UniProtKB/Swiss-Prot protein knowledgebase release 2015_02 statistics





1.  INTRODUCTION



Release 2015_02 of 04-Feb-15 of UniProtKB/Swiss-Prot contains 547599 sequence entries,

comprising 195014757 amino acids abstracted from 234565 references. 



245 sequences have been added since release 2015_01, the sequence data of

69 existing entries has been updated and the annotations of

153039 entries have been revised.



Number of fragments: 9115

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38582





Protein existence (PE):           entries     %



1: Evidence at protein level        85336   15.6%

2: Evidence at transcript level     62729   11.5%

3: Inferred from homology          386076   70.5%

4: Predicted                        11493    2.1%

5: Uncertain                         1965    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: 13179



   The first twenty species represent 115832 sequences:  21.2 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5489

                            2x: 1896

                            3x: 1016

                            4x:  658

                            5x:  481

                            6x:  399

                            7x:  289

                            8x:  224

                            9x:  212

                           10x:  123

                       11- 20x:  711

                       21- 50x:  423

                       51-100x:  212

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20198  Homo sapiens (Human)

       2      16699  Mus musculus (Mouse)

       3      13640  Arabidopsis thaliana (Mouse-ear cress)

       4       7918  Rattus norvegicus (Rat)

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

       6       5990  Bos taurus (Bovine)

       7       5103  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4433  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4131  Dictyostelium discoideum (Slime mold)

      11       3492  Caenorhabditis elegans

      12       3390  Xenopus laevis (African clawed frog)

      13       3321  Oryza sativa subsp. japonica (Rice)

      14       3241  Drosophila melanogaster (Fruit fly)

      15       2938  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2262  Gallus gallus (Chicken)

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

      18       2040  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2027  Escherichia coli O157:H7

      20       1887  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1780  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

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

      24       1701  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      25       1688  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      26       1679  Shigella flexneri

      27       1415  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1282  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      30       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

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

      32       1051  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1025  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

      35        973  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      36        956  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

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

      38        927  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      39        925  Staphylococcus aureus (strain N315)

      40        925  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      41        909  Acanthamoeba polyphaga mimivirus (APMV)

      42        905  Kluyveromyces lactis   

      43        899  Staphylococcus aureus (strain COL)

      44        895  Staphylococcus aureus (strain MW2)

      45        889  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        875  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        841  Escherichia coli O9:H4 (strain HS)

      55        840  Neurospora crassa 

      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        811  Canis familiaris (Dog) (Canis lupus familiaris)

      62        791  Escherichia coli (strain SMS-3-5 / SECEC)

      63        790  Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) 

      64        788  Emericella nidulans  

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

      66        784  Aquifex aeolicus (strain VF5)

      67        776  Pasteurella multocida (strain Pm70)

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

      69        771  Escherichia coli (strain K12 / DH10B)

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

      71        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      72        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      73        762  Escherichia coli (strain 55989 / EAEC)

      74        761  Escherichia coli O8 (strain IAI1)

      75        760  Shigella flexneri serotype 5b (strain 8401)

      76        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      77        758  Staphylococcus epidermidis (strain ATCC 12228)

      78        756  Escherichia coli (strain SE11)

      79        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      80        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      81        750  Zea mays (Maize)

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

      83        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      84        742  Staphylococcus aureus (strain NCTC 8325)

      85        741  Bacillus halodurans 

      86        736  Bacillus anthracis

      87        736  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      88        733  Vibrio vulnificus (strain CMCP6)

      89        731  Escherichia coli O81 (strain ED1a)

      90        722  Salmonella enteritidis PT4 (strain P125109)

      91        717  Vibrio vulnificus (strain YJ016)

      92        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      93        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      94        715  Enterobacter sp. (strain 638)

      95        714  Escherichia coli O1:K1 / APEC

      96        714  Salmonella paratyphi A (strain AKU_12601)

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

      98        713  Salmonella agona (strain SL483)

      99        713  Salmonella newport (strain SL254)

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

     101        712  Salmonella schwarzengrund (strain CVM19633)

     102        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     103        710  Salmonella heidelberg (strain SL476)

     104        704  Pseudomonas putida (strain KT2440)

     105        702  Salmonella dublin (strain CT_02021853)

     106        699  Oryza sativa subsp. indica (Rice)

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

     111        689  Pan troglodytes (Chimpanzee)

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

     117        670  Serratia proteamaculans (strain 568)

     118        668  Mycobacterium leprae (strain TN)

     119        667  Yersinia pestis (strain Pestoides F)

     120        666  Staphylococcus aureus (strain USA300)

     121        665  Escherichia coli

     122        660  Bradyrhizobium diazoefficiens 

     123        659  Bacillus cereus (strain ATCC 14579 / DSM 31)

     124        658  Rhizobium sp. (strain NGR234)

     125        653  Debaryomyces hansenii   

     126        644  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     127        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     128        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     129        640  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     130        638  Shewanella oneidensis (strain MR-1)

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

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

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

     134        620  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

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

     138        607  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     139        606  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     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        591  Bacillus cereus (strain ATCC 10987)

     146        591  Listeria innocua serovar 6a (strain CLIP 11262)

     147        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     148        589  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

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

     154        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     155        568  Caenorhabditis briggsae

     156        568  Caulobacter crescentus (strain ATCC 19089 / CB15)

     157        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     158        567  Pseudomonas syringae pv. syringae (strain B728a)

     159        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     160        564  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     161        564  Vibrio fischeri (strain ATCC 700601 / ES114)

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

     163        561  Bacillus cereus (strain ZK / E33L)

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

     170        545  Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6)

     171        539  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        516  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     179        515  Chromobacterium violaceum 

     180        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     181        515  Corynebacterium glutamicum 

     182        515  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        511  Pseudomonas aeruginosa (strain PA7)

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

     185        508  Staphylococcus aureus (strain Newman)

     186        508  Deinococcus radiodurans 

     187        508  Geobacillus kaustophilus (strain HTA426)

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

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

     190        506  Streptomyces avermitilis 

     191        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     192        500  Pseudomonas entomophila (strain L48)

     193        499  Brucella abortus biovar 1 (strain 9-941)

     194        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     195        496  Bacillus clausii (strain KSM-K16)

     196        495  Burkholderia pseudomallei (strain K96243)

     197        495  Haemophilus influenzae (strain 86-028NP)

     198        494  Proteus mirabilis (strain HI4320)

     199        494  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     200        493  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     201        492  Bacillus amyloliquefaciens subsp. plantarum 

     202        491  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     203        491  Xanthomonas campestris pv. campestris (strain 8004)

     204        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     205        488  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     206        487  Methanosarcina mazei  

     207        487  Shewanella sp. (strain MR-7)

     208        486  Mannheimia succiniciproducens (strain MBEL55E)

     209        484  Pseudomonas aeruginosa (strain LESB58)

     210        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     211        484  Thermosynechococcus elongatus (strain BP-1)

     212        484  Shewanella sp. (strain MR-4)

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

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

     215        481  Pyrococcus horikoshii 

     216        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     217        478  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     218        477  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  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     225        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     226        466  Shewanella frigidimarina (strain NCIMB 400)

     227        466  Pseudomonas putida (strain GB-1)

     228        466  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     229        465  Nicotiana tabacum (Common tobacco)

     230        464  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     231        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     232        464  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     233        463  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     234        463  Shewanella sp. (strain ANA-3)

     235        462  Burkholderia mallei (strain ATCC 23344)

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

     237        460  Enterococcus faecalis (strain ATCC 700802 / V583)

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

     239        457  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     240        456  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     241        455  Staphylococcus aureus (strain JH1)

     242        455  Ovis aries (Sheep)

     243        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     244        453  Pseudomonas putida (strain W619)

     245        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     246        452  Shewanella baltica (strain OS185)

     247        451  Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

     248        451  Aeromonas salmonicida (strain A449)

     249        450  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)

     250        450  Dechloromonas aromatica (strain RCB)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19318 (  4%)

    Bacteria         331909 ( 61%)

    Eukaryota        179875 ( 33%)

    Viruses           16497 (  3%)





   Within Eukaryota:



   



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

     Human                  20199 ( 11%)           (  4%)

     Other Mammalia         46115 ( 26%)           (  8%)

     Other Vertebrata       17772 ( 10%)           (  3%)

     Viridiplantae          36180 ( 20%)           (  7%)

     Fungi                  31457 ( 17%)           (  6%)

     Insecta                 8774 (  5%)           (  2%)

     Nematoda                4370 (  2%)           (  1%)

     Other                  15008 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9113             1001-1100     3807

                 51- 100   41858             1101-1200     2663

                101- 150   58327             1201-1300     2063

                151- 200   58202             1301-1400     1930

                201- 250   57067             1401-1500     1538

                251- 300   50656             1501-1600      757

                301- 350   50852             1601-1700      578

                351- 400   44073             1701-1800      488

                401- 450   36161             1801-1900      441

                451- 500   29030             1901-2000      360

                501- 550   20745             2001-2100      219

                551- 600   14854             2101-2200      296

                601- 650   12445             2201-2300      302

                651- 700    8990             2301-2400      187

                701- 750    7435             2401-2500      142

                751- 800    5315             >2500         1118

                801- 850    4631

                851- 900    5102

                901- 950    3936

                951-1000    2803



   





   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: 2480





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  812

                       2x:  325

                       3x:  167

                       4x:  115

                       5x:   98

                       6x:   78

                       7x:   53

                       8x:   51

                       9x:   33

                      10x:   34

                  11- 20x:  206

                  21- 50x:  196

                  51-100x:  115

                    >100x:  197





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



   Nb    Citations   Journal name

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

    1        22459   Journal of Biological Chemistry

    2        10199   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6102   Journal of Bacteriology

    4         5249   Biochemical and Biophysical Research Communications

    5         4820   Biochemistry

    6         4730   Nucleic Acids Research

    7         4692   Gene

    8         4548   FEBS Letters

    9         4404   The EMBO Journal

   10         4086   Molecular and Cellular Biology

   11         3975   Nature

   12         3865   Journal of Molecular Biology

   13         3359   Biochimica et Biophysica Acta

   14         3305   European Journal of Biochemistry

   15         3223   Cell

   16         2725   Journal of Virology

   17         2668   Science

   18         2642   Biochemical Journal

   19         2517   Genomics

   20         2231   Molecular Microbiology

   21         2088   Plant Physiology

   22         1995   Journal of Cell Biology

   23         1784   The American Journal of Human Genetics

   24         1722   Plant Molecular Biology

   25         1693   Genes and Development

   26         1602   Nature Genetics

   27         1589   Virology

   28         1581   Human Molecular Genetics

   29         1543   The Plant Cell

   30         1481   Oncogene

   31         1455   Molecular Biology of the Cell

   32         1438   Development

   33         1400   The Plant Journal

   34         1391   Human Mutation

   35         1366   Molecular and General Genetics

   36         1295   Molecular Cell

   37         1280   Journal of Biochemistry

   38         1225   Journal of Immunology

   39         1173   Structure

   40         1162   Genetics

   41         1048   Journal of General Virology

   42         1042   Journal of Cell Science

   43         1036   Blood

   44         1024   Infection and Immunity

   45         1011   PLoS ONE

   46          971   Archives of Biochemistry and Biophysics

   47          958   Microbiology

   48          882   Developmental Biology

   49          875   Current Biology

   50          834   Cancer Research

   51          822   Yeast

   52          779   FEMS Microbiology Letters

   53          758   Acta Crystallographica, Section D

   54          731   Applied and Environmental Microbiology

   55          722   Journal of Neuroscience

   56          707   Protein Science

   57          702   Toxicon

   58          652   Human Genetics

   59          635   Nature Structural Biology

   60          632   Neuron

   61          629   Mechanisms of Development

   62          620   Journal of Clinical Investigation

   63          600   American Journal of Physiology

   64          558   The Journal of Experimental Medicine

   65          552   Current Genetics

   66          545   Proteins

   67          542   Plant and Cell Physiology

   68          505   Molecular Endocrinology

   69          492   Journal of Neurochemistry

   70          489   Journal of Medical Genetics

   71          484   Mammalian Genome

   72          483   Nature Cell Biology

   73          479   Bioscience, Biotechnology, and Biochemistry

   74          468   The Journal of Clinical Endocrinology and Metabolism

   75          463   Endocrinology

   76          460   Immunogenetics

   77          443   Molecular and Biochemical Parasitology

   78          405   Experimental Cell Research

   79          403   Journal of Molecular Evolution

   80          398   Nature Structural and Molecular Biology

   81          383   Molecular Biology and Evolution

   82          381   The FEBS Journal

   83          379   DNA and Cell Biology

   84          378   Antimicrobial Agents and Chemotherapy

   85          378   Peptides

   86          375   Developmental Cell

   87          368   DNA Sequence

   88          364   RNA

   89          363   Eukaryotic Cell

   90          344   Planta

   91          341   Journal of Investigative Dermatology

   92          332   Brain Research. Molecular Brain Research

   93          328   Molecular Pharmacology

   94          328   Comparative Biochemistry and Physiology

   95          325   Tissue Antigens

   96          308   Neurology

   97          300   Biology of Reproduction

   98          294   Biological Chemistry Hoppe-Seyler

   99          292   EMBO Reports

  100          285   Developmental Dynamics

  101          284   The FASEB Journal

  102          281   Cytogenetics and Cell Genetics

  103          278   Biochimie

  104          278   PLoS Genetics

  105          278   Immunity

  106          275   The New England Journal of Medicine

  107          275   Genes to Cells

  108          274   Journal of the American Chemical Society

  109          273   Genome Research

  110          272   Virus Research

  111          269   Molecular Plant-Microbe Interactions

  112          263   Journal of General Microbiology

  113          258   Acta Crystallographica, Section F

  114          251   European Journal of Human Genetics

  115          242   Annals of Neurology

  116          239   European Journal of Immunology

  117          234   Journal of Experimental Botany

  118          228   Investigative Ophthalmology and Visual Science

  119          222   Journal of Human Genetics

  120          221   BMC Genomics

  121          220   DNA Research

  122          219   Archives of Microbiology

  123          219   Nature Immunology

  124          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  125          212   American Journal of Medical Genetics. Part A

  126          206   Clinical Genetics

  127          206   Journal of Cellular Biochemistry

  128          203   Glycobiology

  129          202   Journal of Medicinal Chemistry

  130          196   Molecular and Cellular Endocrinology

  131          195   Archives of Virology

  132          192   Molecular Immunology

  133          192   PLoS Pathogens

  134          191   Circulation Research

  135          189   Diabetes

  136          188   Cell Cycle

  137          188   Traffic

  138          182   Applied Microbiology and Biotechnology

  139          182   Molecular Genetics and Metabolism

  140          176   Insect Biochemistry and Molecular Biology

  141          176   Phytochemistry

  142          173   Protein Expression and Purification

  143          170   International Journal of Cancer

  144          170   Molecular Phylogenetics and Evolution

  145          168   American Journal of Medical Genetics

  146          166   PLoS Biology

  147          164   Journal of Lipid Research

  148          164   Proteomics

  149          163   Biological Chemistry

  150          162   Molecular and Cellular Neuroscience





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)                      1095000                 2.00                                         

   Journal                            901055     435480      1.65       1                                 

   Submitted to EMBL/GenBank/DDBJ     183855     162610      0.34       2                                 

   Submitted to other databases         7068       6558      0.01       3                                 

   Book citation                        1467       1453     <0.01       4                                 

   Plant Gene Register                   597        585     <0.01       5                                 

   Thesis                                426        423     <0.01       6                                 

   Unpublished observations              335        331     <0.01       7                                 

   Patent                                191        188     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 359797



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2532311                 4.62                                         

   ALLERGEN                              664        664     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24115      24115      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6270       6270      0.01      21                                 

   BIOTECHNOLOGY                         432        430     <0.01      28                                 

   CATALYTIC ACTIVITY                 253935     228570      0.46       5                                 

   CAUTION                             10096       9903      0.02      18                                 

   COFACTOR                           116825     106937      0.21       7                                 

   DEVELOPMENTAL STAGE                 10440      10440      0.02      17                                 

   DISEASE                              5881       3960      0.01      22                                 

   DISRUPTION PHENOTYPE                 8199       8199      0.01      20                                 

   DOMAIN                              42723      37084      0.08       9                                 

   ENZYME REGULATION                   13045      13045      0.02      16                                 

   FUNCTION                           439324     421453      0.80       2                                 

   INDUCTION                           17023      17023      0.03      14                                 

   INTERACTION                         13206      13206      0.02      15                                 

   MASS SPECTROMETRY                    5864       4463      0.01      23                                 

   MISCELLANEOUS                       34326      31507      0.06      12                                 

   PATHWAY                            134253     121719      0.25       6                                 

   PHARMACEUTICAL                         99         99     <0.01      29                                 

   POLYMORPHISM                         1040        983     <0.01      24                                 

   PTM                                 48233      37011      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42323      42323      0.08      10                                 

   SIMILARITY                         660155     522709      1.21       1                                 

   SUBCELLULAR LOCATION               335460     328969      0.61       3                                 

   SUBUNIT                            257760     257760      0.47       4                                 

   TISSUE SPECIFICITY                  41156      41156      0.08      11                                 

   TOXIC DOSE                            601        556     <0.01      27                                 

   WEB RESOURCE                         8236       6890      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3989519                 7.29                                         

   ACT_SITE                           151875      93031      0.28      10                                 

   BINDING                            339851      89570      0.62       4                                 

   CA_BIND                              3984       1677      0.01      35                                 

   CARBOHYD                           109574      28161      0.20      15                                 

   CHAIN                              555036     541243      1.01       1                                 

   COILED                              21026      14449      0.04      26                                 

   COMPBIAS                            56490      30135      0.10      18                                 

   CONFLICT                           130792      45765      0.24      13                                 

   CROSSLNK                             7213       4104      0.01      34                                 

   DISULFID                           115599      31546      0.21      14                                 

   DNA_BIND                            10755       9768      0.02      31                                 

   DOMAIN                             174826     106011      0.32       7                                 

   HELIX                              202823      19362      0.37       6                                 

   INIT_MET                            17678      17678      0.03      27                                 

   INTRAMEM                             2287       1007     <0.01      37                                 

   LIPID                               12260       7865      0.02      30                                 

   METAL                              346659      85814      0.63       3                                 

   MOD_RES                            174229      62731      0.32       8                                 

   MOTIF                               38581      24916      0.07      24                                 

   MUTAGEN                             51497      11759      0.09      19                                 

   NON_CONS                             2052        757     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12271       9380      0.02      29                                 

   NP_BIND                            134535      78694      0.25      11                                 

   PEPTIDE                             10505       7187      0.02      32                                 

   PROPEP                              13042      11236      0.02      28                                 

   REGION                             166028      79754      0.30       9                                 

   REPEAT                              98505      14314      0.18      16                                 

   SIGNAL                              39508      39498      0.07      23                                 

   SITE                                50358      28025      0.09      20                                 

   STRAND                             212272      18268      0.39       5                                 

   TOPO_DOM                           134084      27566      0.24      12                                 

   TRANSIT                              8830       8717      0.02      33                                 

   TRANSMEM                           362018      74902      0.66       2                                 

   TURN                                49071      15666      0.09      22                                 

   UNSURE                               3643        734      0.01      36                                 

   VAR_SEQ                             50329      21133      0.09      21                                 

   VARIANT                             89245      16952      0.16      17                                 

   ZN_FING                             29830      13176      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)               17494036                31.95                                                           

   Allergome                            1638       1064     <0.01     105      Protein family/group databases               

   ArachnoServer                         789        781     <0.01     115      Organism-specific databases                  

   Bgee                                38839      38839      0.07      51      Gene expression databases                    

   BindingDB                            5440       5440      0.01      88      Chemistry                                    

   BioCyc                             324681     307474      0.59      20      Enzyme and pathway databases                 

   BioGrid                             40645      40280      0.07      50      Protein-protein interaction databases        

   BRENDA                               4375       4362      0.01      95      Enzyme and pathway databases                 

   CAZy                                 7786       7008      0.01      79      Protein family/group databases               

   CCDS                                45571      33404      0.08      47      Sequence databases                           

   CGD                                   956        928     <0.01     111      Organism-specific databases                  

   ChEMBL                               6008       6008      0.01      84      Chemistry                                    

   ChiTaRS                             16448      16439      0.03      70      Other                                        

   CleanEx                             30060      29421      0.05      56      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     131      2D gel databases                             

   ConoServer                            949        866     <0.01     112      Organism-specific databases                  

   CTD                                 72330      71651      0.13      40      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      86      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     129      PTM databases                                

   dictyBase                            4207       4092      0.01      97      Organism-specific databases                  

   DIP                                 15799      15733      0.03      72      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     121      3D structure databases                       

   DMDM                                16400      16400      0.03      71      Polymorphism databases                       

   DNASU                               18785      18715      0.03      66      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     130      2D gel databases                             

   DrugBank                            11195       1762      0.02      76      Chemistry                                    

   EchoBASE                             4161       4161      0.01      98      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      96      Organism-specific databases                  

   eggNOG                             431247     431247      0.79      13      Phylogenomic databases                       

   EMBL                               962250     536373      1.76       3      Sequence databases                           

   Ensembl                             84727      49232      0.15      38      Genome annotation databases                  

   EnsemblBacteria                    352330     333629      0.64      19      Genome annotation databases                  

   EnsemblFungi                        19059      18759      0.03      64      Genome annotation databases                  

   EnsemblMetazoa                      12219       9475      0.02      75      Genome annotation databases                  

   EnsemblPlants                       19738      16796      0.04      63      Genome annotation databases                  

   EnsemblProtists                      4466       4341      0.01      94      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     133      Organism-specific databases                  

   EuPathDB                              819        819     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16503      16502      0.03      69      Other                                        

   ExpressionAtlas                     33718      33718      0.06      52      Gene expression databases                    

   FlyBase                              5943       5569      0.01      85      Organism-specific databases                  

   Gene3D                             463482     341576      0.85       9      Family and domain databases                  

   GeneCards                           20869      19794      0.04      60      Organism-specific databases                  

   GeneFarm                             3325       3313      0.01      99      Organism-specific databases                  

   GeneID                             498189     469754      0.91       7      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     110      Organism-specific databases                  

   GeneTree                            56443      56414      0.10      46      Phylogenomic databases                       

   Genevestigator                      68586      68586      0.13      42      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      77      Other                                        

   GenoList                             7074       7062      0.01      80      Organism-specific databases                  

   GenomeRNAi                          21687      21687      0.04      59      Other                                        

   GO                                2611048     519044      4.77       1      Ontologies                                   

   Gramene                              6254       6254      0.01      82      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2068       2067     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      87      Organism-specific databases                  

   HAMAP                              324357     321405      0.59      21      Family and domain databases                  

   HGNC                                20005      19843      0.04      62      Organism-specific databases                  

   HOGENOM                            386097     386097      0.71      17      Phylogenomic databases                       

   HOVERGEN                            75669      75669      0.14      39      Phylogenomic databases                       

   HPA                                 22347      15977      0.04      58      Organism-specific databases                  

   InParanoid                         135075     135075      0.25      28      Phylogenomic databases                       

   IntAct                              43055      43055      0.08      49      Protein-protein interaction databases        

   InterPro                          1907853     526710      3.48       2      Family and domain databases                  

   KEGG                               474913     449425      0.87       8      Genome annotation databases                  

   KO                                 378987     378496      0.69      18      Phylogenomic databases                       

   LegioList                             765        763     <0.01     117      Organism-specific databases                  

   Leproma                               671        668     <0.01     118      Organism-specific databases                  

   MaizeGDB                              503        498     <0.01     123      Organism-specific databases                  

   MaxQB                               31211      31211      0.06      55      Proteomic databases                          

   MEROPS                              12731      12731      0.02      74      Protein family/group databases               

   MGI                                 16615      16571      0.03      68      Organism-specific databases                  

   MIM                                 19047      14100      0.03      65      Organism-specific databases                  

   MINT                                31603      31603      0.06      54      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     132      Protein family/group databases               

   mycoCLAP                              312        306     <0.01     127      Protein family/group databases               

   NextBio                             71279      71279      0.13      41      Other                                        

   neXtProt                            20035      20035      0.04      61      Organism-specific databases                  

   OGP                                   376        376     <0.01     126      2D gel databases                             

   OMA                                407909     407909      0.74      14      Phylogenomic databases                       

   Orphanet                             6201       3262      0.01      83      Organism-specific databases                  

   OrthoDB                            389434     389434      0.71      16      Phylogenomic databases                       

   PANTHER                            179356     172476      0.33      25      Family and domain databases                  

   PATRIC                             307779     307748      0.56      22      Genome annotation databases                  

   PaxDb                               66646      66645      0.12      43      Proteomic databases                          

   PDB                                115788      21739      0.21      33      3D structure databases                       

   PDBsum                             115788      21739      0.21      32      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      90      Proteomic databases                          

   PeroxiBase                            770        754     <0.01     116      Protein family/group databases               

   Pfam                               740047     507708      1.35       4      Family and domain databases                  

   PharmGKB                            18391      18359      0.03      67      Organism-specific databases                  

   PhosphoSite                         33557      33557      0.06      53      PTM databases                                

   PhosSite                              606        597     <0.01     120      PTM databases                                

   PhylomeDB                           93739      93739      0.17      36      Phylogenomic databases                       

   PIR                                121990     111762      0.22      31      Sequence databases                           

   PIRSF                              102284     101322      0.19      35      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     106      Other                                        

   PomBase                              5127       5091      0.01      91      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     134      Protein family/group databases               

   PRIDE                              122400     122400      0.22      30      Proteomic databases                          

   PRINTS                             136753     120467      0.25      27      Family and domain databases                  

   PRO                                 58105      58105      0.11      45      Other                                        

   ProDom                              29244      29065      0.05      57      Family and domain databases                  

   ProMEX                                395        395     <0.01     125      Proteomic databases                          

   PROSITE                            446636     288123      0.82      10      Family and domain databases                  

   ProteinModelPortal                 441488     441488      0.81      12      3D structure databases                       

   Proteomes                          506987     481499      0.93       6      Other                                        

   PseudoCAP                            1290       1281     <0.01     107      Organism-specific databases                  

   Reactome                            87708      26696      0.16      37      Enzyme and pathway databases                 

   REBASE                                406        406     <0.01     124      Protein family/group databases               

   RefSeq                             648542     479636      1.18       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1258       1037     <0.01     108      2D gel databases                             

   RGD                                  7840       7836      0.01      78      Organism-specific databases                  

   SABIO-RK                             3002       3002      0.01     100      Enzyme and pathway databases                 

   SGD                                  6737       6732      0.01      81      Organism-specific databases                  

   SignaLink                            2970       2961      0.01     101      Enzyme and pathway databases                 

   SMART                              170159     127455      0.31      26      Family and domain databases                  

   SMR                                224029     224029      0.41      24      3D structure databases                       

   STRING                             403051     403050      0.74      15      Protein-protein interaction databases        

   SUPFAM                             442455     340228      0.81      11      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     109      2D gel databases                             

   TAIR                                13623      13567      0.02      73      Organism-specific databases                  

   TCDB                                 5393       5372      0.01      89      Protein family/group databases               

   TIGRFAMs                           291367     271193      0.53      23      Family and domain databases                  

   TreeFam                             44791      44786      0.08      48      Phylogenomic databases                       

   TubercuList                          2063       2027     <0.01     104      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     122      2D gel databases                             

   UCSC                                59283      44792      0.11      44      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     128      PTM databases                                

   UniGene                            103004      92838      0.19      34      Sequence databases                           

   UniPathway                         134050     121525      0.24      29      Enzyme and pathway databases                 

   VectorBase                            615        597     <0.01     119      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     113      2D gel databases                             

   WormBase                             5070       4022      0.01      92      Organism-specific databases                  

   Xenbase                              4768       4762      0.01      93      Organism-specific databases                  

   ZFIN                                 2775       2775      0.01     102      Organism-specific databases                  



Total number of cross-referenced databases: 134



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.26   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.58

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

   Asn (N) 4.05   Gly (G) 7.08   Met (M) 2.41   Trp (W) 1.09

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

   Cys (C) 1.37   Ile (I) 5.94   Pro (P) 4.71   Val (V) 6.87



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



   



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

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





   6.2  Classification of the amino acids by their frequency



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

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4464 entries are encoded on a mitochondrion, and 3799 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: 76488