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         UniProtKB/Swiss-Prot protein knowledgebase release 2014_07 statistics





1.  INTRODUCTION



Release 2014_07 of 09-Jul-14 of UniProtKB/Swiss-Prot contains 546000 sequence entries,

comprising 194259968 amino acids abstracted from 229917 references. 



482 sequences have been added since release 2014_06, the sequence data of

29 existing entries has been updated and the annotations of

96419 entries have been revised.



Number of fragments: 9116

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 37149





Protein existence (PE):           entries     %



1: Evidence at protein level        84172   15.4%

2: Evidence at transcript level     62515   11.4%

3: Inferred from homology          381792   69.9%

4: Predicted                        15648    2.9%

5: Uncertain                         1873    0.3%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 13110



   The first twenty species represent 114928 sequences:    21 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5453

                            2x: 1892

                            3x: 1006

                            4x:  655

                            5x:  475

                            6x:  397

                            7x:  292

                            8x:  222

                            9x:  212

                           10x:  121

                       11- 20x:  707

                       21- 50x:  422

                       51-100x:  210

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20209  Homo sapiens (Human)

       2      16671  Mus musculus (Mouse)

       3      13037  Arabidopsis thaliana (Mouse-ear cress)

       4       7906  Rattus norvegicus (Rat)

       5       6621  Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

       6       5986  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       4127  Dictyostelium discoideum (Slime mold)

      11       3468  Caenorhabditis elegans

      12       3385  Xenopus laevis (African clawed frog)

      13       3231  Drosophila melanogaster (Fruit fly)

      14       3227  Oryza sativa subsp. japonica (Rice)

      15       2926  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2259  Gallus gallus (Chicken)

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

      18       2025  Escherichia coli O157:H7

      19       2025  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      20       1885  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1774  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       1414  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1271  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       1048  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1021  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

      35        956  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      36        938  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

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

      38        926  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      39        925  Staphylococcus aureus (strain N315)

      40        924  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        837  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        810  Canis familiaris (Dog) (Canis lupus familiaris)

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

      63        788  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      64        786  Emericella nidulans  

      65        784  Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) 

      66        783  Aquifex aeolicus (strain VF5)

      67        775  Pasteurella multocida (strain Pm70)

      68        771  Escherichia coli (strain K12 / DH10B)

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

      70        767  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      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  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      82        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      83        741  Zea mays (Maize)

      84        740  Staphylococcus aureus (strain NCTC 8325)

      85        737  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  Salmonella paratyphi A (strain AKU_12601)

      96        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      97        713  Salmonella agona (strain SL483)

      98        713  Escherichia coli O1:K1 / APEC

      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        702  Salmonella dublin (strain CT_02021853)

     105        701  Pseudomonas putida (strain KT2440)

     106        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     107        696  Klebsiella pneumoniae (strain 342)

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

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

     110        689  Pan troglodytes (Chimpanzee)

     111        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     112        684  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     113        679  Oryza sativa subsp. indica (Rice)

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

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

     116        671  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        659  Bradyrhizobium diazoefficiens 

     122        658  Escherichia coli

     123        658  Rhizobium sp. (strain NGR234)

     124        655  Bacillus cereus (strain ATCC 14579 / DSM 31)

     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        619  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

     137        607  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     138        605  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     139        604  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     140        602  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        588  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     149        586  Rickettsia prowazekii (strain Madrid E)

     150        579  Neisseria meningitidis serogroup B (strain MC58)

     151        576  Brucella suis biovar 1 (strain 1330)

     152        573  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     153        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     154        568  Caenorhabditis briggsae

     155        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     156        567  Caulobacter crescentus (strain ATCC 19089 / CB15)

     157        567  Pseudomonas syringae pv. syringae (strain B728a)

     158        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     159        565  Pseudomonas aeruginosa (strain UCBPP-PA14)

     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        552  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        537  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        515  Chromobacterium violaceum 

     179        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     180        514  Corynebacterium glutamicum 

     181        513  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

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

     187        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     188        507  Deinococcus radiodurans 

     189        507  Geobacillus kaustophilus (strain HTA426)

     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  Bacillus amyloliquefaciens subsp. plantarum 

     201        491  Xanthomonas campestris pv. campestris (strain 8004)

     202        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     203        490  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     204        488  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     205        487  Shewanella sp. (strain MR-7)

     206        486  Mannheimia succiniciproducens (strain MBEL55E)

     207        486  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     208        484  Pseudomonas aeruginosa (strain LESB58)

     209        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     210        484  Shewanella sp. (strain MR-4)

     211        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     212        483  Methanosarcina mazei  

     213        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     214        482  Thermosynechococcus elongatus (strain BP-1)

     215        481  Pyrococcus horikoshii 

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

     217        477  Pseudomonas putida (strain F1 / ATCC 700007)

     218        477  Brucella abortus (strain 2308)

     219        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     220        476  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     221        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     222        472  Pyrococcus abyssi (strain GE5 / Orsay)

     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        464  Nicotiana tabacum (Common tobacco)

     229        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     230        463  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     231        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     232        463  Shewanella sp. (strain ANA-3)

     233        462  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     234        462  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

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

     240        456  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     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  Aeromonas salmonicida (strain A449)

     248        450  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)

     249        450  Streptococcus mutans serotype c (strain ATCC 700610 / UA159)

     250        450  Dechloromonas aromatica (strain RCB)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19270 (  4%)

    Bacteria         331559 ( 61%)

    Eukaryota        178692 ( 33%)

    Viruses           16479 (  3%)





   Within Eukaryota:



   



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

     Human                  20210 ( 11%)           (  4%)

     Other Mammalia         46053 ( 26%)           (  8%)

     Other Vertebrata       17731 ( 10%)           (  3%)

     Viridiplantae          35380 ( 20%)           (  6%)

     Fungi                  31281 ( 18%)           (  6%)

     Insecta                 8747 (  5%)           (  2%)

     Nematoda                4344 (  2%)           (  1%)

     Other                  14946 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9092             1001-1100     3792

                 51- 100   41767             1101-1200     2639

                101- 150   58202             1201-1300     2042

                151- 200   58109             1301-1400     1917

                201- 250   56966             1401-1500     1531

                251- 300   50552             1501-1600      749

                301- 350   50721             1601-1700      575

                351- 400   43921             1701-1800      481

                401- 450   36019             1801-1900      438

                451- 500   28915             1901-2000      356

                501- 550   20623             2001-2100      217

                551- 600   14798             2101-2200      297

                601- 650   12393             2201-2300      299

                651- 700    8963             2301-2400      185

                701- 750    7392             2401-2500      140

                751- 800    5283             >2500         1109

                801- 850    4607

                851- 900    5082

                901- 950    3922

                951-1000    2790



   





   The average sequence length in UniProtKB/Swiss-Prot is 355 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: 2428





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  793

                       2x:  319

                       3x:  161

                       4x:  119

                       5x:   91

                       6x:   78

                       7x:   57

                       8x:   46

                       9x:   33

                      10x:   42

                  11- 20x:  190

                  21- 50x:  195

                  51-100x:  110

                    >100x:  194





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



   Nb    Citations   Journal name

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

    1        22064   Journal of Biological Chemistry

    2        10026   Proceedings of the National Academy of Sciences of the U.S.A.

    3         5993   Journal of Bacteriology

    4         5183   Biochemical and Biophysical Research Communications

    5         4684   Nucleic Acids Research

    6         4679   Biochemistry

    7         4660   Gene

    8         4483   FEBS Letters

    9         4364   The EMBO Journal

   10         4042   Molecular and Cellular Biology

   11         3906   Nature

   12         3801   Journal of Molecular Biology

   13         3317   Biochimica et Biophysica Acta

   14         3284   European Journal of Biochemistry

   15         3179   Cell

   16         2699   Journal of Virology

   17         2605   Science

   18         2595   Biochemical Journal

   19         2517   Genomics

   20         2198   Molecular Microbiology

   21         2004   Plant Physiology

   22         1959   Journal of Cell Biology

   23         1735   The American Journal of Human Genetics

   24         1695   Plant Molecular Biology

   25         1667   Genes and Development

   26         1581   Virology

   27         1565   Nature Genetics

   28         1537   Human Molecular Genetics

   29         1470   Oncogene

   30         1466   The Plant Cell

   31         1423   Molecular Biology of the Cell

   32         1402   Development

   33         1356   Molecular and General Genetics

   34         1353   Human Mutation

   35         1323   The Plant Journal

   36         1273   Journal of Biochemistry

   37         1264   Molecular Cell

   38         1218   Journal of Immunology

   39         1146   Structure

   40         1142   Genetics

   41         1043   Journal of General Virology

   42         1022   Blood

   43         1012   Journal of Cell Science

   44         1007   Infection and Immunity

   45          958   Archives of Biochemistry and Biophysics

   46          932   Microbiology

   47          884   PLoS ONE

   48          865   Developmental Biology

   49          858   Current Biology

   50          824   Cancer Research

   51          809   Yeast

   52          764   FEMS Microbiology Letters

   53          733   Acta Crystallographica, Section D

   54          696   Applied and Environmental Microbiology

   55          694   Protein Science

   56          691   Journal of Neuroscience

   57          689   Toxicon

   58          639   Human Genetics

   59          634   Nature Structural Biology

   60          628   Mechanisms of Development

   61          621   Neuron

   62          594   Journal of Clinical Investigation

   63          585   American Journal of Physiology

   64          551   The Journal of Experimental Medicine

   65          549   Current Genetics

   66          532   Proteins

   67          524   Plant and Cell Physiology

   68          504   Molecular Endocrinology

   69          483   Mammalian Genome

   70          482   Journal of Neurochemistry

   71          477   Nature Cell Biology

   72          470   Bioscience, Biotechnology, and Biochemistry

   73          464   Journal of Medical Genetics

   74          460   Immunogenetics

   75          457   Endocrinology

   76          449   The Journal of Clinical Endocrinology and Metabolism

   77          439   Molecular and Biochemical Parasitology

   78          403   Journal of Molecular Evolution

   79          397   Experimental Cell Research

   80          382   Molecular Biology and Evolution

   81          380   Nature Structural and Molecular Biology

   82          378   DNA and Cell Biology

   83          375   Peptides

   84          368   DNA Sequence

   85          360   The FEBS Journal

   86          355   RNA

   87          353   Developmental Cell

   88          340   Eukaryotic Cell

   89          340   Antimicrobial Agents and Chemotherapy

   90          331   Brain Research. Molecular Brain Research

   91          326   Comparative Biochemistry and Physiology

   92          326   Tissue Antigens

   93          324   Planta

   94          323   Journal of Investigative Dermatology

   95          318   Molecular Pharmacology

   96          299   Biology of Reproduction

   97          294   Biological Chemistry Hoppe-Seyler

   98          292   Neurology

   99          282   Developmental Dynamics

  100          281   Cytogenetics and Cell Genetics

  101          279   EMBO Reports

  102          276   Immunity

  103          275   Biochimie

  104          273   The FASEB Journal

  105          271   Genome Research

  106          270   Virus Research

  107          270   Genes to Cells

  108          263   Journal of General Microbiology

  109          259   The New England Journal of Medicine

  110          257   Molecular Plant-Microbe Interactions

  111          245   Journal of the American Chemical Society

  112          243   PLoS Genetics

  113          240   European Journal of Human Genetics

  114          236   Annals of Neurology

  115          236   Acta Crystallographica, Section F

  116          235   European Journal of Immunology

  117          219   DNA Research

  118          219   Investigative Ophthalmology and Visual Science

  119          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  120          215   Nature Immunology

  121          214   Journal of Human Genetics

  122          213   Archives of Microbiology

  123          213   BMC Genomics

  124          211   Journal of Experimental Botany

  125          204   Journal of Cellular Biochemistry

  126          199   American Journal of Medical Genetics. Part A

  127          197   Journal of Medicinal Chemistry

  128          196   Glycobiology

  129          194   Molecular and Cellular Endocrinology

  130          193   Clinical Genetics

  131          193   Archives of Virology

  132          191   Molecular Immunology

  133          184   Diabetes

  134          183   Circulation Research

  135          177   Cell Cycle

  136          176   Insect Biochemistry and Molecular Biology

  137          175   Traffic

  138          173   Applied Microbiology and Biotechnology

  139          173   PLoS Pathogens

  140          173   Molecular Genetics and Metabolism

  141          172   Phytochemistry

  142          169   Molecular Phylogenetics and Evolution

  143          168   American Journal of Medical Genetics

  144          168   International Journal of Cancer

  145          168   Protein Expression and Purification

  146          162   PLoS Biology

  147          160   Molecular Reproduction and Development

  148          160   Biological Chemistry

  149          159   DNA

  150          158   Molecular Genetics and Genomics





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)                      1081151                 1.98                                         

   Journal                            887383     432546      1.63       1                                 

   Submitted to EMBL/GenBank/DDBJ     183769     163018      0.34       2                                 

   Submitted to other databases         7004       6515      0.01       3                                 

   Book citation                        1464       1450     <0.01       4                                 

   Plant Gene Register                   593        581     <0.01       5                                 

   Thesis                                422        419     <0.01       6                                 

   Unpublished observations              320        316     <0.01       7                                 

   Patent                                190        187     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 352269



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2499466                 4.58                                         

   ALLERGEN                              662        662     <0.01      25                                 

   ALTERNATIVE PRODUCTS                23054      23054      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5842       5842      0.01      21                                 

   BIOTECHNOLOGY                         387        385     <0.01      28                                 

   CATALYTIC ACTIVITY                 250412     226053      0.46       5                                 

   CAUTION                              9857       9675      0.02      18                                 

   COFACTOR                           114538     105138      0.21       7                                 

   DEVELOPMENTAL STAGE                 10307      10307      0.02      17                                 

   DISEASE                              5667       3809      0.01      23                                 

   DISRUPTION PHENOTYPE                 7424       7424      0.01      20                                 

   DOMAIN                              41987      36547      0.08       9                                 

   ENZYME REGULATION                   12780      12780      0.02      16                                 

   FUNCTION                           433354     415507      0.79       2                                 

   INDUCTION                           16578      16578      0.03      14                                 

   INTERACTION                         12870      12870      0.02      15                                 

   MASS SPECTROMETRY                    5744       4379      0.01      22                                 

   MISCELLANEOUS                       33692      31120      0.06      12                                 

   PATHWAY                            133364     121360      0.24       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1034        979     <0.01      24                                 

   PTM                                 46916      36219      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    41910      41910      0.08      10                                 

   SIMILARITY                         652045     521149      1.19       1                                 

   SUBCELLULAR LOCATION               333672     327291      0.61       3                                 

   SUBUNIT                            255255     255255      0.47       4                                 

   TISSUE SPECIFICITY                  40527      40527      0.07      11                                 

   TOXIC DOSE                            585        543     <0.01      27                                 

   WEB RESOURCE                         8278       6934      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3902518                 7.15                                         

   ACT_SITE                           149181      91372      0.27      10                                 

   BINDING                            322694      85822      0.59       4                                 

   CA_BIND                              3972       1669      0.01      35                                 

   CARBOHYD                           109129      27958      0.20      15                                 

   CHAIN                              553393     539666      1.01       1                                 

   COILED                              20707      14252      0.04      26                                 

   COMPBIAS                            56011      29822      0.10      18                                 

   CONFLICT                           129966      45453      0.24      13                                 

   CROSSLNK                             7106       4065      0.01      34                                 

   DISULFID                           113512      31081      0.21      14                                 

   DNA_BIND                            10717       9736      0.02      31                                 

   DOMAIN                             166584      99259      0.31       8                                 

   HELIX                              196756      18877      0.36       6                                 

   INIT_MET                            17731      17731      0.03      27                                 

   INTRAMEM                             2215        972     <0.01      37                                 

   LIPID                               12308       7832      0.02      29                                 

   METAL                              339973      84271      0.62       3                                 

   MOD_RES                            173429      62605      0.32       7                                 

   MOTIF                               37631      24435      0.07      24                                 

   MUTAGEN                             49188      11292      0.09      20                                 

   NON_CONS                             2069        759     <0.01      38                                 

   NON_STD                               356        281     <0.01      39                                 

   NON_TER                             12275       9381      0.02      30                                 

   NP_BIND                            130276      77291      0.24      12                                 

   PEPTIDE                             10455       7150      0.02      32                                 

   PROPEP                              12963      11167      0.02      28                                 

   REGION                             150491      75449      0.28       9                                 

   REPEAT                              97284      14333      0.18      16                                 

   SIGNAL                              39203      39193      0.07      23                                 

   SITE                                49663      27638      0.09      19                                 

   STRAND                             206290      17818      0.38       5                                 

   TOPO_DOM                           132664      27527      0.24      11                                 

   TRANSIT                              8670       8557      0.02      33                                 

   TRANSMEM                           360630      74548      0.66       2                                 

   TURN                                47920      15317      0.09      22                                 

   UNSURE                               3402        724      0.01      36                                 

   VAR_SEQ                             48327      20111      0.09      21                                 

   VARIANT                             87733      16885      0.16      17                                 

   ZN_FING                             29644      13089      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)               16558062                30.33                                                           

   Allergome                            1633       1061     <0.01     104      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     117      Organism-specific databases                  

   ArrayExpress                        21894      21894      0.04      56      Gene expression databases                    

   Bgee                                38829      38829      0.07      48      Gene expression databases                    

   BindingDB                            4993       4993      0.01      91      Chemistry                                    

   BioCyc                             324246     307098      0.59      19      Enzyme and pathway databases                 

   BioGrid                             39265      38920      0.07      47      Protein-protein interaction databases        

   BRENDA                               4333       4322      0.01      94      Enzyme and pathway databases                 

   CAZy                                 7737       6961      0.01      77      Protein family/group databases               

   CCDS                                43811      33087      0.08      45      Sequence databases                           

   CGD                                   915        893     <0.01     112      Organism-specific databases                  

   ChEMBL                               5684       5684      0.01      83      Chemistry                                    

   ChiTaRS                             12555      12551      0.02      72      Other                                        

   CleanEx                             30067      29428      0.06      52      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     129      2D gel databases                             

   ConoServer                            948        866     <0.01     110      Organism-specific databases                  

   CTD                                 71870      71175      0.13      37      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      84      Organism-specific databases                  

   dictyBase                            4203       4088      0.01      96      Organism-specific databases                  

   DIP                                 15437      15367      0.03      69      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     120      3D structure databases                       

   DMDM                                16416      16416      0.03      68      Polymorphism databases                       

   DNASU                               18745      18675      0.03      62      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     128      2D gel databases                             

   DrugBank                             5305       1617      0.01      86      Chemistry                                    

   EchoBASE                             4161       4161      0.01      97      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      95      Organism-specific databases                  

   eggNOG                             430525     430525      0.79      12      Phylogenomic databases                       

   EMBL                               954845     534812      1.75       3      Sequence databases                           

   Ensembl                             86180      49124      0.16      35      Genome annotation databases                  

   EnsemblBacteria                    348965     330359      0.64      18      Genome annotation databases                  

   EnsemblFungi                        19021      18681      0.03      61      Genome annotation databases                  

   EnsemblMetazoa                      12137       9427      0.02      73      Genome annotation databases                  

   EnsemblPlants                       18460      15805      0.03      64      Genome annotation databases                  

   EnsemblProtists                      4476       4354      0.01      93      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     130      Organism-specific databases                  

   EuPathDB                              807        807     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16445      16445      0.03      67      Other                                        

   FlyBase                              5933       5559      0.01      82      Organism-specific databases                  

   Gene3D                             466103     343738      0.85       8      Family and domain databases                  

   GeneCards                           20890      19792      0.04      58      Organism-specific databases                  

   GeneFarm                             3267       3256      0.01      98      Organism-specific databases                  

   GeneID                             493884     468998      0.90       6      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     109      Organism-specific databases                  

   GeneTree                            38219      38205      0.07      49      Phylogenomic databases                       

   Genevestigator                      68113      68113      0.12      40      Gene expression databases                    

   GeneWiki                            10376      10289      0.02      75      Other                                        

   GenoList                             7071       7059      0.01      78      Organism-specific databases                  

   GenomeRNAi                          21392      21392      0.04      57      Other                                        

   GO                                2543691     516757      4.66       1      Ontologies                                   

   Gramene                              6207       6207      0.01      80      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  1982       1982     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      85      Organism-specific databases                  

   HAMAP                              323606     320700      0.59      20      Family and domain databases                  

   HGNC                                19928      19763      0.04      60      Organism-specific databases                  

   HOGENOM                            385279     385279      0.71      16      Phylogenomic databases                       

   HOVERGEN                            75643      75643      0.14      36      Phylogenomic databases                       

   HPA                                 22354      15984      0.04      55      Organism-specific databases                  

   InParanoid                          70843      70843      0.13      39      Phylogenomic databases                       

   IntAct                              41857      41857      0.08      46      Protein-protein interaction databases        

   InterPro                          1899754     525060      3.48       2      Family and domain databases                  

   KEGG                               470449     443609      0.86       7      Genome annotation databases                  

   KO                                 371868     371388      0.68      17      Phylogenomic databases                       

   LegioList                             765        763     <0.01     116      Organism-specific databases                  

   Leproma                               671        668     <0.01     118      Organism-specific databases                  

   MaizeGDB                              503        498     <0.01     123      Organism-specific databases                  

   MaxQB                               27064      27064      0.05      54      Proteomic databases                          

   MEROPS                              11916      11916      0.02      74      Protein family/group databases               

   MGI                                 16584      16540      0.03      66      Organism-specific databases                  

   MIM                                 18678      13932      0.03      63      Organism-specific databases                  

   MINT                                31576      31576      0.06      51      Protein-protein interaction databases        

   mycoCLAP                              329        322     <0.01     126      Protein family/group databases               

   NextBio                             71181      71181      0.13      38      Other                                        

   neXtProt                            20068      20068      0.04      59      Organism-specific databases                  

   OGP                                   377        377     <0.01     125      2D gel databases                             

   OMA                                402920     402920      0.74      13      Phylogenomic databases                       

   Orphanet                             6018       3167      0.01      81      Organism-specific databases                  

   OrthoDB                            389105     389105      0.71      15      Phylogenomic databases                       

   PANTHER                            171238     165525      0.31      24      Family and domain databases                  

   PATRIC                             307582     307553      0.56      21      Genome annotation databases                  

   PaxDb                               66589      66589      0.12      41      Proteomic databases                          

   PDB                                108180      20979      0.20      31      3D structure databases                       

   PDBsum                             108180      20979      0.20      30      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      88      Proteomic databases                          

   PeroxiBase                            769        753     <0.01     115      Protein family/group databases               

   Pfam                               738992     506836      1.35       4      Family and domain databases                  

   PharmGKB                            18385      18357      0.03      65      Organism-specific databases                  

   PhosphoSite                         33563      33563      0.06      50      PTM databases                                

   PhosSite                              604        595     <0.01     121      PTM databases                                

   PhylomeDB                           93232      93232      0.17      34      Phylogenomic databases                       

   PIR                                121486     111285      0.22      29      Sequence databases                           

   PIRSF                              102145     101183      0.19      33      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     105      Other                                        

   PomBase                              5138       5102      0.01      89      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     131      Protein family/group databases               

   PRIDE                              122254     122254      0.22      28      Proteomic databases                          

   PRINTS                             136689     120395      0.25      26      Family and domain databases                  

   PRO                                 57961      57961      0.11      43      Other                                        

   ProDom                              29452      29273      0.05      53      Family and domain databases                  

   ProMEX                                870        870     <0.01     113      Proteomic databases                          

   PROSITE                            439008     286046      0.80      11      Family and domain databases                  

   ProteinModelPortal                 439534     439534      0.81      10      3D structure databases                       

   PseudoCAP                            1279       1270     <0.01     106      Organism-specific databases                  

   Reactome                            14323       8358      0.03      70      Enzyme and pathway databases                 

   REBASE                                405        405     <0.01     124      Protein family/group databases               

   RefSeq                             564005     478065      1.03       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1258       1037     <0.01     107      2D gel databases                             

   RGD                                  7827       7823      0.01      76      Organism-specific databases                  

   SABIO-RK                             2893       2893      0.01     100      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      79      Organism-specific databases                  

   SignaLink                            2962       2959      0.01      99      Enzyme and pathway databases                 

   SMART                              169624     127048      0.31      25      Family and domain databases                  

   SMR                                218299     218299      0.40      23      3D structure databases                       

   STRING                             402452     402451      0.74      14      Protein-protein interaction databases        

   SUPFAM                             441681     339548      0.81       9      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     108      2D gel databases                             

   TAIR                                13037      12981      0.02      71      Organism-specific databases                  

   TCDB                                 5269       5246      0.01      87      Protein family/group databases               

   TIGRFAMs                           291284     271103      0.53      22      Family and domain databases                  

   TreeFam                             44727      44722      0.08      44      Phylogenomic databases                       

   TubercuList                          2058       2022     <0.01     102      Organism-specific databases                  

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

   UCSC                                58414      44714      0.11      42      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     127      PTM databases                                

   UniGene                            102184      92234      0.19      32      Sequence databases                           

   UniPathway                         133208     121209      0.24      27      Enzyme and pathway databases                 

   VectorBase                            607        589     <0.01     119      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     111      2D gel databases                             

   WormBase                             5028       3998      0.01      90      Organism-specific databases                  

   Xenbase                              4763       4757      0.01      92      Organism-specific databases                  

   ZFIN                                 2763       2763      0.01     101      Organism-specific databases                  



Total number of cross-referenced databases: 131



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) 6.57

   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) 5.95   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



4465 entries are encoded on a mitochondrion, and 3773 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: 75887