UniProtKB/Swiss-Prot protein knowledgebase release 2015_03 statistics





1.  INTRODUCTION



Release 2015_03 of 04-Mar-15 of UniProtKB/Swiss-Prot contains 547964 sequence entries,

comprising 195174196 amino acids abstracted from 235228 references. 



367 sequences have been added since release 2015_02, the sequence data of

12 existing entries has been updated and the annotations of

132045 entries have been revised.



Number of fragments: 9116

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38619





Protein existence (PE):           entries     %



1: Evidence at protein level        85660   15.6%

2: Evidence at transcript level     62660   11.4%

3: Inferred from homology          386183   70.5%

4: Predicted                        11498    2.1%

5: Uncertain                         1963    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: 13194



   The first twenty species represent 115969 sequences:  21.2 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5494

                            2x: 1900

                            3x: 1016

                            4x:  655

                            5x:  483

                            6x:  403

                            7x:  290

                            8x:  224

                            9x:  213

                           10x:  124

                       11- 20x:  710

                       21- 50x:  423

                       51-100x:  213

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20202  Homo sapiens (Human)

       2      16704  Mus musculus (Mouse)

       3      13738  Arabidopsis thaliana (Mouse-ear cress)

       4       7918  Rattus norvegicus (Rat)

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

       6       5990  Bos taurus (Bovine)

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

       8       4433  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4131  Dictyostelium discoideum (Slime mold)

      11       3505  Caenorhabditis elegans

      12       3392  Xenopus laevis (African clawed frog)

      13       3332  Oryza sativa subsp. japonica (Rice)

      14       3243  Drosophila melanogaster (Fruit fly)

      15       2940  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2262  Gallus gallus (Chicken)

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

      18       2040  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2027  Escherichia coli O157:H7

      20       1887  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

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

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

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

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

      26       1680  Shigella flexneri

      27       1415  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1283  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       1052  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1025  Archaeoglobus fulgidus 

      34       1022  Yersinia pestis

      35        974  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

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

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

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

      39        925  Staphylococcus aureus (strain N315)

      40        925  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      41        910  Kluyveromyces lactis   

      42        909  Acanthamoeba polyphaga mimivirus (APMV)

      43        899  Staphylococcus aureus (strain COL)

      44        895  Staphylococcus aureus (strain MW2)

      45        892  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      46        889  Staphylococcus aureus (strain MSSA476)

      47        889  Oryctolagus cuniculus (Rabbit)

      48        888  Staphylococcus aureus (strain MRSA252)

      49        882  Salmonella choleraesuis (strain SC-B67)

      50        878  Shigella sonnei (strain Ss046)

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

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        841  Neurospora crassa 

      55        841  Escherichia coli O9:H4 (strain HS)

      56        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      57        829  Shigella boydii serotype 4 (strain Sb227)

      58        825  Escherichia coli (strain UTI89 / UPEC)

      59        822  Shigella dysenteriae serotype 1 (strain Sd197)

      60        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      61        811  Canis familiaris (Dog) (Canis lupus familiaris)

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

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

      64        788  Emericella nidulans  

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

      66        784  Aquifex aeolicus (strain VF5)

      67        776  Pasteurella multocida (strain Pm70)

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

      69        771  Escherichia coli (strain K12 / DH10B)

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

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

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

      73        762  Escherichia coli (strain 55989 / EAEC)

      74        761  Escherichia coli O8 (strain IAI1)

      75        760  Shigella flexneri serotype 5b (strain 8401)

      76        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      77        758  Staphylococcus epidermidis (strain ATCC 12228)

      78        756  Escherichia coli (strain SE11)

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

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

      81        750  Zea mays (Maize)

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

      83        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      84        742  Staphylococcus aureus (strain NCTC 8325)

      85        741  Bacillus halodurans 

      86        736  Bacillus anthracis

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

      88        733  Vibrio vulnificus (strain CMCP6)

      89        731  Escherichia coli O81 (strain ED1a)

      90        722  Salmonella enteritidis PT4 (strain P125109)

      91        717  Vibrio vulnificus (strain YJ016)

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

      93        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      94        715  Enterobacter sp. (strain 638)

      95        714  Escherichia coli O1:K1 / APEC

      96        714  Salmonella paratyphi A (strain AKU_12601)

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

      98        713  Salmonella agona (strain SL483)

      99        713  Salmonella newport (strain SL254)

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

     101        712  Salmonella schwarzengrund (strain CVM19633)

     102        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     103        710  Salmonella heidelberg (strain SL476)

     104        704  Pseudomonas putida (strain KT2440)

     105        702  Oryza sativa subsp. indica (Rice)

     106        702  Salmonella dublin (strain CT_02021853)

     107        698  Klebsiella pneumoniae (strain 342)

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

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

     110        691  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     111        689  Pan troglodytes (Chimpanzee)

     112        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

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

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

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

     116        674  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     117        670  Serratia proteamaculans (strain 568)

     118        668  Escherichia coli

     119        668  Mycobacterium leprae (strain TN)

     120        667  Yersinia pestis (strain Pestoides F)

     121        666  Staphylococcus aureus (strain USA300)

     122        661  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        660  Bradyrhizobium diazoefficiens 

     124        658  Rhizobium sp. (strain NGR234)

     125        653  Debaryomyces hansenii   

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

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

     128        643  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     129        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     130        638  Shewanella oneidensis (strain MR-1)

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

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

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

     134        620  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

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

     138        607  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     139        607  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

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

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

     142        602  Staphylococcus saprophyticus subsp. saprophyticus 

     143        601  Salmonella paratyphi C (strain RKS4594)

     144        600  Yersinia pestis bv. Antiqua (strain Angola)

     145        593  Bacillus cereus (strain ATCC 10987)

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

     147        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

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

     149        589  Pseudomonas aeruginosa (strain UCBPP-PA14)

     150        586  Rickettsia prowazekii (strain Madrid E)

     151        579  Neisseria meningitidis serogroup B (strain MC58)

     152        576  Brucella suis biovar 1 (strain 1330)

     153        573  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

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

     155        569  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     156        568  Caenorhabditis briggsae

     157        568  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        567  Pseudomonas syringae pv. syringae (strain B728a)

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

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

     161        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     162        562  Bacillus cereus (strain ZK / E33L)

     163        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     164        558  Clostridium acetobutylicum 

     165        556  Xanthomonas axonopodis pv. citri (strain 306)

     166        553  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     167        553  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     168        552  Pseudomonas fluorescens (strain Pf0-1)

     169        548  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

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

     171        539  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     172        535  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

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

     174        529  Sodalis glossinidius (strain morsitans)

     175        529  Listeria monocytogenes serotype 4b (strain F2365)

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

     177        522  Xylella fastidiosa (strain 9a5c)

     178        516  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     179        516  Chromobacterium violaceum 

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

     181        515  Corynebacterium glutamicum 

     182        515  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        511  Pseudomonas aeruginosa (strain PA7)

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

     185        509  Deinococcus radiodurans 

     186        508  Staphylococcus aureus (strain Newman)

     187        508  Geobacillus kaustophilus (strain HTA426)

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

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

     190        506  Streptomyces avermitilis 

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

     192        500  Pseudomonas entomophila (strain L48)

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

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

     195        496  Bacillus clausii (strain KSM-K16)

     196        495  Burkholderia pseudomallei (strain K96243)

     197        495  Haemophilus influenzae (strain 86-028NP)

     198        494  Proteus mirabilis (strain HI4320)

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

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

     201        492  Bacillus amyloliquefaciens subsp. plantarum 

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

     203        491  Xanthomonas campestris pv. campestris (strain 8004)

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

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

     206        487  Methanosarcina mazei  

     207        487  Shewanella sp. (strain MR-7)

     208        486  Mannheimia succiniciproducens (strain MBEL55E)

     209        484  Pseudomonas aeruginosa (strain LESB58)

     210        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     211        484  Thermosynechococcus elongatus (strain BP-1)

     212        484  Shewanella sp. (strain MR-4)

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

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

     215        481  Pyrococcus horikoshii 

     216        479  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

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

     218        478  Pseudomonas putida (strain F1 / ATCC 700007)

     219        477  Pyrococcus abyssi (strain GE5 / Orsay)

     220        477  Brucella abortus (strain 2308)

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

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

     223        468  Clostridium perfringens (strain 13 / Type A)

     224        467  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

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

     226        466  Shewanella frigidimarina (strain NCIMB 400)

     227        466  Pseudomonas putida (strain GB-1)

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

     229        465  Nicotiana tabacum (Common tobacco)

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

     231        464  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     232        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     233        464  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     234        463  Shewanella sp. (strain ANA-3)

     235        462  Burkholderia mallei (strain ATCC 23344)

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

     237        460  Enterococcus faecalis (strain ATCC 700802 / V583)

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

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

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

     241        456  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     242        455  Staphylococcus aureus (strain JH1)

     243        455  Ovis aries (Sheep)

     244        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     245        453  Pseudomonas putida (strain W619)

     246        452  Shewanella baltica (strain OS185)

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

     248        451  Aeromonas salmonicida (strain A449)

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

     250        450  Dechloromonas aromatica (strain RCB)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19338 (  4%)

    Bacteria         332008 ( 61%)

    Eukaryota        180086 ( 33%)

    Viruses           16532 (  3%)





   Within Eukaryota:



   



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

     Human                  20203 ( 11%)           (  4%)

     Other Mammalia         46128 ( 26%)           (  8%)

     Other Vertebrata       17791 ( 10%)           (  3%)

     Viridiplantae          36305 ( 20%)           (  7%)

     Fungi                  31485 ( 17%)           (  6%)

     Insecta                 8777 (  5%)           (  2%)

     Nematoda                4383 (  2%)           (  1%)

     Other                  15014 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9114             1001-1100     3812

                 51- 100   41877             1101-1200     2666

                101- 150   58346             1201-1300     2067

                151- 200   58231             1301-1400     1933

                201- 250   57087             1401-1500     1540

                251- 300   50707             1501-1600      758

                301- 350   50955             1601-1700      578

                351- 400   44098             1701-1800      488

                401- 450   36183             1801-1900      441

                451- 500   29040             1901-2000      360

                501- 550   20749             2001-2100      219

                551- 600   14864             2101-2200      299

                601- 650   12447             2201-2300      302

                651- 700    8992             2301-2400      187

                701- 750    7438             2401-2500      142

                751- 800    5321             >2500         1124

                801- 850    4635

                851- 900    5105

                901- 950    3938

                951-1000    2805



   





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



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

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





4.  JOURNAL CITATIONS



   Note: the following citation statistics reflect the number of distinct

         journal citations.



   Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2486





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  809

                       2x:  329

                       3x:  169

                       4x:  113

                       5x:  100

                       6x:   80

                       7x:   53

                       8x:   46

                       9x:   37

                      10x:   34

                  11- 20x:  206

                  21- 50x:  198

                  51-100x:  113

                    >100x:  199





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



   Nb    Citations   Journal name

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

    1        22509   Journal of Biological Chemistry

    2        10218   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6114   Journal of Bacteriology

    4         5259   Biochemical and Biophysical Research Communications

    5         4830   Biochemistry

    6         4732   Nucleic Acids Research

    7         4694   Gene

    8         4556   FEBS Letters

    9         4410   The EMBO Journal

   10         4087   Molecular and Cellular Biology

   11         3989   Nature

   12         3874   Journal of Molecular Biology

   13         3367   Biochimica et Biophysica Acta

   14         3306   European Journal of Biochemistry

   15         3224   Cell

   16         2744   Journal of Virology

   17         2675   Science

   18         2643   Biochemical Journal

   19         2517   Genomics

   20         2238   Molecular Microbiology

   21         2098   Plant Physiology

   22         1998   Journal of Cell Biology

   23         1795   The American Journal of Human Genetics

   24         1725   Plant Molecular Biology

   25         1696   Genes and Development

   26         1607   Nature Genetics

   27         1593   Virology

   28         1590   Human Molecular Genetics

   29         1559   The Plant Cell

   30         1482   Oncogene

   31         1456   Molecular Biology of the Cell

   32         1445   Development

   33         1423   The Plant Journal

   34         1395   Human Mutation

   35         1366   Molecular and General Genetics

   36         1302   Molecular Cell

   37         1280   Journal of Biochemistry

   38         1229   Journal of Immunology

   39         1182   Structure

   40         1165   Genetics

   41         1051   Journal of General Virology

   42         1045   Journal of Cell Science

   43         1040   Blood

   44         1029   PLoS ONE

   45         1024   Infection and Immunity

   46          973   Archives of Biochemistry and Biophysics

   47          960   Microbiology

   48          889   Developmental Biology

   49          879   Current Biology

   50          834   Cancer Research

   51          822   Yeast

   52          780   FEMS Microbiology Letters

   53          763   Acta Crystallographica, Section D

   54          734   Journal of Neuroscience

   55          732   Applied and Environmental Microbiology

   56          709   Protein Science

   57          705   Toxicon

   58          653   Human Genetics

   59          635   Nature Structural Biology

   60          634   Neuron

   61          629   Mechanisms of Development

   62          627   Journal of Clinical Investigation

   63          602   American Journal of Physiology

   64          558   The Journal of Experimental Medicine

   65          552   Current Genetics

   66          545   Proteins

   67          544   Plant and Cell Physiology

   68          505   Molecular Endocrinology

   69          493   Journal of Neurochemistry

   70          491   Journal of Medical Genetics

   71          484   Mammalian Genome

   72          483   Nature Cell Biology

   73          481   Bioscience, Biotechnology, and Biochemistry

   74          469   The Journal of Clinical Endocrinology and Metabolism

   75          463   Endocrinology

   76          460   Immunogenetics

   77          443   Molecular and Biochemical Parasitology

   78          406   Experimental Cell Research

   79          403   Journal of Molecular Evolution

   80          398   Nature Structural and Molecular Biology

   81          383   Molecular Biology and Evolution

   82          383   The FEBS Journal

   83          381   Peptides

   84          379   DNA and Cell Biology

   85          378   Antimicrobial Agents and Chemotherapy

   86          375   Developmental Cell

   87          368   DNA Sequence

   88          365   RNA

   89          364   Eukaryotic Cell

   90          347   Planta

   91          342   Journal of Investigative Dermatology

   92          332   Brain Research. Molecular Brain Research

   93          329   Molecular Pharmacology

   94          328   Comparative Biochemistry and Physiology

   95          325   Tissue Antigens

   96          308   Neurology

   97          300   Biology of Reproduction

   98          294   Biological Chemistry Hoppe-Seyler

   99          292   EMBO Reports

  100          286   The FASEB Journal

  101          285   PLoS Genetics

  102          285   Developmental Dynamics

  103          281   Cytogenetics and Cell Genetics

  104          279   Biochimie

  105          279   Immunity

  106          277   Journal of the American Chemical Society

  107          276   The New England Journal of Medicine

  108          276   Genes to Cells

  109          274   Virus Research

  110          273   Molecular Plant-Microbe Interactions

  111          273   Genome Research

  112          263   Journal of General Microbiology

  113          260   Acta Crystallographica, Section F

  114          253   European Journal of Human Genetics

  115          242   Annals of Neurology

  116          239   European Journal of Immunology

  117          235   Journal of Experimental Botany

  118          228   Investigative Ophthalmology and Visual Science

  119          222   Journal of Human Genetics

  120          221   BMC Genomics

  121          220   DNA Research

  122          219   Archives of Microbiology

  123          219   Nature Immunology

  124          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  125          212   American Journal of Medical Genetics. Part A

  126          207   Clinical Genetics

  127          206   Journal of Cellular Biochemistry

  128          203   Glycobiology

  129          202   Journal of Medicinal Chemistry

  130          196   Molecular and Cellular Endocrinology

  131          195   PLoS Pathogens

  132          195   Archives of Virology

  133          193   Circulation Research

  134          192   Molecular Immunology

  135          189   Diabetes

  136          188   Cell Cycle

  137          188   Traffic

  138          183   Applied Microbiology and Biotechnology

  139          182   Molecular Genetics and Metabolism

  140          176   Insect Biochemistry and Molecular Biology

  141          176   Phytochemistry

  142          175   Protein Expression and Purification

  143          171   International Journal of Cancer

  144          170   Molecular Phylogenetics and Evolution

  145          168   American Journal of Medical Genetics

  146          168   PLoS Biology

  147          165   Journal of Lipid Research

  148          164   Proteomics

  149          163   Molecular and Cellular Neuroscience

  150          163   Biological Chemistry





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)                      1101112                 2.01                                         

   Journal                            906896     435841      1.66       1                                 

   Submitted to EMBL/GenBank/DDBJ     184109     162780      0.34       2                                 

   Submitted to other databases         7078       6566      0.01       3                                 

   Book citation                        1467       1453     <0.01       4                                 

   Plant Gene Register                   598        586     <0.01       5                                 

   Thesis                                426        423     <0.01       6                                 

   Unpublished observations              341        337     <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: 360916



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2536268                 4.63                                         

   ALLERGEN                              664        664     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24142      24142      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6385       6385      0.01      21                                 

   BIOTECHNOLOGY                         435        433     <0.01      28                                 

   CATALYTIC ACTIVITY                 253683     228839      0.46       5                                 

   CAUTION                             10105       9912      0.02      18                                 

   COFACTOR                           116995     107100      0.21       7                                 

   DEVELOPMENTAL STAGE                 10464      10464      0.02      17                                 

   DISEASE                              5921       3981      0.01      22                                 

   DISRUPTION PHENOTYPE                 8357       8357      0.02      19                                 

   DOMAIN                              42844      37181      0.08       9                                 

   ENZYME REGULATION                   13074      13074      0.02      16                                 

   FUNCTION                           440034     422081      0.80       2                                 

   INDUCTION                           17108      17108      0.03      14                                 

   INTERACTION                         13303      13303      0.02      15                                 

   MASS SPECTROMETRY                    5870       4467      0.01      23                                 

   MISCELLANEOUS                       34378      31591      0.06      12                                 

   PATHWAY                            134618     122057      0.25       6                                 

   PHARMACEUTICAL                         99         99     <0.01      29                                 

   POLYMORPHISM                         1042        985     <0.01      24                                 

   PTM                                 48442      37079      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42375      42375      0.08      10                                 

   SIMILARITY                         660808     523039      1.21       1                                 

   SUBCELLULAR LOCATION               335868     329318      0.61       3                                 

   SUBUNIT                            258483     258483      0.47       4                                 

   TISSUE SPECIFICITY                  41253      41253      0.08      11                                 

   TOXIC DOSE                            604        558     <0.01      27                                 

   WEB RESOURCE                         8287       6940      0.02      20                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        4010740                 7.32                                         

   ACT_SITE                           152146      93192      0.28      10                                 

   BINDING                            340966      90005      0.62       4                                 

   CA_BIND                              3984       1677      0.01      35                                 

   CARBOHYD                           109702      28187      0.20      15                                 

   CHAIN                              555423     541599      1.01       1                                 

   COILED                              20991      14474      0.04      26                                 

   COMPBIAS                            56611      30200      0.10      18                                 

   CONFLICT                           130867      45803      0.24      13                                 

   CROSSLNK                             7216       4107      0.01      34                                 

   DISULFID                           115671      31569      0.21      14                                 

   DNA_BIND                            10796       9800      0.02      31                                 

   DOMAIN                             175162     106143      0.32       8                                 

   HELIX                              204621      19453      0.37       6                                 

   INIT_MET                            17956      17956      0.03      27                                 

   INTRAMEM                             2318       1020     <0.01      37                                 

   LIPID                               12262       7866      0.02      30                                 

   METAL                              347191      86138      0.63       3                                 

   MOD_RES                            185478      64077      0.34       7                                 

   MOTIF                               38690      24997      0.07      24                                 

   MUTAGEN                             51861      11836      0.09      19                                 

   NON_CONS                             2052        757     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12273       9381      0.02      29                                 

   NP_BIND                            134788      78768      0.25      11                                 

   PEPTIDE                             10516       7198      0.02      32                                 

   PROPEP                              13062      11256      0.02      28                                 

   REGION                             167069      80128      0.30       9                                 

   REPEAT                              98886      14339      0.18      16                                 

   SIGNAL                              39571      39561      0.07      23                                 

   SITE                                50366      28035      0.09      21                                 

   STRAND                             213961      18347      0.39       5                                 

   TOPO_DOM                           134316      27593      0.25      12                                 

   TRANSIT                              8838       8725      0.02      33                                 

   TRANSMEM                           362099      74938      0.66       2                                 

   TURN                                49498      15769      0.09      22                                 

   UNSURE                               3643        734      0.01      36                                 

   VAR_SEQ                             50368      21149      0.09      20                                 

   VARIANT                             89333      16960      0.16      17                                 

   ZN_FING                             29831      13177      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)               17515074                31.96                                                           

   Allergome                            1639       1065     <0.01     105      Protein family/group databases               

   ArachnoServer                         789        781     <0.01     115      Organism-specific databases                  

   Bgee                                38841      38841      0.07      51      Gene expression databases                    

   BindingDB                            5473       5473      0.01      88      Chemistry                                    

   BioCyc                             324815     307600      0.59      20      Enzyme and pathway databases                 

   BioGrid                             40719      40351      0.07      50      Protein-protein interaction databases        

   BRENDA                               4378       4365      0.01      95      Enzyme and pathway databases                 

   CAZy                                 7789       7010      0.01      79      Protein family/group databases               

   CCDS                                45688      33436      0.08      47      Sequence databases                           

   CGD                                   958        929     <0.01     111      Organism-specific databases                  

   ChEMBL                               6008       6008      0.01      84      Chemistry                                    

   ChiTaRS                             16450      16441      0.03      70      Other                                        

   CleanEx                             30060      29421      0.05      56      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     130      2D gel databases                             

   ConoServer                            949        866     <0.01     112      Organism-specific databases                  

   CTD                                 72425      71732      0.13      40      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      86      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     128      PTM databases                                

   dictyBase                            4207       4092      0.01      97      Organism-specific databases                  

   DIP                                 15992      15931      0.03      72      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     120      3D structure databases                       

   DMDM                                16400      16400      0.03      71      Polymorphism databases                       

   DNASU                               18791      18721      0.03      66      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     129      2D gel databases                             

   DrugBank                            11195       1762      0.02      76      Chemistry                                    

   EchoBASE                             4161       4161      0.01      98      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      96      Organism-specific databases                  

   eggNOG                             431416     431416      0.79      13      Phylogenomic databases                       

   EMBL                               963157     536740      1.76       3      Sequence databases                           

   Ensembl                             82907      48342      0.15      38      Genome annotation databases                  

   EnsemblBacteria                    352456     333739      0.64      19      Genome annotation databases                  

   EnsemblFungi                        19316      18979      0.04      64      Genome annotation databases                  

   EnsemblMetazoa                      12635       9479      0.02      75      Genome annotation databases                  

   EnsemblPlants                       20350      17371      0.04      61      Genome annotation databases                  

   EnsemblProtists                      4440       4315      0.01      94      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     132      Organism-specific databases                  

   EuPathDB                              819        819     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16509      16508      0.03      69      Other                                        

   ExpressionAtlas                     33697      33697      0.06      52      Gene expression databases                    

   FlyBase                              5945       5571      0.01      85      Organism-specific databases                  

   Gene3D                             463649     341722      0.85       9      Family and domain databases                  

   GeneCards                           20869      19794      0.04      60      Organism-specific databases                  

   GeneFarm                             3373       3361      0.01      99      Organism-specific databases                  

   GeneID                             499401     470464      0.91       7      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     110      Organism-specific databases                  

   GeneTree                            55172      55148      0.10      46      Phylogenomic databases                       

   Genevestigator                      68680      68680      0.13      42      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      77      Other                                        

   GenoList                             7074       7062      0.01      80      Organism-specific databases                  

   GenomeRNAi                          21690      21690      0.04      59      Other                                        

   GO                                2627568     519314      4.80       1      Ontologies                                   

   Gramene                              6260       6260      0.01      82      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2068       2067     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      87      Organism-specific databases                  

   HAMAP                              324381     321429      0.59      21      Family and domain databases                  

   HGNC                                20008      19846      0.04      63      Organism-specific databases                  

   HOGENOM                            386297     386297      0.70      17      Phylogenomic databases                       

   HOVERGEN                            75681      75681      0.14      39      Phylogenomic databases                       

   HPA                                 24723      16226      0.05      58      Organism-specific databases                  

   InParanoid                         135115     135115      0.25      28      Phylogenomic databases                       

   IntAct                              43276      43276      0.08      49      Protein-protein interaction databases        

   InterPro                          1908624     527026      3.48       2      Family and domain databases                  

   KEGG                               475352     449783      0.87       8      Genome annotation databases                  

   KO                                 379401     378910      0.69      18      Phylogenomic databases                       

   LegioList                             765        763     <0.01     117      Organism-specific databases                  

   Leproma                               671        668     <0.01     118      Organism-specific databases                  

   MaizeGDB                              503        498     <0.01     122      Organism-specific databases                  

   MaxQB                               31648      31648      0.06      54      Proteomic databases                          

   MEROPS                              12861      12861      0.02      74      Protein family/group databases               

   MGI                                 16620      16576      0.03      68      Organism-specific databases                  

   MIM                                 19153      14160      0.03      65      Organism-specific databases                  

   MINT                                31611      31611      0.06      55      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     131      Protein family/group databases               

   mycoCLAP                              306        297     <0.01     126      Protein family/group databases               

   NextBio                             71306      71306      0.13      41      Other                                        

   neXtProt                            20059      20059      0.04      62      Organism-specific databases                  

   OGP                                   376        376     <0.01     125      2D gel databases                             

   OMA                                408146     408146      0.74      14      Phylogenomic databases                       

   Orphanet                             6148       3289      0.01      83      Organism-specific databases                  

   OrthoDB                            389557     389557      0.71      16      Phylogenomic databases                       

   PANTHER                            179396     172513      0.33      25      Family and domain databases                  

   PATRIC                             307864     307832      0.56      22      Genome annotation databases                  

   PaxDb                               66662      66661      0.12      43      Proteomic databases                          

   PDB                                112263      21826      0.20      33      3D structure databases                       

   PDBsum                             112263      21826      0.20      32      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      90      Proteomic databases                          

   PeroxiBase                            770        754     <0.01     116      Protein family/group databases               

   Pfam                               740412     507995      1.35       4      Family and domain databases                  

   PharmGKB                            18391      18359      0.03      67      Organism-specific databases                  

   PhosphoSite                         33557      33557      0.06      53      PTM databases                                

   PhylomeDB                           93839      93839      0.17      36      Phylogenomic databases                       

   PIR                                122079     111846      0.22      31      Sequence databases                           

   PIRSF                              102387     101425      0.19      35      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     106      Other                                        

   PomBase                              5127       5091      0.01      91      Organism-specific databases                  

   PRIDE                              122418     122418      0.22      30      Proteomic databases                          

   PRINTS                             136824     120518      0.25      27      Family and domain databases                  

   PRO                                 58122      58122      0.11      45      Other                                        

   ProDom                              29254      29075      0.05      57      Family and domain databases                  

   ProMEX                                399        399     <0.01     124      Proteomic databases                          

   PROSITE                            447042     288281      0.82      10      Family and domain databases                  

   ProteinModelPortal                 441652     441652      0.81      12      3D structure databases                       

   Proteomes                          507446     481954      0.93       6      Other                                        

   PseudoCAP                            1291       1282     <0.01     107      Organism-specific databases                  

   Reactome                            87724      26707      0.16      37      Enzyme and pathway databases                 

   REBASE                                406        406     <0.01     123      Protein family/group databases               

   RefSeq                             650358     480422      1.19       5      Sequence databases                           

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

   RGD                                  7841       7837      0.01      78      Organism-specific databases                  

   SABIO-RK                             3002       3002      0.01     100      Enzyme and pathway databases                 

   SGD                                  6737       6732      0.01      81      Organism-specific databases                  

   SignaLink                            2976       2965      0.01     101      Enzyme and pathway databases                 

   SMART                              170257     127528      0.31      26      Family and domain databases                  

   SMR                                224118     224118      0.41      24      3D structure databases                       

   STRING                             403216     403215      0.74      15      Protein-protein interaction databases        

   SUPFAM                             442590     340350      0.81      11      Family and domain databases                  

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

   TAIR                                13721      13665      0.03      73      Organism-specific databases                  

   TCDB                                 5394       5373      0.01      89      Protein family/group databases               

   TIGRFAMs                           291414     271231      0.53      23      Family and domain databases                  

   TreeFam                             44804      44799      0.08      48      Phylogenomic databases                       

   TubercuList                          2063       2027     <0.01     104      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     121      2D gel databases                             

   UCSC                                59375      44810      0.11      44      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     127      PTM databases                                

   UniGene                            103208      92974      0.19      34      Sequence databases                           

   UniPathway                         134408     121856      0.25      29      Enzyme and pathway databases                 

   VectorBase                            615        597     <0.01     119      Genome annotation databases                  

   World-2DPAGE                          922        911     <0.01     113      2D gel databases                             

   WormBase                             5098       4035      0.01      92      Organism-specific databases                  

   Xenbase                              4769       4763      0.01      93      Organism-specific databases                  

   ZFIN                                 2779       2779      0.01     102      Organism-specific databases                  



Total number of cross-referenced databases: 132



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



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

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

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

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

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



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



   



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

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





   6.2  Classification of the amino acids by their frequency



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

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4464 entries are encoded on a mitochondrion, and 3814 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: 76561