UniProtKB/Swiss-Prot protein knowledgebase release 2016_01 statistics





1.  INTRODUCTION



Release 2016_01 of 20-Jan-16 of UniProtKB/Swiss-Prot contains 550299 sequence entries,

comprising 196347838 amino acids abstracted from 241721 references. 



193 sequences have been added since release 2015_12, the sequence data of

24 existing entries has been updated and the annotations of

91566 entries have been revised.



Number of fragments: 9151

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 39035





Protein existence (PE):           entries     %



1: Evidence at protein level        91610   16.6%

2: Evidence at transcript level     57689   10.5%

3: Inferred from homology          387626   70.4%

4: Predicted                        11427    2.1%

5: Uncertain                         1947    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: 13260



   The first twenty species represent 117174 sequences:  21.3 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5511

                            2x: 1902

                            3x: 1038

                            4x:  659

                            5x:  488

                            6x:  398

                            7x:  289

                            8x:  232

                            9x:  212

                           10x:  128

                       11- 20x:  714

                       21- 50x:  429

                       51-100x:  213

                         >100x: 1047





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20186  Homo sapiens (Human)

       2      16754  Mus musculus (Mouse)

       3      14430  Arabidopsis thaliana (Mouse-ear cress)

       4       7942  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       3671  Caenorhabditis elegans

      12       3453  Oryza sativa subsp. japonica (Rice)

      13       3402  Xenopus laevis (African clawed frog)

      14       3273  Drosophila melanogaster (Fruit fly)

      15       2961  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2273  Gallus gallus (Chicken)

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

      18       2103  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2028  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       1702  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       1299  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

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

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

      32       1057  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1027  Archaeoglobus fulgidus 

      34       1022  Yersinia pestis

      35        985  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      36        969  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        889  Staphylococcus aureus (strain MSSA476)

      47        889  Oryctolagus cuniculus (Rabbit)

      48        888  Staphylococcus aureus (strain MRSA252)

      49        882  Salmonella choleraesuis (strain SC-B67)

      50        878  Shigella sonnei (strain Ss046)

      51        878  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        846  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        791  Escherichia coli (strain SMS-3-5 / SECEC)

      63        791  Emericella nidulans  

      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        776  Pasteurella multocida (strain Pm70)

      68        773  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      69        771  Escherichia coli (strain K12 / DH10B)

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

      71        771  Oryza sativa subsp. indica (Rice)

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

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

      74        762  Escherichia coli (strain 55989 / EAEC)

      75        761  Escherichia coli O8 (strain IAI1)

      76        760  Shigella flexneri serotype 5b (strain 8401)

      77        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      78        758  Staphylococcus epidermidis (strain ATCC 12228)

      79        757  Zea mays (Maize)

      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 TT01)

      85        743  Staphylococcus aureus (strain NCTC 8325)

      86        741  Bacillus halodurans 

      87        739  Bacillus anthracis

      88        736  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        704  Pseudomonas putida (strain KT2440)

     106        702  Salmonella dublin (strain CT_02021853)

     107        698  Klebsiella pneumoniae (strain 342)

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

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

     110        693  Pan troglodytes (Chimpanzee)

     111        692  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     112        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

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

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

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

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

     117        670  Serratia proteamaculans (strain 568)

     118        669  Escherichia coli

     119        669  Mycobacterium leprae (strain TN)

     120        667  Yersinia pestis (strain Pestoides F)

     121        666  Staphylococcus aureus (strain USA300)

     122        664  Bacillus cereus 

     123        661  Bradyrhizobium diazoefficiens 

     124        658  Rhizobium sp. (strain NGR234)

     125        653  Debaryomyces hansenii   

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

     127        645  Shewanella oneidensis (strain MR-1)

     128        644  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        607  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     139        607  Xanthomonas campestris pv. campestris 

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

     141        602  Photobacterium profundum (Photobacterium sp. (strain SS9))

     142        602  Staphylococcus saprophyticus subsp. saprophyticus 

     143        601  Salmonella paratyphi C (strain RKS4594)

     144        600  Yersinia pestis bv. Antiqua (strain Angola)

     145        593  Bacillus cereus (strain ATCC 10987 / NRS 248)

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

     147        592  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     148        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     149        589  Pseudomonas aeruginosa (strain UCBPP-PA14)

     150        586  Rickettsia prowazekii (strain Madrid E)

     151        579  Neisseria meningitidis serogroup B (strain MC58)

     152        576  Brucella suis biovar 1 (strain 1330)

     153        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        535  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     173        531  Erwinia tasmaniensis (strain DSM 17950 / Et1/99)

     174        529  Sodalis glossinidius (strain morsitans)

     175        529  Listeria monocytogenes serotype 4b (strain F2365)

     176        525  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     177        522  Xylella fastidiosa (strain 9a5c)

     178        518  Corynebacterium glutamicum 

     179        517  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     180        517  Chromobacterium violaceum 

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

     182        515  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        512  Pseudomonas aeruginosa (strain PA7)

     184        512  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     185        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     186        509  Deinococcus radiodurans 

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

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

     204        491  Xanthomonas campestris pv. campestris (strain 8004)

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

     206        489  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     207        487  Methanosarcina mazei  

     208        487  Shewanella sp. (strain MR-7)

     209        486  Mannheimia succiniciproducens (strain MBEL55E)

     210        484  Pseudomonas aeruginosa (strain LESB58)

     211        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     212        484  Thermosynechococcus elongatus (strain BP-1)

     213        484  Shewanella sp. (strain MR-4)

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

     215        482  Pyrococcus horikoshii 

     216        480  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

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

     218        478  Pseudomonas putida (strain F1 / ATCC 700007)

     219        477  Pyrococcus abyssi (strain GE5 / Orsay)

     220        477  Brucella abortus (strain 2308)

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

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

     223        468  Clostridium perfringens (strain 13 / Type A)

     224        467  Nicotiana tabacum (Common tobacco)

     225        467  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

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

     227        466  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     228        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     229        466  Shewanella frigidimarina (strain NCIMB 400)

     230        466  Pseudomonas putida (strain GB-1)

     231        466  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     232        466  Shewanella sp. (strain ANA-3)

     233        464  Aeromonas hydrophila subsp. hydrophila 

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

     235        462  Burkholderia mallei (strain ATCC 23344)

     236        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     237        460  Enterococcus faecalis (strain ATCC 700802 / V583)

     238        459  Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Ralstonia eutropha 

     239        457  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     240        457  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     241        457  Campylobacter jejuni subsp. jejuni serotype O:2 

     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           19371 (  4%)

    Bacteria         332372 ( 60%)

    Eukaryota        181951 ( 33%)

    Viruses           16605 (  3%)





   Within Eukaryota:



   



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

     Human                  20187 ( 11%)           (  4%)

     Other Mammalia         46244 ( 25%)           (  8%)

     Other Vertebrata       17891 ( 10%)           (  3%)

     Viridiplantae          37284 ( 20%)           (  7%)

     Fungi                  31747 ( 17%)           (  6%)

     Insecta                 8832 (  5%)           (  2%)

     Nematoda                4556 (  3%)           (  1%)

     Other                  15210 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9133             1001-1100     3857

                 51- 100   42072             1101-1200     2720

                101- 150   58465             1201-1300     2091

                151- 200   58408             1301-1400     1944

                201- 250   57234             1401-1500     1565

                251- 300   50843             1501-1600      761

                301- 350   51095             1601-1700      586

                351- 400   44275             1701-1800      495

                401- 450   36332             1801-1900      446

                451- 500   29242             1901-2000      365

                501- 550   20918             2001-2100      224

                551- 600   14952             2101-2200      303

                601- 650   12525             2201-2300      303

                651- 700    9050             2301-2400      187

                701- 750    7499             2401-2500      143

                751- 800    5387             >2500         1144

                801- 850    4657

                851- 900    5133

                901- 950    3961

                951-1000    2833



   





   The average sequence length in UniProtKB/Swiss-Prot is 356 amino acids.



   The shortest sequence is   GWA_SEPOF (P83570):     2 amino acids.

   The longest sequence is  TITIN_MOUSE (A2ASS6): 35213 amino acids.





4.  JOURNAL CITATIONS



   Note: the following citation statistics reflect the number of distinct

         journal citations.



   Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2545





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  826

                       2x:  328

                       3x:  168

                       4x:  127

                       5x:  102

                       6x:   83

                       7x:   57

                       8x:   52

                       9x:   29

                      10x:   40

                  11- 20x:  207

                  21- 50x:  203

                  51-100x:  113

                    >100x:  210





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



   Nb    Citations   Journal name

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

    1        22963   Journal of Biological Chemistry

    2        10472   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6233   Journal of Bacteriology

    4         5330   Biochemical and Biophysical Research Communications

    5         4921   Biochemistry

    6         4795   Nucleic Acids Research

    7         4725   Gene

    8         4628   FEBS Letters

    9         4477   The EMBO Journal

   10         4152   Molecular and Cellular Biology

   11         4097   Nature

   12         3956   Journal of Molecular Biology

   13         3446   Biochimica et Biophysica Acta

   14         3327   European Journal of Biochemistry

   15         3308   Cell

   16         2865   Journal of Virology

   17         2749   Science

   18         2691   Biochemical Journal

   19         2524   Genomics

   20         2303   Molecular Microbiology

   21         2210   Plant Physiology

   22         2030   Journal of Cell Biology

   23         1865   The American Journal of Human Genetics

   24         1758   Plant Molecular Biology

   25         1736   Genes and Development

   26         1682   The Plant Cell

   27         1644   Nature Genetics

   28         1642   Human Molecular Genetics

   29         1630   Virology

   30         1535   The Plant Journal

   31         1511   Development

   32         1502   Molecular Biology of the Cell

   33         1498   Oncogene

   34         1434   Human Mutation

   35         1371   Molecular and General Genetics

   36         1352   Molecular Cell

   37         1289   Journal of Biochemistry

   38         1283   Journal of Immunology

   39         1245   PLoS ONE

   40         1212   Structure

   41         1211   Genetics

   42         1093   Journal of Cell Science

   43         1074   Blood

   44         1064   Journal of General Virology

   45         1047   Infection and Immunity

   46          990   Microbiology

   47          984   Archives of Biochemistry and Biophysics

   48          926   Current Biology

   49          923   Developmental Biology

   50          849   Cancer Research

   51          825   Yeast

   52          794   FEMS Microbiology Letters

   53          785   Acta Crystallographica, Section D

   54          784   Journal of Neuroscience

   55          742   Applied and Environmental Microbiology

   56          724   Toxicon

   57          720   Protein Science

   58          661   Journal of Clinical Investigation

   59          661   Human Genetics

   60          659   Neuron

   61          637   Nature Structural Biology

   62          634   Mechanisms of Development

   63          623   American Journal of Physiology

   64          578   The Journal of Experimental Medicine

   65          576   Plant and Cell Physiology

   66          563   Proteins

   67          555   Current Genetics

   68          516   Journal of Medical Genetics

   69          513   Molecular Endocrinology

   70          508   Nature Cell Biology

   71          506   Journal of Neurochemistry

   72          502   Bioscience, Biotechnology, and Biochemistry

   73          487   Mammalian Genome

   74          484   The Journal of Clinical Endocrinology and Metabolism

   75          472   Endocrinology

   76          462   Immunogenetics

   77          444   Molecular and Biochemical Parasitology

   78          422   Nature Structural and Molecular Biology

   79          418   Experimental Cell Research

   80          411   The FEBS Journal

   81          408   Developmental Cell

   82          404   Journal of Molecular Evolution

   83          402   Antimicrobial Agents and Chemotherapy

   84          386   Molecular Biology and Evolution

   85          386   Peptides

   86          381   DNA and Cell Biology

   87          376   Eukaryotic Cell

   88          370   RNA

   89          370   DNA Sequence

   90          362   PLoS Genetics

   91          360   Planta

   92          347   Journal of Investigative Dermatology

   93          342   Molecular Pharmacology

   94          336   Comparative Biochemistry and Physiology

   95          334   Brain Research. Molecular Brain Research

   96          326   Neurology

   97          325   Tissue Antigens

   98          316   EMBO Reports

   99          305   Biology of Reproduction

  100          301   The FASEB Journal

  101          294   Biological Chemistry Hoppe-Seyler

  102          294   Immunity

  103          289   The New England Journal of Medicine

  104          289   Genes to Cells

  105          288   Developmental Dynamics

  106          288   Journal of the American Chemical Society

  107          287   Biochimie

  108          285   Virus Research

  109          281   Cytogenetics and Cell Genetics

  110          281   Acta Crystallographica, Section F

  111          280   Molecular Plant-Microbe Interactions

  112          279   Genome Research

  113          273   Journal of Experimental Botany

  114          272   European Journal of Human Genetics

  115          265   Journal of General Microbiology

  116          252   Annals of Neurology

  117          249   European Journal of Immunology

  118          236   Investigative Ophthalmology and Visual Science

  119          236   PLoS Pathogens

  120          235   American Journal of Medical Genetics. Part A

  121          235   Nature Immunology

  122          234   BMC Genomics

  123          229   Journal of Human Genetics

  124          227   Clinical Genetics

  125          224   Archives of Microbiology

  126          220   DNA Research

  127          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  128          217   Journal of Medicinal Chemistry

  129          211   Journal of Cellular Biochemistry

  130          208   Glycobiology

  131          202   Traffic

  132          199   Molecular and Cellular Endocrinology

  133          198   Circulation Research

  134          198   Archives of Virology

  135          196   Molecular Immunology

  136          196   Diabetes

  137          195   Applied Microbiology and Biotechnology

  138          195   Cell Cycle

  139          191   Molecular Genetics and Metabolism

  140          188   PLoS Biology

  141          185   Phytochemistry

  142          184   Protein Expression and Purification

  143          181   Journal of Lipid Research

  144          178   Insect Biochemistry and Molecular Biology

  145          173   International Journal of Cancer

  146          172   Molecular Phylogenetics and Evolution

  147          170   Hemoglobin

  148          170   Nature Medicine

  149          170   Molecular and Cellular Neuroscience

  150          169   Proteomics





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)                      1134324                 2.06                                         

   Journal                            938865     439069      1.71       1                                 

   Submitted to EMBL/GenBank/DDBJ     185209     163365      0.34       2                                 

   Submitted to other databases         7148       6631      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              384        380     <0.01       7                                 

   Patent                                192        189     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 371463



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2567260                 4.67                                         

   ALLERGEN                              692        692     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24455      24455      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6825       6825      0.01      21                                 

   BIOTECHNOLOGY                         473        471     <0.01      28                                 

   CATALYTIC ACTIVITY                 255872     229826      0.46       5                                 

   CAUTION                             10329      10122      0.02      18                                 

   COFACTOR                           118019     108030      0.21       7                                 

   DEVELOPMENTAL STAGE                 10807      10807      0.02      17                                 

   DISEASE                              6138       4103      0.01      22                                 

   DISRUPTION PHENOTYPE                 9609       9609      0.02      19                                 

   DOMAIN                              43837      37945      0.08       9                                 

   ENZYME REGULATION                   13338      13338      0.02      16                                 

   FUNCTION                           443994     425665      0.81       2                                 

   INDUCTION                           17826      17826      0.03      14                                 

   INTERACTION                         15899      15899      0.03      15                                 

   MASS SPECTROMETRY                    6057       4568      0.01      23                                 

   MISCELLANEOUS                       34901      32092      0.06      12                                 

   PATHWAY                            135093     122440      0.25       6                                 

   PHARMACEUTICAL                         99         99     <0.01      29                                 

   POLYMORPHISM                         1040        984     <0.01      24                                 

   PTM                                 49980      38040      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42861      42861      0.08      10                                 

   SIMILARITY                         665844     525393      1.21       1                                 

   SUBCELLULAR LOCATION               338442     331789      0.62       3                                 

   SUBUNIT                            263021     263021      0.48       4                                 

   TISSUE SPECIFICITY                  42328      42328      0.08      11                                 

   TOXIC DOSE                            622        576     <0.01      27                                 

   WEB RESOURCE                         8232       6884      0.01      20                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        4123030                 7.49                                         

   ACT_SITE                           154405      94652      0.28      10                                 

   BINDING                            348457      92759      0.63       4                                 

   CA_BIND                              3984       1675      0.01      36                                 

   CARBOHYD                           111780      28623      0.20      15                                 

   CHAIN                              557834     543884      1.01       1                                 

   COILED                              21319      14702      0.04      26                                 

   COMPBIAS                            57294      30637      0.10      18                                 

   CONFLICT                           131686      46168      0.24      13                                 

   CROSSLNK                            10052       5277      0.02      33                                 

   DISULFID                           117337      32069      0.21      14                                 

   DNA_BIND                            11175      10153      0.02      31                                 

   DOMAIN                             178038     107940      0.32       8                                 

   HELIX                              215154      20332      0.39       7                                 

   INIT_MET                            18266      18266      0.03      27                                 

   INTRAMEM                             2400       1031     <0.01      37                                 

   LIPID                               12537       8064      0.02      29                                 

   METAL                              353396      87789      0.64       3                                 

   MOD_RES                            215642      68288      0.39       6                                 

   MOTIF                               39529      25522      0.07      24                                 

   MUTAGEN                             55460      12612      0.10      19                                 

   NON_CONS                             2238        776     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12285       9399      0.02      30                                 

   NP_BIND                            138623      79607      0.25      11                                 

   PEPTIDE                             10712       7276      0.02      32                                 

   PROPEP                              13435      11517      0.02      28                                 

   REGION                             174857      82987      0.32       9                                 

   REPEAT                             100163      14298      0.18      16                                 

   SIGNAL                              40186      40176      0.07      23                                 

   SITE                                51853      28897      0.09      21                                 

   STRAND                             224571      19167      0.41       5                                 

   TOPO_DOM                           135321      27870      0.25      12                                 

   TRANSIT                              9032       8919      0.02      34                                 

   TRANSMEM                           364916      75641      0.66       2                                 

   TURN                                51926      16487      0.09      20                                 

   UNSURE                               4277        756      0.01      35                                 

   VAR_SEQ                             50857      21394      0.09      22                                 

   VARIANT                             91750      17022      0.17      17                                 

   ZN_FING                             29925      13236      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)               17736421                32.23                                                           

   Allergome                            1675       1093     <0.01     110      Protein family/group databases               

   ArachnoServer                        1146       1136     <0.01     116      Organism-specific databases                  

   Bgee                                38850      38850      0.07      51      Gene expression databases                    

   BindingDB                            5686       5686      0.01      91      Chemistry                                    

   BioCyc                             325313     308039      0.59      19      Enzyme and pathway databases                 

   BioGrid                             47257      46813      0.09      47      Protein-protein interaction databases        

   BioMuta                             17246      17245      0.03      69      Polymorphism and mutation databases          

   BRENDA                              12713      11946      0.02      79      Enzyme and pathway databases                 

   CAZy                                 7875       7084      0.01      82      Protein family/group databases               

   CCDS                                46534      33554      0.08      48      Sequence databases                           

   CGD                                  1705       1689     <0.01     109      Organism-specific databases                  

   ChEMBL                               6160       6160      0.01      87      Chemistry                                    

   ChiTaRS                             16463      16453      0.03      74      Other                                        

   CleanEx                             30045      29405      0.05      58      Gene expression databases                    

   CollecTF                              132        132     <0.01     135      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     136      2D gel databases                             

   ConoServer                            949        866     <0.01     117      Organism-specific databases                  

   CTD                                 73291      72549      0.13      42      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     133      PTM databases                                

   dictyBase                            4207       4092      0.01      99      Organism-specific databases                  

   DIP                                 16694      16636      0.03      70      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     124      3D structure databases                       

   DMDM                                16376      16375      0.03      75      Polymorphism and mutation databases          

   DNASU                               18854      18783      0.03      67      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     146        146     <0.01     134      2D gel databases                             

   DrugBank                            11528       1852      0.02      80      Chemistry                                    

   EchoBASE                             4161       4161      0.01     100      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      98      Organism-specific databases                  

   eggNOG                             655830     327343      1.19       5      Phylogenomic databases                       

   EMBL                               969882     538982      1.76       3      Sequence databases                           

   Ensembl                             84120      48349      0.15      40      Genome annotation databases                  

   EnsemblBacteria                    354326     335330      0.64      17      Genome annotation databases                  

   EnsemblFungi                        30187      27827      0.05      57      Genome annotation databases                  

   EnsemblMetazoa                      13148       9754      0.02      77      Genome annotation databases                  

   EnsemblPlants                       21702      18490      0.04      62      Genome annotation databases                  

   EnsemblProtists                      5015       4852      0.01      96      Genome annotation databases                  

   ESTHER                               2427       2425     <0.01     106      Protein family/group databases               

   euHCVdb                                55         44     <0.01     138      Organism-specific databases                  

   EuPathDB                            16692      16692      0.03      71      Organism-specific databases                  

   EvolutionaryTrace                   16539      16537      0.03      73      Other                                        

   ExpressionAtlas                     30774      30774      0.06      56      Gene expression databases                    

   FlyBase                              5965       5603      0.01      89      Organism-specific databases                  

   Gene3D                             471352     347438      0.86       9      Family and domain databases                  

   GeneCards                           20026      19851      0.04      64      Organism-specific databases                  

   GeneDB                                386        349     <0.01     130      Genome annotation databases                  

   GeneFarm                             3478       3466      0.01     102      Organism-specific databases                  

   GeneID                             279420     269765      0.51      23      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     115      Organism-specific databases                  

   GeneTree                            55409      55371      0.10      45      Phylogenomic databases                       

   Genevisible                         55117      55117      0.10      46      Gene expression databases                    

   GeneWiki                            10368      10282      0.02      81      Other                                        

   GenoList                             7075       7063      0.01      84      Organism-specific databases                  

   GenomeRNAi                          21738      21738      0.04      61      Other                                        

   GO                                2712101     522051      4.93       1      Ontologies                                   

   Gramene                              6632       6632      0.01      86      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  1829       1829     <0.01     108      Chemistry                                    

   H-InvDB                              5589       4768      0.01      92      Organism-specific databases                  

   HAMAP                              325227     322155      0.59      20      Family and domain databases                  

   HGNC                                19993      19843      0.04      65      Organism-specific databases                  

   HOGENOM                            388267     388267      0.71      15      Phylogenomic databases                       

   HOVERGEN                            75749      75749      0.14      41      Phylogenomic databases                       

   HPA                                 24700      16208      0.04      60      Organism-specific databases                  

   InParanoid                         135780     135780      0.25      27      Phylogenomic databases                       

   IntAct                              45378      45378      0.08      49      Protein-protein interaction databases        

   InterPro                          1933160     530388      3.51       2      Family and domain databases                  

   iPTMnet                             35769      35769      0.06      52      PTM databases                                

   KEGG                               492092     459186      0.89       7      Genome annotation databases                  

   KO                                 383973     383503      0.70      16      Phylogenomic databases                       

   LegioList                             765        763     <0.01     121      Organism-specific databases                  

   Leproma                               672        669     <0.01     122      Organism-specific databases                  

   MaizeGDB                              506        501     <0.01     127      Organism-specific databases                  

   MalaCards                            3775       3773      0.01     101      Organism-specific databases                  

   MaxQB                               33374      33374      0.06      54      Proteomic databases                          

   MEROPS                              12882      12882      0.02      78      Protein family/group databases               

   MGI                                 16670      16626      0.03      72      Organism-specific databases                  

   MIM                                 19583      14382      0.04      66      Organism-specific databases                  

   MINT                                31688      31688      0.06      55      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     137      Protein family/group databases               

   mycoCLAP                              347        343     <0.01     132      Protein family/group databases               

   NextBio                             71584      71584      0.13      43      Other                                        

   neXtProt                            20040      20040      0.04      63      Organism-specific databases                  

   OGP                                   375        375     <0.01     131      2D gel databases                             

   OMA                                406667     406667      0.74      13      Phylogenomic databases                       

   Orphanet                             6148       3289      0.01      88      Organism-specific databases                  

   OrthoDB                            390694     390694      0.71      14      Phylogenomic databases                       

   PANTHER                            167392     161295      0.30      26      Family and domain databases                  

   PATRIC                             308108     308073      0.56      21      Genome annotation databases                  

   PaxDb                              110328     110325      0.20      34      Proteomic databases                          

   PDB                                123712      22941      0.22      32      3D structure databases                       

   PDBsum                             123712      22941      0.22      31      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      94      Proteomic databases                          

   PeroxiBase                            771        755     <0.01     120      Protein family/group databases               

   Pfam                               743915     508650      1.35       4      Family and domain databases                  

   PharmGKB                            18383      18342      0.03      68      Organism-specific databases                  

   PhosphoSite                         33543      33543      0.06      53      PTM databases                                

   PhylomeDB                           94576      94576      0.17      37      Phylogenomic databases                       

   PIR                                122749     112469      0.22      33      Sequence databases                           

   PIRSF                              104307     103269      0.19      36      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     111      Other                                        

   PomBase                              5139       5120      0.01      95      Organism-specific databases                  

   PRIDE                              123812     123812      0.22      30      Proteomic databases                          

   PRINTS                             134145     118238      0.24      29      Family and domain databases                  

   PRO                                 88796      88796      0.16      39      Other                                        

   ProDom                              28597      28416      0.05      59      Family and domain databases                  

   ProMEX                                423        423     <0.01     128      Proteomic databases                          

   PROSITE                            451239     290299      0.82      11      Family and domain databases                  

   ProteinModelPortal                 443498     443498      0.81      12      3D structure databases                       

   Proteomes                          467965     447185      0.85      10      Other                                        

   PseudoCAP                            1307       1298     <0.01     112      Organism-specific databases                  

   Reactome                            92202      27896      0.17      38      Enzyme and pathway databases                 

   REBASE                                410        410     <0.01     129      Protein family/group databases               

   RefSeq                             596949     460129      1.08       6      Sequence databases                           

   REPRODUCTION-2DPAGE                  1259       1038     <0.01     113      2D gel databases                             

   RGD                                  7865       7862      0.01      83      Organism-specific databases                  

   SABIO-RK                             3274       3274      0.01     103      Enzyme and pathway databases                 

   SGD                                  6739       6734      0.01      85      Organism-specific databases                  

   SignaLink                            2997       2997      0.01     104      Enzyme and pathway databases                 

   SMART                              171247     128221      0.31      25      Family and domain databases                  

   SMR                                225837     225837      0.41      24      3D structure databases                       

   STRING                             325466     325466      0.59      18      Protein-protein interaction databases        

   SUPFAM                             477838     362466      0.87       8      Family and domain databases                  

   SWISS-2DPAGE                         1180       1180     <0.01     114      2D gel databases                             

   SwissLipids                           907        836     <0.01     119      Chemistry                                    

   TAIR                                14414      14358      0.03      76      Organism-specific databases                  

   TCDB                                 5902       5874      0.01      90      Protein family/group databases               

   TIGRFAMs                           291418     271190      0.53      22      Family and domain databases                  

   TreeFam                             44903      44898      0.08      50      Phylogenomic databases                       

   TubercuList                          2121       2085     <0.01     107      Organism-specific databases                  

   UCD-2DPAGE                            508        499     <0.01     126      2D gel databases                             

   UCSC                                60396      45054      0.11      44      Genome annotation databases                  

   UniCarbKB                             584        584     <0.01     125      PTM databases                                

   UniGene                            105026      93663      0.19      35      Sequence databases                           

   UniPathway                         134873     122229      0.25      28      Enzyme and pathway databases                 

   VectorBase                            615        597     <0.01     123      Genome annotation databases                  

   WBParaSite                             22         22     <0.01     139      Genome annotation databases                  

   World-2DPAGE                          924        913     <0.01     118      2D gel databases                             

   WormBase                             5429       4209      0.01      93      Organism-specific databases                  

   Xenbase                              4773       4767      0.01      97      Organism-specific databases                  

   ZFIN                                 2803       2802      0.01     105      Organism-specific databases                  



Total number of cross-referenced databases: 139



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) 4.71   Val (V) 6.87



   Asx (B) 0.000  Glx (Z) 0.000  Xaa (X) 0.00



   



   Legend: gray = aliphatic, red = acidic, green = small hydroxy,

           blue = basic, black = aromatic, white = amide, yellow = sulfur





   6.2  Classification of the amino acids by their frequency



   Leu, Ala, Gly, Val, Glu, Ser, Ile, Lys, Arg, Asp, Thr, Pro, Asn, Gln,

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4463 entries are encoded on a mitochondrion, and 3831 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: 77260