UniProtKB/Swiss-Prot protein knowledgebase release 2015_01 statistics





1.  INTRODUCTION



Release 2015_01 of 07-Jan-15 of UniProtKB/Swiss-Prot contains 547357 sequence entries,

comprising 194874700 amino acids abstracted from 233684 references. 



274 sequences have been added since release 2014_11, the sequence data of

37 existing entries has been updated and the annotations of

527803 entries have been revised.



Number of fragments: 9117

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38511





Protein existence (PE):           entries     %



1: Evidence at protein level        85123   15.6%

2: Evidence at transcript level     62731   11.5%

3: Inferred from homology          386038   70.5%

4: Predicted                        11499    2.1%

5: Uncertain                         1966    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: 13165



   The first twenty species represent 115679 sequences:  21.1 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5480

                            2x: 1897

                            3x: 1012

                            4x:  657

                            5x:  480

                            6x:  399

                            7x:  290

                            8x:  224

                            9x:  212

                           10x:  122

                       11- 20x:  712

                       21- 50x:  422

                       51-100x:  212

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20199  Homo sapiens (Human)

       2      16695  Mus musculus (Mouse)

       3      13530  Arabidopsis thaliana (Mouse-ear cress)

       4       7916  Rattus norvegicus (Rat)

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

       6       5988  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       4128  Dictyostelium discoideum (Slime mold)

      11       3487  Caenorhabditis elegans

      12       3390  Xenopus laevis (African clawed frog)

      13       3297  Oryza sativa subsp. japonica (Rice)

      14       3241  Drosophila melanogaster (Fruit fly)

      15       2937  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2262  Gallus gallus (Chicken)

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

      18       2037  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       1280  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       1050  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1025  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

      35        969  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        748  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        698  Klebsiella pneumoniae (strain 342)

     107        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     108        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     109        691  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     110        690  Oryza sativa subsp. indica (Rice)

     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        672  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        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     130        638  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     131        636  Shewanella oneidensis (strain MR-1)

     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        588  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        512  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        492  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        464  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           19312 (  4%)

    Bacteria         331887 ( 61%)

    Eukaryota        179679 ( 33%)

    Viruses           16479 (  3%)





   Within Eukaryota:



   



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

     Human                  20200 ( 11%)           (  4%)

     Other Mammalia         46106 ( 26%)           (  8%)

     Other Vertebrata       17769 ( 10%)           (  3%)

     Viridiplantae          36021 ( 20%)           (  7%)

     Fungi                  31451 ( 18%)           (  6%)

     Insecta                 8773 (  5%)           (  2%)

     Nematoda                4363 (  2%)           (  1%)

     Other                  14996 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9109             1001-1100     3806

                 51- 100   41847             1101-1200     2659

                101- 150   58319             1201-1300     2060

                151- 200   58184             1301-1400     1927

                201- 250   57047             1401-1500     1537

                251- 300   50637             1501-1600      752

                301- 350   50837             1601-1700      577

                351- 400   44058             1701-1800      485

                401- 450   36137             1801-1900      441

                451- 500   29019             1901-2000      358

                501- 550   20723             2001-2100      218

                551- 600   14847             2101-2200      296

                601- 650   12437             2201-2300      301

                651- 700    8990             2301-2400      187

                701- 750    7420             2401-2500      142

                751- 800    5316             >2500         1113

                801- 850    4624

                851- 900    5098

                901- 950    3931

                951-1000    2801



   





   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: 2466





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  805

                       2x:  323

                       3x:  170

                       4x:  114

                       5x:   94

                       6x:   78

                       7x:   57

                       8x:   49

                       9x:   31

                      10x:   38

                  11- 20x:  200

                  21- 50x:  198

                  51-100x:  113

                    >100x:  196





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



   Nb    Citations   Journal name

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

    1        22401   Journal of Biological Chemistry

    2        10159   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6091   Journal of Bacteriology

    4         5238   Biochemical and Biophysical Research Communications

    5         4798   Biochemistry

    6         4727   Nucleic Acids Research

    7         4683   Gene

    8         4536   FEBS Letters

    9         4394   The EMBO Journal

   10         4075   Molecular and Cellular Biology

   11         3966   Nature

   12         3847   Journal of Molecular Biology

   13         3357   Biochimica et Biophysica Acta

   14         3301   European Journal of Biochemistry

   15         3217   Cell

   16         2718   Journal of Virology

   17         2660   Science

   18         2635   Biochemical Journal

   19         2517   Genomics

   20         2228   Molecular Microbiology

   21         2077   Plant Physiology

   22         1988   Journal of Cell Biology

   23         1777   The American Journal of Human Genetics

   24         1717   Plant Molecular Biology

   25         1690   Genes and Development

   26         1597   Nature Genetics

   27         1585   Virology

   28         1569   Human Molecular Genetics

   29         1531   The Plant Cell

   30         1478   Oncogene

   31         1448   Molecular Biology of the Cell

   32         1435   Development

   33         1388   The Plant Journal

   34         1374   Human Mutation

   35         1364   Molecular and General Genetics

   36         1290   Molecular Cell

   37         1279   Journal of Biochemistry

   38         1224   Journal of Immunology

   39         1170   Structure

   40         1160   Genetics

   41         1046   Journal of General Virology

   42         1035   Blood

   43         1034   Journal of Cell Science

   44         1023   Infection and Immunity

   45          980   PLoS ONE

   46          971   Archives of Biochemistry and Biophysics

   47          956   Microbiology

   48          882   Developmental Biology

   49          873   Current Biology

   50          832   Cancer Research

   51          822   Yeast

   52          779   FEMS Microbiology Letters

   53          752   Acta Crystallographica, Section D

   54          729   Applied and Environmental Microbiology

   55          714   Journal of Neuroscience

   56          705   Protein Science

   57          700   Toxicon

   58          646   Human Genetics

   59          635   Nature Structural Biology

   60          630   Neuron

   61          629   Mechanisms of Development

   62          614   Journal of Clinical Investigation

   63          595   American Journal of Physiology

   64          557   The Journal of Experimental Medicine

   65          552   Current Genetics

   66          543   Proteins

   67          539   Plant and Cell Physiology

   68          505   Molecular Endocrinology

   69          491   Journal of Neurochemistry

   70          483   Mammalian Genome

   71          483   Nature Cell Biology

   72          477   Journal of Medical Genetics

   73          474   Bioscience, Biotechnology, and Biochemistry

   74          463   Endocrinology

   75          460   Immunogenetics

   76          458   The Journal of Clinical Endocrinology and Metabolism

   77          442   Molecular and Biochemical Parasitology

   78          403   Journal of Molecular Evolution

   79          402   Experimental Cell Research

   80          395   Nature Structural and Molecular Biology

   81          383   Molecular Biology and Evolution

   82          379   DNA and Cell Biology

   83          379   The FEBS Journal

   84          378   Antimicrobial Agents and Chemotherapy

   85          377   Peptides

   86          372   Developmental Cell

   87          368   DNA Sequence

   88          362   RNA

   89          357   Eukaryotic Cell

   90          341   Planta

   91          332   Journal of Investigative Dermatology

   92          331   Brain Research. Molecular Brain Research

   93          328   Comparative Biochemistry and Physiology

   94          325   Molecular Pharmacology

   95          325   Tissue Antigens

   96          302   Neurology

   97          300   Biology of Reproduction

   98          294   Biological Chemistry Hoppe-Seyler

   99          290   EMBO Reports

  100          284   Developmental Dynamics

  101          283   The FASEB Journal

  102          281   Cytogenetics and Cell Genetics

  103          278   Biochimie

  104          277   Immunity

  105          274   Genes to Cells

  106          272   Genome Research

  107          272   PLoS Genetics

  108          271   The New England Journal of Medicine

  109          271   Virus Research

  110          267   Molecular Plant-Microbe Interactions

  111          266   Journal of the American Chemical Society

  112          263   Journal of General Microbiology

  113          252   Acta Crystallographica, Section F

  114          247   European Journal of Human Genetics

  115          239   Annals of Neurology

  116          238   European Journal of Immunology

  117          231   Journal of Experimental Botany

  118          226   Investigative Ophthalmology and Visual Science

  119          221   BMC Genomics

  120          220   DNA Research

  121          219   Archives of Microbiology

  122          219   Nature Immunology

  123          219   Journal of Human Genetics

  124          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  125          209   American Journal of Medical Genetics. Part A

  126          206   Journal of Cellular Biochemistry

  127          203   Glycobiology

  128          201   Journal of Medicinal Chemistry

  129          196   Molecular and Cellular Endocrinology

  130          196   Clinical Genetics

  131          195   Archives of Virology

  132          192   Molecular Immunology

  133          191   Circulation Research

  134          190   PLoS Pathogens

  135          189   Diabetes

  136          188   Traffic

  137          186   Cell Cycle

  138          182   Applied Microbiology and Biotechnology

  139          177   Molecular Genetics and Metabolism

  140          176   Insect Biochemistry and Molecular Biology

  141          175   Phytochemistry

  142          173   Protein Expression and Purification

  143          170   International Journal of Cancer

  144          169   Molecular Phylogenetics and Evolution

  145          168   American Journal of Medical Genetics

  146          166   PLoS Biology

  147          164   Proteomics

  148          163   Journal of Lipid Research

  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)                      1092817                 2.00                                         

   Journal                            898764     434903      1.64       1                                 

   Submitted to EMBL/GenBank/DDBJ     183974     162815      0.34       2                                 

   Submitted to other databases         7057       6547      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: 358048



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2528536                 4.62                                         

   ALLERGEN                              664        664     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24080      24080      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6218       6218      0.01      21                                 

   BIOTECHNOLOGY                         430        428     <0.01      28                                 

   CATALYTIC ACTIVITY                 253069     228018      0.46       5                                 

   CAUTION                             10078       9888      0.02      18                                 

   COFACTOR                           116440     106558      0.21       7                                 

   DEVELOPMENTAL STAGE                 10423      10423      0.02      17                                 

   DISEASE                              5829       3934      0.01      23                                 

   DISRUPTION PHENOTYPE                 8074       8074      0.01      20                                 

   DOMAIN                              42520      37001      0.08       9                                 

   ENZYME REGULATION                   12993      12993      0.02      16                                 

   FUNCTION                           439178     421130      0.80       2                                 

   INDUCTION                           16970      16970      0.03      14                                 

   INTERACTION                         13204      13204      0.02      15                                 

   MASS SPECTROMETRY                    5859       4458      0.01      22                                 

   MISCELLANEOUS                       34309      31483      0.06      12                                 

   PATHWAY                            134208     121674      0.25       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1040        983     <0.01      24                                 

   PTM                                 48108      36972      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42220      42220      0.08      10                                 

   SIMILARITY                         659278     522475      1.20       1                                 

   SUBCELLULAR LOCATION               335146     328717      0.61       3                                 

   SUBUNIT                            257589     257589      0.47       4                                 

   TISSUE SPECIFICITY                  41054      41054      0.08      11                                 

   TOXIC DOSE                            597        555     <0.01      27                                 

   WEB RESOURCE                         8233       6887      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3980520                 7.27                                         

   ACT_SITE                           151437      92704      0.28      10                                 

   BINDING                            338783      89307      0.62       4                                 

   CA_BIND                              3974       1671      0.01      35                                 

   CARBOHYD                           109502      28132      0.20      15                                 

   CHAIN                              554788     541002      1.01       1                                 

   COILED                              20898      14396      0.04      26                                 

   COMPBIAS                            56368      30068      0.10      18                                 

   CONFLICT                           130645      45724      0.24      13                                 

   CROSSLNK                             7176       4093      0.01      34                                 

   DISULFID                           115519      31528      0.21      14                                 

   DNA_BIND                            10752       9766      0.02      31                                 

   DOMAIN                             173433     105399      0.32       8                                 

   HELIX                              201944      19248      0.37       6                                 

   INIT_MET                            17712      17712      0.03      27                                 

   INTRAMEM                             2275       1001     <0.01      37                                 

   LIPID                               12256       7861      0.02      30                                 

   METAL                              346314      85748      0.63       3                                 

   MOD_RES                            174117      62718      0.32       7                                 

   MOTIF                               38000      24662      0.07      24                                 

   MUTAGEN                             51164      11690      0.09      19                                 

   NON_CONS                             2069        758     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12272       9382      0.02      29                                 

   NP_BIND                            134474      78657      0.25      12                                 

   PEPTIDE                             10505       7185      0.02      32                                 

   PROPEP                              13037      11232      0.02      28                                 

   REGION                             164974      79338      0.30       9                                 

   REPEAT                              98135      14299      0.18      16                                 

   SIGNAL                              39465      39455      0.07      23                                 

   SITE                                50315      28006      0.09      20                                 

   STRAND                             211468      18163      0.39       5                                 

   TOPO_DOM                           134627      27857      0.25      11                                 

   TRANSIT                              8795       8682      0.02      33                                 

   TRANSMEM                           361852      74854      0.66       2                                 

   TURN                                48848      15594      0.09      22                                 

   UNSURE                               3642        733      0.01      36                                 

   VAR_SEQ                             50233      21106      0.09      21                                 

   VARIANT                             88587      16939      0.16      17                                 

   ZN_FING                             29807      13164      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)               17440704                31.86                                                           

   Allergome                            1638       1064     <0.01     105      Protein family/group databases               

   ArachnoServer                         789        781     <0.01     115      Organism-specific databases                  

   Bgee                                38842      38842      0.07      51      Gene expression databases                    

   BindingDB                            5440       5440      0.01      88      Chemistry                                    

   BioCyc                             324644     307442      0.59      20      Enzyme and pathway databases                 

   BioGrid                             40309      39946      0.07      50      Protein-protein interaction databases        

   BRENDA                               4373       4361      0.01      95      Enzyme and pathway databases                 

   CAZy                                 7783       7005      0.01      79      Protein family/group databases               

   CCDS                                45585      33409      0.08      47      Sequence databases                           

   CGD                                   950        924     <0.01     111      Organism-specific databases                  

   ChEMBL                               6008       6008      0.01      84      Chemistry                                    

   ChiTaRS                             16448      16439      0.03      70      Other                                        

   CleanEx                             30067      29428      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                                 72316      71637      0.13      40      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      86      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     129      PTM databases                                

   dictyBase                            4204       4088      0.01      97      Organism-specific databases                  

   DIP                                 15795      15730      0.03      72      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     121      3D structure databases                       

   DMDM                                16404      16404      0.03      71      Polymorphism databases                       

   DNASU                               18781      18711      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                             431111     431111      0.79      13      Phylogenomic databases                       

   EMBL                               961244     536136      1.76       3      Sequence databases                           

   Ensembl                             84530      49200      0.15      38      Genome annotation databases                  

   EnsemblBacteria                    349592     330962      0.64      19      Genome annotation databases                  

   EnsemblFungi                        19098      18756      0.03      64      Genome annotation databases                  

   EnsemblMetazoa                      12210       9468      0.02      75      Genome annotation databases                  

   EnsemblPlants                       19294      16454      0.04      63      Genome annotation databases                  

   EnsemblProtists                      4461       4336      0.01      94      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     133      Organism-specific databases                  

   EuPathDB                              817        817     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16500      16499      0.03      69      Other                                        

   ExpressionAtlas                     33327      33327      0.06      53      Gene expression databases                    

   FlyBase                              5943       5569      0.01      85      Organism-specific databases                  

   Gene3D                             463374     341490      0.85       9      Family and domain databases                  

   GeneCards                           20872      19797      0.04      60      Organism-specific databases                  

   GeneFarm                             3325       3313      0.01      99      Organism-specific databases                  

   GeneID                             498295     469855      0.91       7      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     110      Organism-specific databases                  

   GeneTree                            56476      56445      0.10      46      Phylogenomic databases                       

   Genevestigator                      68504      68504      0.13      42      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      77      Other                                        

   GenoList                             7074       7062      0.01      80      Organism-specific databases                  

   GenomeRNAi                          21688      21688      0.04      59      Other                                        

   GO                                2562452     518603      4.68       1      Ontologies                                   

   Gramene                              6243       6243      0.01      82      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2068       2067     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      87      Organism-specific databases                  

   HAMAP                              324303     321355      0.59      21      Family and domain databases                  

   HGNC                                20005      19843      0.04      62      Organism-specific databases                  

   HOGENOM                            385974     385974      0.71      17      Phylogenomic databases                       

   HOVERGEN                            75670      75670      0.14      39      Phylogenomic databases                       

   HPA                                 22351      15981      0.04      58      Organism-specific databases                  

   InParanoid                         135030     135030      0.25      28      Phylogenomic databases                       

   IntAct                              43053      43053      0.08      49      Protein-protein interaction databases        

   InterPro                          1907330     526498      3.48       2      Family and domain databases                  

   KEGG                               473665     448842      0.87       8      Genome annotation databases                  

   KO                                 378130     377644      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                               31218      31218      0.06      55      Proteomic databases                          

   MEROPS                              12727      12727      0.02      74      Protein family/group databases               

   MGI                                 16611      16567      0.03      68      Organism-specific databases                  

   MIM                                 18981      14081      0.03      65      Organism-specific databases                  

   MINT                                31600      31600      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                             71264      71264      0.13      41      Other                                        

   neXtProt                            20039      20039      0.04      61      Organism-specific databases                  

   OGP                                   376        376     <0.01     126      2D gel databases                             

   OMA                                407742     407742      0.74      14      Phylogenomic databases                       

   Orphanet                             6201       3262      0.01      83      Organism-specific databases                  

   OrthoDB                            389404     389404      0.71      16      Phylogenomic databases                       

   PANTHER                            179314     172436      0.33      25      Family and domain databases                  

   PATRIC                             307766     307735      0.56      22      Genome annotation databases                  

   PaxDb                               66633      66632      0.12      43      Proteomic databases                          

   PDB                                118037      21636      0.22      33      3D structure databases                       

   PDBsum                             118037      21636      0.22      32      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      90      Proteomic databases                          

   PeroxiBase                            770        754     <0.01     116      Protein family/group databases               

   Pfam                               739788     507509      1.35       4      Family and domain databases                  

   PharmGKB                            18384      18356      0.03      67      Organism-specific databases                  

   PhosphoSite                         33560      33560      0.06      52      PTM databases                                

   PhosSite                              606        597     <0.01     120      PTM databases                                

   PhylomeDB                           93644      93644      0.17      36      Phylogenomic databases                       

   PIR                                121901     111679      0.22      31      Sequence databases                           

   PIRSF                              102253     101291      0.19      35      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     106      Other                                        

   PomBase                              5134       5098      0.01      91      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     134      Protein family/group databases               

   PRIDE                              122373     122373      0.22      30      Proteomic databases                          

   PRINTS                             136729     120447      0.25      27      Family and domain databases                  

   PRO                                 58086      58086      0.11      45      Other                                        

   ProDom                              29244      29065      0.05      57      Family and domain databases                  

   ProMEX                                389        389     <0.01     125      Proteomic databases                          

   PROSITE                            446002     287562      0.81      10      Family and domain databases                  

   ProteinModelPortal                 441268     441268      0.81      12      3D structure databases                       

   Proteomes                          506613     481138      0.93       6      Other                                        

   PseudoCAP                            1288       1279     <0.01     107      Organism-specific databases                  

   Reactome                            87661      26673      0.16      37      Enzyme and pathway databases                 

   REBASE                                406        406     <0.01     124      Protein family/group databases               

   RefSeq                             650265     479656      1.19       5      Sequence databases                           

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

   RGD                                  7837       7833      0.01      78      Organism-specific databases                  

   SABIO-RK                             3000       3000      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                              170119     127420      0.31      26      Family and domain databases                  

   SMR                                224068     224068      0.41      24      3D structure databases                       

   STRING                             402955     402954      0.74      15      Protein-protein interaction databases        

   SUPFAM                             442341     340130      0.81      11      Family and domain databases                  

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

   TAIR                                13513      13457      0.02      73      Organism-specific databases                  

   TCDB                                 5369       5348      0.01      89      Protein family/group databases               

   TIGRFAMs                           291339     271165      0.53      23      Family and domain databases                  

   TreeFam                             44782      44777      0.08      48      Phylogenomic databases                       

   TubercuList                          2062       2026     <0.01     104      Organism-specific databases                  

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

   UCSC                                59281      44788      0.11      44      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     128      PTM databases                                

   UniGene                            102836      92692      0.19      34      Sequence databases                           

   UniPathway                         134007     121482      0.24      29      Enzyme and pathway databases                 

   VectorBase                            614        596     <0.01     119      Genome annotation databases                  

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

   WormBase                             5064       4017      0.01      92      Organism-specific databases                  

   Xenbase                              4768       4762      0.01      93      Organism-specific databases                  

   ZFIN                                 2774       2774      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 3797 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: 76372