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         UniProtKB/Swiss-Prot protein knowledgebase release 2013_08 statistics





1.  INTRODUCTION



Release 2013_08 of 24-Jul-13 of UniProtKB/Swiss-Prot contains 540732 sequence entries,

comprising 192091492 amino acids abstracted from 221115 references. 



187 sequences have been added since release 2013_07, the sequence data of

60 existing entries has been updated and the annotations of

96142 entries have been revised.



Number of fragments: 9065

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 35297





Protein existence (PE):           entries     %



1: Evidence at protein level        79739   14.7%

2: Evidence at transcript level     64210   11.9%

3: Inferred from homology          379215   70.1%

4: Predicted                        15667    2.9%

5: Uncertain                         1901    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: 13004



   The first twenty species represent 113672 sequences:    21 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5430

                            2x: 1892

                            3x:  991

                            4x:  643

                            5x:  469

                            6x:  394

                            7x:  285

                            8x:  217

                            9x:  208

                           10x:  121

                       11- 20x:  695

                       21- 50x:  406

                       51-100x:  212

                         >100x: 1041





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20266  Homo sapiens (Human)

       2      16618  Mus musculus (Mouse)

       3      12224  Arabidopsis thaliana (Mouse-ear cress)

       4       7858  Rattus norvegicus (Rat)

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

       6       5980  Bos taurus (Bovine)

       7       5089  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4431  Escherichia coli (strain K12)

       9       4188  Bacillus subtilis (strain 168)

      10       4126  Dictyostelium discoideum (Slime mold)

      11       3431  Caenorhabditis elegans

      12       3371  Xenopus laevis (African clawed frog)

      13       3198  Drosophila melanogaster (Fruit fly)

      14       3065  Oryza sativa subsp. japonica (Rice)

      15       2898  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2256  Gallus gallus (Chicken)

      17       2218  Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)

      18       2032  Mycobacterium tuberculosis

      19       2015  Escherichia coli O157:H7

      20       1787  Methanocaldococcus jannaschii  

      21       1771  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

      22       1707  Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

      23       1694  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      24       1684  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      25       1678  Shigella flexneri

      26       1413  Sus scrofa (Pig)

      27       1346  Salmonella typhi

      28       1247  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      29       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

      30       1170  Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)

      31       1036  Synechocystis sp. (strain PCC 6803 / Kazusa)

      32       1018  Yersinia pestis

      33       1015  Archaeoglobus fulgidus 

      34        950  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      35        930  Salmonella paratyphi A (strain ATCC 9150 / SARB42)

      36        926  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      37        925  Staphylococcus aureus (strain N315)

      38        923  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      39        909  Acanthamoeba polyphaga mimivirus (APMV)

      40        905  Kluyveromyces lactis   

      41        899  Staphylococcus aureus (strain COL)

      42        895  Staphylococcus aureus (strain MW2)

      43        889  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      44        889  Staphylococcus aureus (strain MSSA476)

      45        889  Oryctolagus cuniculus (Rabbit)

      46        888  Staphylococcus aureus (strain MRSA252)

      47        882  Salmonella choleraesuis (strain SC-B67)

      48        878  Shigella sonnei (strain Ss046)

      49        869  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      50        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      51        862  Candida glabrata   

      52        841  Escherichia coli O9:H4 (strain HS)

      53        836  Neurospora crassa 

      54        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      55        829  Shigella boydii serotype 4 (strain Sb227)

      56        825  Escherichia coli (strain UTI89 / UPEC)

      57        821  Shigella dysenteriae serotype 1 (strain Sd197)

      58        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      59        803  Canis familiaris (Dog) (Canis lupus familiaris)

      60        791  Escherichia coli (strain SMS-3-5 / SECEC)

      61        787  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      62        783  Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) 

      63        782  Aquifex aeolicus (strain VF5)

      64        775  Pasteurella multocida (strain Pm70)

      65        775  Emericella nidulans  

      66        771  Escherichia coli (strain K12 / DH10B)

      67        765  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      68        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      69        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      70        762  Escherichia coli (strain 55989 / EAEC)

      71        761  Escherichia coli O8 (strain IAI1)

      72        760  Shigella flexneri serotype 5b (strain 8401)

      73        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      74        758  Staphylococcus epidermidis (strain ATCC 12228)

      75        757  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      76        756  Escherichia coli (strain SE11)

      77        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      78        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      79        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      80        744  Photorhabdus luminescens subsp. laumondii (strain TT01)

      81        740  Staphylococcus aureus (strain NCTC 8325)

      82        739  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      83        736  Bacillus anthracis

      84        736  Bacillus halodurans 

      85        735  Yersinia enterocolitica serotype O:8 / biotype 1B (strain 8081)

      86        733  Vibrio vulnificus (strain CMCP6)

      87        731  Escherichia coli O81 (strain ED1a)

      88        721  Salmonella enteritidis PT4 (strain P125109)

      89        718  Zea mays (Maize)

      90        717  Vibrio vulnificus (strain YJ016)

      91        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      92        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      93        714  Salmonella paratyphi A (strain AKU_12601)

      94        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      95        713  Enterobacter sp. (strain 638)

      96        713  Salmonella agona (strain SL483)

      97        713  Escherichia coli O1:K1 / APEC

      98        713  Salmonella newport (strain SL254)

      99        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     100        712  Salmonella schwarzengrund (strain CVM19633)

     101        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     102        710  Salmonella heidelberg (strain SL476)

     103        702  Salmonella dublin (strain CT_02021853)

     104        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     105        696  Klebsiella pneumoniae (strain 342)

     106        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     107        693  Pseudomonas putida (strain KT2440)

     108        689  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     109        688  Pan troglodytes (Chimpanzee)

     110        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     111        683  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     112        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     113        675  Pseudomonas syringae pv. tomato (strain DC3000)

     114        670  Serratia proteamaculans (strain 568)

     115        668  Mycobacterium leprae (strain TN)

     116        667  Yersinia pestis (strain Pestoides F)

     117        666  Staphylococcus aureus (strain USA300)

     118        658  Rhizobium sp. (strain NGR234)

     119        658  Bradyrhizobium japonicum (strain USDA 110)

     120        656  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     121        653  Debaryomyces hansenii   

     122        652  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        646  Escherichia coli

     124        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     125        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     126        642  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     127        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     128        635  Shewanella oneidensis (strain MR-1)

     129        634  Yersinia pseudotuberculosis serotype IB (strain PB1/+)

     130        632  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     131        623  Oryza sativa subsp. indica (Rice)

     132        622  Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)

     133        616  Treponema pallidum (strain Nichols)

     134        614  Methanothermobacter thermautotrophicus  

     135        612  Staphylococcus haemolyticus (strain JCSC1435)

     136        606  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     137        605  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     138        602  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

     139        602  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     140        602  Photobacterium profundum (Photobacterium sp. (strain SS9))

     141        602  Staphylococcus saprophyticus subsp. saprophyticus 

     142        601  Salmonella paratyphi C (strain RKS4594)

     143        600  Yersinia pestis bv. Antiqua (strain Angola)

     144        591  Listeria innocua serovar 6a (strain CLIP 11262)

     145        590  Bacillus cereus (strain ATCC 10987)

     146        589  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     147        586  Rickettsia prowazekii (strain Madrid E)

     148        581  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     149        579  Neisseria meningitidis serogroup B (strain MC58)

     150        576  Brucella suis biovar 1 (strain 1330)

     151        572  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     152        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     153        568  Caenorhabditis briggsae

     154        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     155        566  Pseudomonas syringae pv. syringae (strain B728a)

     156        565  Helicobacter pylori (strain J99) (Campylobacter pylori J99)

     157        565  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     159        564  Pseudomonas aeruginosa (strain UCBPP-PA14)

     160        563  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     161        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     162        561  Bacillus cereus (strain ZK / E33L)

     163        557  Clostridium acetobutylicum 

     164        556  Xanthomonas axonopodis pv. citri (strain 306)

     165        552  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     166        552  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     167        552  Pseudomonas fluorescens (strain Pf0-1)

     168        546  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

     169        545  Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6)

     170        533  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     171        532  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     172        531  Erwinia tasmaniensis (strain DSM 17950 / Et1/99)

     173        529  Sodalis glossinidius (strain morsitans)

     174        529  Listeria monocytogenes serotype 4b (strain F2365)

     175        523  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     176        522  Xylella fastidiosa (strain 9a5c)

     177        515  Chromobacterium violaceum 

     178        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     179        513  Corynebacterium glutamicum 

     180        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     181        511  Pseudomonas aeruginosa (strain PA7)

     182        511  Vibrio cholerae serotype O1 (strain ATCC 39541 / Ogawa 395 / O395)

     183        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     184        508  Staphylococcus aureus (strain Newman)

     185        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     186        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     187        507  Geobacillus kaustophilus (strain HTA426)

     188        505  Streptomyces avermitilis 

     189        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     190        502  Deinococcus radiodurans 

     191        500  Pseudomonas entomophila (strain L48)

     192        499  Brucella abortus biovar 1 (strain 9-941)

     193        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     194        496  Bacillus clausii (strain KSM-K16)

     195        495  Burkholderia pseudomallei (strain K96243)

     196        495  Haemophilus influenzae (strain 86-028NP)

     197        494  Proteus mirabilis (strain HI4320)

     198        492  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     199        492  Bacillus amyloliquefaciens (strain FZB42)

     200        491  Xanthomonas campestris pv. campestris (strain 8004)

     201        490  Vibrio harveyi (strain ATCC BAA-1116 / BB120)

     202        487  Shewanella sp. (strain MR-7)

     203        486  Mannheimia succiniciproducens (strain MBEL55E)

     204        484  Pseudomonas aeruginosa (strain LESB58)

     205        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     206        484  Shewanella sp. (strain MR-4)

     207        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     208        482  Thermosynechococcus elongatus (strain BP-1)

     209        480  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     210        480  Acinetobacter sp. (strain ADP1)

     211        479  Pyrococcus horikoshii 

     212        478  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     213        475  Pseudomonas putida (strain F1 / ATCC 700007)

     214        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     215        474  Brucella abortus (strain 2308)

     216        473  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     217        473  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     218        471  Methanosarcina mazei  

     219        469  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     220        468  Pyrococcus abyssi (strain GE5 / Orsay)

     221        468  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     222        468  Clostridium perfringens (strain 13 / Type A)

     223        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     224        466  Shewanella frigidimarina (strain NCIMB 400)

     225        466  Pseudomonas putida (strain GB-1)

     226        466  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     227        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     228        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     229        463  Shewanella sp. (strain ANA-3)

     230        462  Burkholderia mallei (strain ATCC 23344)

     231        462  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     232        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     233        460  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     234        459  Cupriavidus pinatubonensis (strain JMP134 / LMG 1197) (Alcaligenes eutrophus) 

     235        458  Enterococcus faecalis (strain ATCC 700802 / V583)

     236        455  Staphylococcus aureus (strain JH1)

     237        455  Nicotiana tabacum (Common tobacco)

     238        454  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     239        454  Ovis aries (Sheep)

     240        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     241        453  Pseudomonas putida (strain W619)

     242        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     243        452  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     244        452  Shewanella baltica (strain OS185)

     245        451  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     246        451  Aeromonas salmonicida (strain A449)

     247        449  Thermoanaerobacter tengcongensis  

     248        449  Staphylococcus aureus (strain JH9)

     249        449  Hahella chejuensis (strain KCTC 2396)

     250        449  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19038 (  4%)

    Bacteria         329008 ( 61%)

    Eukaryota        176340 ( 33%)

    Viruses           16346 (  3%)





   Within Eukaryota:



   



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

     Human                  20267 ( 11%)           (  4%)

     Other Mammalia         45907 ( 26%)           (  8%)

     Other Vertebrata       17498 ( 10%)           (  3%)

     Viridiplantae          34107 ( 19%)           (  6%)

     Fungi                  30859 ( 17%)           (  6%)

     Insecta                 8693 (  5%)           (  2%)

     Nematoda                4306 (  2%)           (  1%)

     Other                  14703 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9065             1001-1100     3752

                 51- 100   41424             1101-1200     2600

                101- 150   57705             1201-1300     2025

                151- 200   57795             1301-1400     1885

                201- 250   56516             1401-1500     1512

                251- 300   50017             1501-1600      737

                301- 350   50203             1601-1700      567

                351- 400   43443             1701-1800      470

                401- 450   35542             1801-1900      432

                451- 500   28608             1901-2000      352

                501- 550   20364             2001-2100      214

                551- 600   14625             2101-2200      288

                601- 650   12274             2201-2300      297

                651- 700    8854             2301-2400      181

                701- 750    7298             2401-2500      138

                751- 800    5188             >2500         1090

                801- 850    4537

                851- 900    5031

                901- 950    3881

                951-1000    2757



   





   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: 2336





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  758

                       2x:  311

                       3x:  156

                       4x:  114

                       5x:   90

                       6x:   72

                       7x:   60

                       8x:   41

                       9x:   39

                      10x:   32

                  11- 20x:  183

                  21- 50x:  190

                  51-100x:  101

                    >100x:  189





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



   Nb    Citations   Journal name

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

    1        21269   Journal of Biological Chemistry

    2         9611   Proceedings of the National Academy of Sciences of the U.S.A.

    3         5754   Journal of Bacteriology

    4         5063   Biochemical and Biophysical Research Communications

    5         4609   Gene

    6         4582   Nucleic Acids Research

    7         4489   Biochemistry

    8         4384   FEBS Letters

    9         4244   The EMBO Journal

   10         3937   Molecular and Cellular Biology

   11         3745   Nature

   12         3601   Journal of Molecular Biology

   13         3246   European Journal of Biochemistry

   14         3235   Biochimica et Biophysica Acta

   15         3061   Cell

   16         2610   Journal of Virology

   17         2519   Biochemical Journal

   18         2511   Genomics

   19         2487   Science

   20         2078   Molecular Microbiology

   21         1894   Plant Physiology

   22         1890   Journal of Cell Biology

   23         1657   Plant Molecular Biology

   24         1615   The American Journal of Human Genetics

   25         1608   Genes and Development

   26         1543   Virology

   27         1522   Nature Genetics

   28         1461   Human Molecular Genetics

   29         1446   Oncogene

   30         1354   Development

   31         1349   Molecular and General Genetics

   32         1346   Molecular Biology of the Cell

   33         1319   Human Mutation

   34         1318   The Plant Cell

   35         1243   Journal of Biochemistry

   36         1208   The Plant Journal

   37         1193   Journal of Immunology

   38         1177   Molecular Cell

   39         1112   Genetics

   40         1093   Structure

   41         1035   Journal of General Virology

   42          984   Blood

   43          960   Journal of Cell Science

   44          958   Infection and Immunity

   45          933   Archives of Biochemistry and Biophysics

   46          873   Microbiology

   47          845   Developmental Biology

   48          814   Cancer Research

   49          805   Current Biology

   50          789   Yeast

   51          737   FEMS Microbiology Letters

   52          691   Acta Crystallographica, Section D

   53          664   Protein Science

   54          654   Journal of Neuroscience

   55          652   Toxicon

   56          649   Applied and Environmental Microbiology

   57          628   Human Genetics

   58          627   Nature Structural Biology

   59          626   Mechanisms of Development

   60          622   PLoS ONE

   61          594   Neuron

   62          577   Journal of Clinical Investigation

   63          548   American Journal of Physiology

   64          541   Current Genetics

   65          532   The Journal of Experimental Medicine

   66          504   Proteins

   67          490   Molecular Endocrinology

   68          486   Plant and Cell Physiology

   69          479   Mammalian Genome

   70          468   Journal of Neurochemistry

   71          459   Immunogenetics

   72          453   Nature Cell Biology

   73          450   Bioscience, Biotechnology, and Biochemistry

   74          446   The Journal of Clinical Endocrinology and Metabolism

   75          438   Endocrinology

   76          430   Journal of Medical Genetics

   77          430   Molecular and Biochemical Parasitology

   78          400   Journal of Molecular Evolution

   79          381   Experimental Cell Research

   80          379   Molecular Biology and Evolution

   81          377   DNA and Cell Biology

   82          366   DNA Sequence

   83          354   Peptides

   84          344   Nature Structural and Molecular Biology

   85          333   RNA

   86          330   Developmental Cell

   87          329   Brain Research. Molecular Brain Research

   88          328   The FEBS Journal

   89          325   Tissue Antigens

   90          320   Antimicrobial Agents and Chemotherapy

   91          320   Comparative Biochemistry and Physiology

   92          310   Journal of Investigative Dermatology

   93          306   Planta

   94          305   Molecular Pharmacology

   95          294   Biological Chemistry Hoppe-Seyler

   96          287   Biology of Reproduction

   97          283   Neurology

   98          279   Cytogenetics and Cell Genetics

   99          274   Eukaryotic Cell

  100          273   Developmental Dynamics

  101          269   Virus Research

  102          267   Genome Research

  103          263   EMBO Reports

  104          260   Immunity

  105          259   Biochimie

  106          257   Journal of General Microbiology

  107          255   Genes to Cells

  108          245   Molecular Plant-Microbe Interactions

  109          245   The FASEB Journal

  110          240   The New England Journal of Medicine

  111          234   European Journal of Immunology

  112          227   Annals of Neurology

  113          224   European Journal of Human Genetics

  114          221   Journal of the American Chemical Society

  115          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  116          215   DNA Research

  117          212   Journal of Human Genetics

  118          203   Investigative Ophthalmology and Visual Science

  119          202   Archives of Microbiology

  120          202   Acta Crystallographica, Section F

  121          198   Nature Immunology

  122          197   Journal of Experimental Botany

  123          195   Journal of Cellular Biochemistry

  124          193   BMC Genomics

  125          191   Archives of Virology

  126          190   American Journal of Medical Genetics. Part A

  127          189   Molecular and Cellular Endocrinology

  128          184   Journal of Medicinal Chemistry

  129          183   Molecular Immunology

  130          181   Glycobiology

  131          180   Clinical Genetics

  132          175   PLoS Genetics

  133          174   Diabetes

  134          172   Insect Biochemistry and Molecular Biology

  135          170   Circulation Research

  136          168   American Journal of Medical Genetics

  137          168   Molecular Phylogenetics and Evolution

  138          166   International Journal of Cancer

  139          165   Traffic

  140          163   Phytochemistry

  141          161   Molecular Genetics and Metabolism

  142          159   Molecular Reproduction and Development

  143          159   DNA

  144          158   Protein Expression and Purification

  145          156   Molecular Genetics and Genomics

  146          155   Cell Cycle

  147          155   Hemoglobin

  148          155   Biological Chemistry

  149          154   Bioorganicheskaia Khimiia

  150          153   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)                      1049336                 1.94                                         

   Journal                            843721     419229      1.56       1                                 

   Submitted to EMBL/GenBank/DDBJ     196528     175896      0.36       2                                 

   Submitted to other databases         6855       6379      0.01       3                                 

   Book citation                         724        710     <0.01       4                                 

   Plant Gene Register                   589        577     <0.01       5                                 

   Thesis                                417        414     <0.01       6                                 

   Unpublished observations              305        301     <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: 338670



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2438141                 4.51                                         

   ALLERGEN                              530        530     <0.01      27                                 

   ALTERNATIVE PRODUCTS                22302      22302      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5065       5065      0.01      23                                 

   BIOTECHNOLOGY                         357        355     <0.01      28                                 

   CATALYTIC ACTIVITY                 244649     221349      0.45       5                                 

   CAUTION                              9407       9233      0.02      19                                 

   COFACTOR                           108529      99008      0.20       7                                 

   DEVELOPMENTAL STAGE                  9961       9961      0.02      17                                 

   DISEASE                              5300       3563      0.01      22                                 

   DISRUPTION PHENOTYPE                 5926       5926      0.01      20                                 

   DOMAIN                              39827      35049      0.07      10                                 

   ENZYME REGULATION                   11252      11252      0.02      15                                 

   FUNCTION                           423680     406170      0.78       2                                 

   INDUCTION                           15418      15418      0.03      14                                 

   INTERACTION                         10252      10252      0.02      16                                 

   MASS SPECTROMETRY                    5595       4264      0.01      21                                 

   MISCELLANEOUS                       32840      30340      0.06      12                                 

   PATHWAY                            131818     119944      0.24       6                                 

   PHARMACEUTICAL                         93         93     <0.01      29                                 

   POLYMORPHISM                          903        849     <0.01      24                                 

   PTM                                 44663      34880      0.08       8                                 

   RNA EDITING                           627        627     <0.01      25                                 

   SEQUENCE CAUTION                    41227      41227      0.08       9                                 

   SIMILARITY                         642910     516142      1.19       1                                 

   SUBCELLULAR LOCATION               328115     322055      0.61       3                                 

   SUBUNIT                            247842     247842      0.46       4                                 

   TISSUE SPECIFICITY                  39039      39039      0.07      11                                 

   TOXIC DOSE                            553        516     <0.01      26                                 

   WEB RESOURCE                         9461       7526      0.02      18                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3739710                 6.92                                         

   ACT_SITE                           142893      87334      0.26       9                                 

   BINDING                            295926      78871      0.55       4                                 

   CA_BIND                              3922       1643      0.01      35                                 

   CARBOHYD                           107482      27558      0.20      15                                 

   CHAIN                              547732     534506      1.01       1                                 

   COILED                              20320      13967      0.04      26                                 

   COMPBIAS                            54569      28993      0.10      18                                 

   CONFLICT                           128279      44911      0.24      12                                 

   CROSSLNK                             6821       3943      0.01      34                                 

   DISULFID                           109793      30194      0.20      14                                 

   DNA_BIND                            10402       9477      0.02      31                                 

   DOMAIN                             161917      96376      0.30       8                                 

   HELIX                              183644      17855      0.34       6                                 

   INIT_MET                            15661      15661      0.03      27                                 

   INTRAMEM                             2176        940     <0.01      37                                 

   LIPID                               11947       7581      0.02      30                                 

   METAL                              319832      78521      0.59       3                                 

   MOD_RES                            162694      60981      0.30       7                                 

   MOTIF                               36043      23364      0.07      24                                 

   MUTAGEN                             44311      10294      0.08      22                                 

   NON_CONS                             2043        751     <0.01      38                                 

   NON_STD                               354        279     <0.01      39                                 

   NON_TER                             12212       9330      0.02      29                                 

   NP_BIND                            121600      73992      0.22      13                                 

   PEPTIDE                             10326       7038      0.02      32                                 

   PROPEP                              12690      10921      0.02      28                                 

   REGION                             135870      68866      0.25      10                                 

   REPEAT                              95940      14190      0.18      16                                 

   SIGNAL                              38387      38377      0.07      23                                 

   SITE                                46891      26000      0.09      19                                 

   STRAND                             191913      16862      0.35       5                                 

   TOPO_DOM                           130602      27079      0.24      11                                 

   TRANSIT                              8414       8309      0.02      33                                 

   TRANSMEM                           356568      73621      0.66       2                                 

   TURN                                44662      14468      0.08      21                                 

   UNSURE                               3361        717      0.01      36                                 

   VAR_SEQ                             46159      19412      0.09      20                                 

   VARIANT                             85929      16796      0.16      17                                 

   ZN_FING                             29425      12940      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)               15985728                29.56                                                           

   Allergome                            1505        946     <0.01     101      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     111      Organism-specific databases                  

   ArrayExpress                        36302      36302      0.07      46      Gene expression databases                    

   Bgee                                38784      38784      0.07      44      Gene expression databases                    

   BindingDB                            5033       5033      0.01      85      Other                                        

   BioCyc                             311803     301117      0.58      20      Enzyme and pathway databases                 

   BRENDA                               4325       4315      0.01      92      Enzyme and pathway databases                 

   CAZy                                 7635       6875      0.01      74      Protein family/group databases               

   CGD                                   719        697     <0.01     113      Organism-specific databases                  

   ChEMBL                               5636       5636      0.01      79      Other                                        

   ChiTaRS                             12537      12532      0.02      68      Other                                        

   CleanEx                             30084      29443      0.06      50      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     125      2D gel databases                             

   ConoServer                            926        844     <0.01     106      Organism-specific databases                  

   CTD                                 70313      69629      0.13      39      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      80      Organism-specific databases                  

   dictyBase                            4203       4086      0.01      94      Organism-specific databases                  

   DIP                                 14377      14290      0.03      66      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     117      3D structure databases                       

   DMDM                                16758      16755      0.03      62      Polymorphism databases                       

   DNASU                               18711      18640      0.03      58      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     124      2D gel databases                             

   DrugBank                             5319       1628      0.01      82      Other                                        

   EchoBASE                             4161       4161      0.01      95      Organism-specific databases                  

   EcoGene                              4292       4290      0.01      93      Organism-specific databases                  

   eggNOG                             430938     430938      0.80      10      Phylogenomic databases                       

   EMBL                               941400     529462      1.74       3      Sequence databases                           

   Ensembl                             84576      48712      0.16      35      Genome annotation databases                  

   EnsemblBacteria                    342894     324723      0.63      18      Genome annotation databases                  

   EnsemblFungi                        17644      17352      0.03      61      Genome annotation databases                  

   EnsemblMetazoa                      12381       9279      0.02      69      Genome annotation databases                  

   EnsemblPlants                       16665      14700      0.03      63      Genome annotation databases                  

   EnsemblProtists                      4499       4372      0.01      91      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     126      Organism-specific databases                  

   EuPathDB                              755        755     <0.01     112      Organism-specific databases                  

   EvolutionaryTrace                   16608      16608      0.03      64      Other                                        

   FlyBase                              5901       5527      0.01      78      Organism-specific databases                  

   Gene3D                             359072     274282      0.66      16      Family and domain databases                  

   GeneCards                           20056      19784      0.04      55      Organism-specific databases                  

   GeneFarm                             3198       3187      0.01      96      Organism-specific databases                  

   GeneID                             499324     468423      0.92       6      Genome annotation databases                  

   GeneTree                            38242      38226      0.07      45      Phylogenomic databases                       

   Genevestigator                      67485      67485      0.12      41      Gene expression databases                    

   GeneWiki                            10348      10260      0.02      72      Other                                        

   GenoList                             7071       7059      0.01      75      Organism-specific databases                  

   GenomeRNAi                          21302      21300      0.04      53      Other                                        

   GO                                2439884     511058      4.51       1      Ontologies                                   

   Gramene                              6029       6029      0.01      77      Organism-specific databases                  

   H-InvDB                              5593       4772      0.01      81      Organism-specific databases                  

   HAMAP                              316206     315795      0.58      19      Family and domain databases                  

   HGNC                                19862      19694      0.04      56      Organism-specific databases                  

   HOGENOM                            385619     385619      0.71      13      Phylogenomic databases                       

   HOVERGEN                            75578      75578      0.14      37      Phylogenomic databases                       

   HPA                                 19101      14749      0.04      57      Organism-specific databases                  

   InParanoid                          70124      70124      0.13      40      Phylogenomic databases                       

   IntAct                              35160      35160      0.07      47      Protein-protein interaction databases        

   InterPro                          1825171     517699      3.38       2      Family and domain databases                  

   IPI                                 97999      67985      0.18      32      Sequence databases                           

   KEGG                               480847     451146      0.89       8      Genome annotation databases                  

   KO                                 374760     374333      0.69      14      Phylogenomic databases                       

   LegioList                             765        763     <0.01     110      Organism-specific databases                  

   Leproma                               671        668     <0.01     114      Organism-specific databases                  

   MaizeGDB                              499        494     <0.01     119      Organism-specific databases                  

   MEROPS                              11893      11893      0.02      71      Protein family/group databases               

   MGI                                 16532      16486      0.03      65      Organism-specific databases                  

   MIM                                 18156      13736      0.03      60      Organism-specific databases                  

   MINT                                31528      31528      0.06      49      Protein-protein interaction databases        

   mycoCLAP                              282        277     <0.01     122      Protein family/group databases               

   NextBio                             70890      70890      0.13      38      Other                                        

   neXtProt                            20118      20118      0.04      54      Organism-specific databases                  

   OGP                                   377        377     <0.01     121      2D gel databases                             

   OMA                                394962     394962      0.73      12      Phylogenomic databases                       

   Orphanet                             5193       2816      0.01      83      Organism-specific databases                  

   OrthoDB                             78246      78246      0.14      36      Phylogenomic databases                       

   PANTHER                            203652     189817      0.38      24      Family and domain databases                  

   Pathway_Interaction_DB               4568       1666      0.01      90      Enzyme and pathway databases                 

   PATRIC                             308993     308962      0.57      21      Genome annotation databases                  

   PaxDb                               66693      66693      0.12      42      Proteomic databases                          

   PDB                                 96838      19818      0.18      34      3D structure databases                       

   PDBsum                              96838      19818      0.18      33      3D structure databases                       

   PeptideAtlas                         5162       5162      0.01      84      Proteomic databases                          

   PeroxiBase                            772        756     <0.01     109      Protein family/group databases               

   Pfam                               722868     499306      1.34       4      Family and domain databases                  

   PharmGKB                            18388      18360      0.03      59      Organism-specific databases                  

   PhosphoSite                         33568      33568      0.06      48      PTM databases                                

   PhosSite                              660        648     <0.01     115      PTM databases                                

   PhylomeDB                           27689      27689      0.05      52      Phylogenomic databases                       

   PIR                                118851     108690      0.22      29      Sequence databases                           

   PIRSF                               99530      99336      0.18      30      Family and domain databases                  

   PMAP-CutDB                           1457       1457     <0.01     102      Other                                        

   PomBase                              5011       4960      0.01      86      Organism-specific databases                  

   PptaseDB                               40         40     <0.01     127      Protein family/group databases               

   PRIDE                              120516     120516      0.22      28      Proteomic databases                          

   PRINTS                             137384     120372      0.25      26      Family and domain databases                  

   ProDom                              29313      29132      0.05      51      Family and domain databases                  

   ProMEX                                824        824     <0.01     108      Proteomic databases                          

   PROSITE                            484548     305298      0.90       7      Family and domain databases                  

   ProtClustDB                        344173     344173      0.64      17      Phylogenomic databases                       

   ProteinModelPortal                 433690     433690      0.80       9      3D structure databases                       

   PseudoCAP                            1255       1246     <0.01     104      Organism-specific databases                  

   Reactome                            13102       7882      0.02      67      Enzyme and pathway databases                 

   REBASE                                403        403     <0.01     120      Protein family/group databases               

   RefSeq                             525275     468769      0.97       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1257       1036     <0.01     103      2D gel databases                             

   RGD                                  7773       7769      0.01      73      Organism-specific databases                  

   SABIO-RK                             2544       2544     <0.01      99      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      76      Organism-specific databases                  

   SignaLink                            2959       2959      0.01      97      Enzyme and pathway databases                 

   SMART                              167945     125724      0.31      25      Family and domain databases                  

   SMR                                219593     219593      0.41      23      3D structure databases                       

   STRING                             396704     396704      0.73      11      Protein-protein interaction databases        

   SUPFAM                             374004     289054      0.69      15      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     105      2D gel databases                             

   TAIR                                12205      12150      0.02      70      Organism-specific databases                  

   TCDB                                 5004       4983      0.01      87      Protein family/group databases               

   TIGRFAMs                           290501     269894      0.54      22      Family and domain databases                  

   TubercuList                          2045       2009     <0.01     100      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     118      2D gel databases                             

   UCSC                                44662      44662      0.08      43      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     123      PTM databases                                

   UniGene                             99093      90020      0.18      31      Sequence databases                           

   UniPathway                         131680     119816      0.24      27      Enzyme and pathway databases                 

   VectorBase                            606        588     <0.01     116      Genome annotation databases                  

   World-2DPAGE                          920        909     <0.01     107      2D gel databases                             

   WormBase                             4922       3959      0.01      88      Organism-specific databases                  

   Xenbase                              4742       4737      0.01      89      Organism-specific databases                  

   ZFIN                                 2811       2811      0.01      98      Organism-specific databases                  



Total number of cross-referenced databases: 127



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.25   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.57

   Arg (R) 5.53   Glu (E) 6.75   Lys (K) 5.84   Thr (T) 5.34

   Asn (N) 4.06   Gly (G) 7.07   Met (M) 2.42   Trp (W) 1.08

   Asp (D) 5.45   His (H) 2.27   Phe (F) 3.86   Tyr (Y) 2.92

   Cys (C) 1.37   Ile (I) 5.96   Pro (P) 4.70   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



4461 entries are encoded on a mitochondrion, and 3722 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: 74890