical and Biophysical Research Communications

    5         4974   Biochemistry

    6         4829   Nucleic Acids Research

    7         4747   Gene

    8         4654   FEBS Letters

    9         4507   The EMBO Journal

   10         4184   Molecular and Cellular Biology

   11         4147   Nature

   12         4003   Journal of Molecular Biology

   13         3467   Biochimica et Biophysica Acta

   14         3343   Cell

   15         3333   European Journal of Biochemistry

   16         2893   Journal of Virology

   17         2781   Science

   18         2712   Biochemical Journal

   19         2525   Genomics

   20         2342   Molecular Microbiology

   21         2264   Plant Physiology

   22         2052   Journal of Cell Biology

   23         1882   The American Journal of Human Genetics

   24         1774   Plant Molecular Biology

   25         1753   Genes and Development

   26         1733   The Plant Cell

   27         1653   Human Molecular Genetics

   28         1650   Nature Genetics

   29         1640   Virology

   30         1576   The Plant Journal

   31         1528   Development

   32         1524   Molecular Biology of the Cell

   33         1503   Oncogene

   34         1451   Human Mutation

   35         1378   Molecular and General Genetics

   36         1370   Molecular Cell

   37         1338   PLoS ONE

   38         1308   Journal of Immunology

   39         1294   Journal of Biochemistry

   40         1226   Genetics

   41         1221   Structure

   42         1113   Journal of Cell Science

   43         1088   Blood

   44         1068   Journal of General Virology

   45         1058   Infection and Immunity

   46         1004   Microbiology

   47          993   Archives of Biochemistry and Biophysics

   48          940   Developmental Biology

   49          938   Current Biology

   50          854   Cancer Research

   51          826   Yeast

   52          797   FEMS Microbiology Letters

   53          795   Acta Crystallographica, Section D

   54          794   Journal of Neuroscience

   55          765   Applied and Environmental Microbiology

   56          724   Toxicon

   57          721   Protein Science

   58          676   Journal of Clinical Investigation

   59          667   Neuron

   60          663   Human Genetics

   61          637   Nature Structural Biology

   62          634   Mechanisms of Development

   63          628   American Journal of Physiology

   64          591   Plant and Cell Physiology

   65          587   The Journal of Experimental Medicine

   66          569   Proteins

   67          559   Current Genetics

   68          525   Journal of Medical Genetics

   69          523   Molecular Endocrinology

   70          514   Nature Cell Biology

   71          511   Bioscience, Biotechnology, and Biochemistry

   72          508   Journal of Neurochemistry

   73          494   The Journal of Clinical Endocrinology and Metabolism

   74          487   Mammalian Genome

   75          477   Endocrinology

   76          462   Immunogenetics

   77          445   Molecular and Biochemical Parasitology

   78          435   Nature Structural and Molecular Biology

   79          429   The FEBS Journal

   80          424   Experimental Cell Research

   81          421   Developmental Cell

   82          417   Antimicrobial Agents and Chemotherapy

   83          406   Journal of Molecular Evolution

   84          403   Eukaryotic Cell

   85          401   PLoS Genetics

   86          388   Peptides

   87          386   Molecular Biology and Evolution

   88          383   DNA and Cell Biology

   89          373   RNA

   90          370   DNA Sequence

   91          369   Planta

   92          348   Journal of Investigative Dermatology

   93          346   Molecular Pharmacology

   94          336   Comparative Biochemistry and Physiology

   95          334   Brain Research. Molecular Brain Research

   96          334   Neurology

   97          325   Tissue Antigens

   98          323   EMBO Reports

   99          316   Biology of Reproduction

  100          305   The FASEB Journal

  101          303   Journal of the American Chemical Society

  102          296   Molecular Plant-Microbe Interactions

  103          295   Immunity

  104          294   Biological Chemistry Hoppe-Seyler

  105          292   The New England Journal of Medicine

  106          292   Biochimie

  107          291   Developmental Dynamics

  108          291   Genes to Cells

  109          288   Acta Crystallographica, Section F

  110          288   Virus Research

  111          281   Cytogenetics and Cell Genetics

  112          280   Genome Research

  113          278   European Journal of Human Genetics

  114          277   Journal of Experimental Botany

  115          266   Journal of General Microbiology

  116          255   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          243   BMC Genomics

  122          240   Investigative Ophthalmology and Visual Science

  123          238   Nature Immunology

  124          231   Journal of Human Genetics

  125          229   Archives of Microbiology

  126          221   DNA Research

  127          219   Journal of Medicinal Chemistry

  128          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  129          217   Journal of Cellular Biochemistry

  130          216   Applied Microbiology and Biotechnology

  131          209   Glycobiology

  132          202   Traffic

  133          200   Cell Cycle

  134          200   Circulation Research

  135          200   Molecular Genetics and Metabolism

  136          200   Archives of Virology

  137          199   Molecular and Cellular Endocrinology

  138          197   Molecular Immunology

  139          197   Diabetes

  140          192   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)                      1146735                 2.08                                         

   Journal                            951062     440359      1.73       1                                 

   Submitted to EMBL/GenBank/DDBJ     185399     163406      0.34       2                                 

   Submitted to other databases         7165       6646      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: 376110



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2581672                 4.68                                         

   ALLERGEN                              696        696     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24534      24534      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        7017       7017      0.01      21                                 

   BIOTECHNOLOGY                         569        567     <0.01      28                                 

   CATALYTIC ACTIVITY                 257758     231387      0.47       5                                 

   CAUTION                             10375      10169      0.02      18                                 

   COFACTOR                           118836     108777      0.22       7                                 

   DEVELOPMENTAL STAGE                 10923      10923      0.02      17                                 

   DISEASE                              6201       4152      0.01      22                                 

   DISRUPTION PHENOTYPE                10158      10158      0.02      19                                 

   DOMAIN                              44213      38295      0.08       9                                 

   ENZYME REGULATION                   13470      13469      0.02      16                                 

   FUNCTION                           446550     428071      0.81       2                                 

   INDUCTION                           18162      18161      0.03      14                                 

   INTERACTION                         16020      16020      0.03      15                                 

   MASS SPECTROMETRY                    6086       4590      0.01      23                                 

   MISCELLANEOUS                       35125      32302      0.06      12                                 

   PATHWAY                            135454     122717      0.25       6                                 

   PHARMACEUTICAL                         99         99     <0.01      29                                 

   POLYMORPHISM                         1045        989     <0.01      24                                 

   PTM                                 50897      38764      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    43107      43107      0.08      10                                 

   SIMILARITY                         667737     526280      1.21       1                                 

   SUBCELLULAR LOCATION               339881     333167      0.62       3                                 

   SUBUNIT                            264648     264512      0.48       4                                 

   TISSUE SPECIFICITY                  42672      42672      0.08      11                                 

   TOXIC DOSE                            623        577     <0.01      27                                 

   WEB RESOURCE                         8189       6867      0.01      20                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        4157447                 7.54                                         

   ACT_SITE                           157133      96019      0.29      10                                 

   BINDING                            352926      93520      0.64       4                                 

   CA_BIND                              3987       1677      0.01      36                                 

   CARBOHYD                           112064      28712      0.20      15                                 

   CHAIN                              558769     544770      1.01       1                                 

   COILED                              21412      14772      0.04      26                                 

   COMPBIAS                            57521      30793      0.10      18                                 

   CONFLICT                           132035      46296      0.24      13                                 

   CROSSLNK                            11117       5572      0.02      32                                 

   DISULFID                           117849      32199      0.21      14                                 

   DNA_BIND                            11217      10193      0.02      31                                 

   DOMAIN                             179223     108662      0.33       8                                 

   HELIX                              219782      20684      0.40       6                                 

   INIT_MET                            18282      18282      0.03      27                                 

   INTRAMEM                             2430       1061     <0.01      37                                 

   LIPID                               12546       8066      0.02      29                                 

   METAL                              356568      88564      0.65       3                                 

   MOD_RES                            215857      68412      0.39       7                                 

   MOTIF                               40088      25906      0.07      24                                 

   MUTAGEN                             57084      12928      0.10      19                                 

   NON_CONS                             2235        775     <0.01      38                                 

   NON_STD                               359        284     <0.01      39                                 

   NON_TER                             12286       9402      0.02      30                                 

   NP_BIND                            139480      79923      0.25      11                                 

   PEPTIDE                             10722       7285      0.02      33                                 

   PROPEP                              13451      11535      0.02      28                                 

   REGION                             177608      84365      0.32       9                                 

   REPEAT                             100597      14334      0.18      16                                 

   SIGNAL                              40297      40287      0.07      23                                 

   SITE                                52474      29287      0.10      21                                 

   STRAND                             229028      19502      0.42       5                                 

   TOPO_DOM                           135788      27992      0.25      12                                 

   TRANSIT                              9085       8972      0.02      34                                 

   TRANSMEM                           365393      75786      0.66       2                                 

   TURN                                52882      16756      0.10      20                                 

   UNSURE                               4277        756      0.01      35                                 

   VAR_SEQ                             51008      21460      0.09      22                                 

   VARIANT                             92549      17032      0.17      17                                 

   ZN_FING                             30038      13314      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)               17838866                32.36                                                           

   Allergome                            1691       1106     <0.01     111      Protein family/group databases               

   ArachnoServer                        1145       1135     <0.01     117      Organism-specific databases                  

   Bgee                                38878      38878      0.07      51      Gene expression databases                    

   BindingDB                            5687       5687      0.01      91      Chemistry                                    

   BioCyc                             325522     308227      0.59      20      Enzyme and pathway databases                 

   BioGrid                             48218      47763      0.09      47      Protein-protein interaction databases        

   BioMuta                             17246      17245      0.03      72      Polymorphism and mutation databases          

   BRENDA                              12753      11984      0.02      81      Enzyme and pathway databases                 

   CAZy                                 7891       7100      0.01      84      Protein family/group databases               

   CCDS                                46587      33595      0.08      48      Sequence databases                           

   CGD                                  1708       1692     <0.01     110      Organism-specific databases                  

   ChEMBL                               6391       6391      0.01      87      Chemistry                                    

   ChiTaRS                             16470      16460      0.03      76      Other                                        

   CleanEx                             30044      29404      0.05      58      Gene expression databases                    

   CollecTF                              133        133     <0.01     137      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     138      2D gel databases                             

   ConoServer                            949        866     <0.01     119      Organism-specific databases                  

   CTD                                 73431      72687      0.13      42      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     135      PTM databases                                

   dictyBase                            4207       4092      0.01     100      Organism-specific databases                  

   DIP                                 16825      16768      0.03      73      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     125      3D structure databases                       

   DMDM                                16376      16375      0.03      77      Polymorphism and mutation databases          

   DNASU                               18879      18808      0.03      68      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     146        146     <0.01     136      2D gel databases                             

   DrugBank                            11766       1908      0.02      82      Chemistry                                    

   EchoBASE                             4161       4161      0.01     101      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      99      Organism-specific databases                  

   eggNOG                             656894     327870      1.19       5      Phylogenomic databases                       

   EMBL                               977007     539858      1.77       3      Sequence databases                           

   Ensembl                             84498      48453      0.15      40      Genome annotation databases                  

   EnsemblBacteria                    354755     335746      0.64      17      Genome annotation databases                  

   EnsemblFungi                        30171      27750      0.05      57      Genome annotation databases                  

   EnsemblMetazoa                      13085       9803      0.02      79      Genome annotation databases                  

   EnsemblPlants                       21939      18692      0.04      62      Genome annotation databases                  

   EnsemblProtists                      4881       4718      0.01      97      Genome annotation databases                  

   EPD                                 23377      23377      0.04      61      Proteomic databases                          

   ESTHER                               2434       2432     <0.01     107      Protein family/group databases               

   euHCVdb                                55         44     <0.01     140      Organism-specific databases                  

   EuPathDB                            17987      17986      0.03      71      Organism-specific databases                  

   EvolutionaryTrace                   16549      16547      0.03      75      Other                                        

   ExpressionAtlas                     32024      32024      0.06      55      Gene expression databases                    

   FlyBase                              5987       5625      0.01      90      Organism-specific databases                  

   Gene3D                             471993     347891      0.86       9      Family and domain databases                  

   GeneCards                           20023      19849      0.04      65      Organism-specific databases                  

   GeneDB                                389        350     <0.01     132      Genome annotation databases                  

   GeneID                             273781     264890      0.50      23      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     116      Organism-specific databases                  

   GeneTree                            55431      55388      0.10      44      Phylogenomic databases                       

   Genevisible                         55139      55139      0.10      45      Gene expression databases                    

   GeneWiki                            10368      10282      0.02      83      Other                                        

   GenomeRNAi                          21785      21785      0.04      63      Other                                        

   GO                                2722846     522972      4.94       1      Ontologies                                   

   Gramene                             18122      15750      0.03      70      Genome annotation databases                  

   GuidetoPHARMACOLOGY                  1874       1874     <0.01     109      Chemistry                                    

   H-InvDB                              5589       4768      0.01      92      Organism-specific databases                  

   HAMAP                              325789     322717      0.59      19      Family and domain databases                  

   HGNC                                20012      19864      0.04      66      Organism-specific databases                  

   HOGENOM                            388664     388664      0.71      15      Phylogenomic databases                       

   HOVERGEN                            75772      75772      0.14      41      Phylogenomic databases                       

   HPA                                 24700      16208      0.04      60      Organism-specific databases                  

   InParanoid                         135948     135948      0.25      27      Phylogenomic databases                       

   IntAct                              46027      46027      0.08      49      Protein-protein interaction databases        

   InterPro                          1938104     531484      3.52       2      Family and domain databases                  

   iPTMnet                             35791      35791      0.06      52      PTM databases                                

   KEGG                               496695     463009      0.90       7      Genome annotation databases                  

   KO                                 387568     387125      0.70      16      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                            3775       3773      0.01     102      Organism-specific databases                  

   MaxQB                               32300      32299      0.06      54      Proteomic databases                          

   MEROPS                              12930      12930      0.02      80      Protein family/group databases               

   MGI                                 16700      16656      0.03      74      Organism-specific databases                  

   MIM                                 19746      14488      0.04      67      Organism-specific databases                  

   MINT                                31705      31705      0.06      56      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     139      Protein family/group databases               

   mycoCLAP                              347        343     <0.01     134      Protein family/group databases               

   NextBio                             71649      71649      0.13      43      Other                                        

   neXtProt                            20043      20043      0.04      64      Organism-specific databases                  

   OGP                                   375        375     <0.01     133      2D gel databases                             

   OMA                                407184     407184      0.74      13      Phylogenomic databases                       

   Orphanet                             6148       3289      0.01      88      Organism-specific databases                  

   OrthoDB                            391003     391003      0.71      14      Phylogenomic databases                       

   PANTHER                            172432     165592      0.31      26      Family and domain databases                  

   PATRIC                             308212     308177      0.56      21      Genome annotation databases                  

   PaxDb                              110694     110577      0.20      34      Proteomic databases                          

   PDB                                128587      23398      0.23      31      3D structure databases                       

   PDBsum                             128587      23398      0.23      30      3D structure databases                       

   PeptideAtlas                         5159       5159      0.01      95      Proteomic databases                          

   PeroxiBase                            771        755     <0.01     121      Protein family/group databases               

   Pfam                               744441     509823      1.35       4      Family and domain databases                  

   PharmGKB                            18381      18341      0.03      69      Organism-specific databases                  

   PhosphoSite                         33545      33545      0.06      53      PTM databases                                

   PhylomeDB                           94811      94811      0.17      37      Phylogenomic databases                       

   PIR                                122964     112670      0.22      33      Sequence databases                           

   PIRSF                              104392     103354      0.19      36      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     112      Other                                        

   PomBase                              5139       5120      0.01      96      Organism-specific databases                  

   PRIDE                              123906     123906      0.22      32      Proteomic databases                          

   PRINTS                             133784     118010      0.24      29      Family and domain databases                  

   PRO                                 88802      88802      0.16      39      Other                                        

   ProDom                              29139      28958      0.05      59      Family and domain databases                  

   ProMEX                                436        436     <0.01     130      Proteomic databases                          

   PROSITE                            452775     291108      0.82      11      Family and domain databases                  

   ProteinModelPortal                 443885     443885      0.81      12      3D structure databases                       

   Proteomes                          469104     448301      0.85      10      Other                                        

   PseudoCAP                            1308       1299     <0.01     113      Organism-specific databases                  

   Reactome                            93539      28523      0.17      38      Enzyme and pathway databases                 

   REBASE                                405        405     <0.01     131      Protein family/group databases               

   RefSeq                             599793     462265      1.09       6      Sequence databases                           

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

   RGD                                  7883       7880      0.01      85      Organism-specific databases                  

   SABIO-RK                             3329       3329      0.01     103      Enzyme and pathway databases                 

   SGD                                  6739       6734      0.01      86      Organism-specific databases                  

   SignaLink                            3002       3002      0.01     105      Enzyme and pathway databases                 

   SIGNOR                                502        502     <0.01     129      Enzyme and pathway databases                 

   SMART                              189084     139604      0.34      25      Family and domain databases                  

   SMR                                225970     225970      0.41      24      3D structure databases                       

   STRING                             325936     325936      0.59      18      Protein-protein interaction databases        

   SUPFAM                             479503     363643      0.87       8      Family and domain databases                  

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

   SwissLipids                           984        909     <0.01     118      Chemistry                                    

   SwissPalm                            5342       5342      0.01      94      PTM databases                                

   TAIR                                14623      14567      0.03      78      Organism-specific databases                  

   TCDB                                 5990       5960      0.01      89      Protein family/group databases               

   TIGRFAMs                           292163     272013      0.53      22      Family and domain databases                  

   TopDownProteomics                    3138       2862      0.01     104      Proteomic databases                          

   TreeFam                             44951      44946      0.08      50      Phylogenomic databases                       

   TubercuList                          2122       2086     <0.01     108      Organism-specific databases                  

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

   UCSC                                48704      44697      0.09      46      Genome annotation databases                  

   UniCarbKB                             584        584     <0.01     126      PTM databases                                

   UniGene                            105970      94287      0.19      35      Sequence databases                           

   UniPathway                         135175     122449      0.25      28      Enzyme and pathway databases                 

   VectorBase                            618        600     <0.01     124      Genome annotation databases                  

   WBParaSite                             22         22     <0.01     141      Genome annotation databases                  

   World-2DPAGE                          924        913     <0.01     120      2D gel databases                             

   WormBase                             5494       4246      0.01      93      Organism-specific databases                  

   Xenbase                              4450       4444      0.01      98      Organism-specific databases                  

   ZFIN                                 2804       2804      0.01     106      Organism-specific databases                  



Total number of cross-referenced databases: 141



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) 5.83   Thr (T) 5.34

   Asn (N) 4.06   Gly (G) 7.08   Met (M) 2.41   Trp (W) 1.09

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

   Cys (C) 1.37   Ile (I) 5.94   Pro (P) 4.72   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: 77573