UniProtKB/Swiss-Prot protein knowledgebase release 2015_04 statistics





1.  INTRODUCTION



Release 2015_04 of 01-Apr-15 of UniProtKB/Swiss-Prot contains 548208 sequence entries,

comprising 195282524 amino acids abstracted from 235893 references. 



247 sequences have been added since release 2015_03, the sequence data of

51 existing entries has been updated and the annotations of

318715 entries have been revised.



Number of fragments: 9118

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38661





Protein existence (PE):           entries     %



1: Evidence at protein level        85854   15.7%

2: Evidence at transcript level     62618   11.4%

3: Inferred from homology          386290   70.5%

4: Predicted                        11480    2.1%

5: Uncertain                         1966    0.4%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 13198



   The first twenty species represent 116098 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: 1017

                            4x:  654

                            5x:  486

                            6x:  403

                            7x:  289

                            8x:  225

                            9x:  214

                           10x:  122

                       11- 20x:  710

                       21- 50x:  425

                       51-100x:  213

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20204  Homo sapiens (Human)

       2      16707  Mus musculus (Mouse)

       3      13822  Arabidopsis thaliana (Mouse-ear cress)

       4       7921  Rattus norvegicus (Rat)

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

       6       5991  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       3518  Caenorhabditis elegans

      12       3392  Xenopus laevis (African clawed frog)

      13       3334  Oryza sativa subsp. japonica (Rice)

      14       3245  Drosophila melanogaster (Fruit fly)

      15       2941  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2262  Gallus gallus (Chicken)

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

      18       2057  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2027  Escherichia coli O157:H7

      20       1888  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1781  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       1243  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

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

      32       1053  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1026  Archaeoglobus fulgidus 

      34       1022  Yersinia pestis

      35        980  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        790  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        752  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        704  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        690  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        662  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        661  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        592  Listeria innocua serovar 6a (strain CLIP 11262)

     147        591  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     148        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     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        570  Caenorhabditis briggsae

     156        569  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     157        568  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        568  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     159        567  Pseudomonas syringae pv. syringae (strain B728a)

     160        566  Vibrio fischeri (strain ATCC 700601 / ES114)

     161        564  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     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        540  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        490  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           19340 (  4%)

    Bacteria         332062 ( 61%)

    Eukaryota        180260 ( 33%)

    Viruses           16546 (  3%)





   Within Eukaryota:



   



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

     Human                  20205 ( 11%)           (  4%)

     Other Mammalia         46136 ( 26%)           (  8%)

     Other Vertebrata       17805 ( 10%)           (  3%)

     Viridiplantae          36397 ( 20%)           (  7%)

     Fungi                  31512 ( 17%)           (  6%)

     Insecta                 8780 (  5%)           (  2%)

     Nematoda                4398 (  2%)           (  1%)

     Other                  15027 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9115             1001-1100     3815

                 51- 100   41891             1101-1200     2668

                101- 150   58361             1201-1300     2067

                151- 200   58248             1301-1400     1933

                201- 250   57122             1401-1500     1540

                251- 300   50725             1501-1600      758

                301- 350   50968             1601-1700      580

                351- 400   44115             1701-1800      488

                401- 450   36204             1801-1900      442

                451- 500   29056             1901-2000      360

                501- 550   20771             2001-2100      220

                551- 600   14879             2101-2200      299

                601- 650   12451             2201-2300      301

                651- 700    8996             2301-2400      187

                701- 750    7441             2401-2500      142

                751- 800    5331             >2500         1130

                801- 850    4637

                851- 900    5105

                901- 950    3939

                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: 2493





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  812

                       2x:  328

                       3x:  171

                       4x:  115

                       5x:  100

                       6x:   79

                       7x:   52

                       8x:   48

                       9x:   35

                      10x:   35

                  11- 20x:  206

                  21- 50x:  200

                  51-100x:  112

                    >100x:  200





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



   Nb    Citations   Journal name

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

    1        22557   Journal of Biological Chemistry

    2        10252   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6127   Journal of Bacteriology

    4         5268   Biochemical and Biophysical Research Communications

    5         4838   Biochemistry

    6         4745   Nucleic Acids Research

    7         4699   Gene

    8         4560   FEBS Letters

    9         4417   The EMBO Journal

   10         4098   Molecular and Cellular Biology

   11         4002   Nature

   12         3880   Journal of Molecular Biology

   13         3372   Biochimica et Biophysica Acta

   14         3307   European Journal of Biochemistry

   15         3229   Cell

   16         2774   Journal of Virology

   17         2686   Science

   18         2652   Biochemical Journal

   19         2517   Genomics

   20         2246   Molecular Microbiology

   21         2111   Plant Physiology

   22         1999   Journal of Cell Biology

   23         1801   The American Journal of Human Genetics

   24         1732   Plant Molecular Biology

   25         1702   Genes and Development

   26         1610   Nature Genetics

   27         1596   Virology

   28         1595   Human Molecular Genetics

   29         1569   The Plant Cell

   30         1482   Oncogene

   31         1467   Molecular Biology of the Cell

   32         1450   Development

   33         1433   The Plant Journal

   34         1398   Human Mutation

   35         1368   Molecular and General Genetics

   36         1310   Molecular Cell

   37         1283   Journal of Biochemistry

   38         1233   Journal of Immunology

   39         1183   Structure

   40         1174   Genetics

   41         1052   Journal of General Virology

   42         1051   Journal of Cell Science

   43         1044   Blood

   44         1040   PLoS ONE

   45         1026   Infection and Immunity

   46          974   Archives of Biochemistry and Biophysics

   47          962   Microbiology

   48          891   Developmental Biology

   49          882   Current Biology

   50          834   Cancer Research

   51          823   Yeast

   52          780   FEMS Microbiology Letters

   53          764   Acta Crystallographica, Section D

   54          735   Applied and Environmental Microbiology

   55          734   Journal of Neuroscience

   56          709   Protein Science

   57          708   Toxicon

   58          653   Human Genetics

   59          635   Nature Structural Biology

   60          635   Neuron

   61          629   Mechanisms of Development

   62          628   Journal of Clinical Investigation

   63          603   American Journal of Physiology

   64          560   The Journal of Experimental Medicine

   65          554   Current Genetics

   66          547   Plant and Cell Physiology

   67          547   Proteins

   68          506   Molecular Endocrinology

   69          494   Journal of Neurochemistry

   70          492   Journal of Medical Genetics

   71          484   Mammalian Genome

   72          484   Nature Cell Biology

   73          484   Bioscience, Biotechnology, and Biochemistry

   74          469   The Journal of Clinical Endocrinology and Metabolism

   75          464   Endocrinology

   76          460   Immunogenetics

   77          443   Molecular and Biochemical Parasitology

   78          409   Experimental Cell Research

   79          404   Nature Structural and Molecular Biology

   80          403   Journal of Molecular Evolution

   81          386   Antimicrobial Agents and Chemotherapy

   82          386   The FEBS Journal

   83          384   Molecular Biology and Evolution

   84          381   Peptides

   85          379   DNA and Cell Biology

   86          376   Developmental Cell

   87          373   Eukaryotic Cell

   88          368   DNA Sequence

   89          366   RNA

   90          347   Planta

   91          342   Journal of Investigative Dermatology

   92          333   Brain Research. Molecular Brain Research

   93          330   Molecular Pharmacology

   94          328   Comparative Biochemistry and Physiology

   95          325   Tissue Antigens

   96          310   Neurology

   97          300   Biology of Reproduction

   98          294   Biological Chemistry Hoppe-Seyler

   99          294   PLoS Genetics

  100          294   EMBO Reports

  101          288   The FASEB Journal

  102          285   Developmental Dynamics

  103          282   Immunity

  104          281   Biochimie

  105          281   Cytogenetics and Cell Genetics

  106          279   Journal of the American Chemical Society

  107          278   Genes to Cells

  108          277   The New England Journal of Medicine

  109          276   Virus Research

  110          275   Molecular Plant-Microbe Interactions

  111          274   Genome Research

  112          263   Journal of General Microbiology

  113          261   Acta Crystallographica, Section F

  114          256   European Journal of Human Genetics

  115          244   Annals of Neurology

  116          240   European Journal of Immunology

  117          239   Journal of Experimental Botany

  118          229   Investigative Ophthalmology and Visual Science

  119          223   BMC Genomics

  120          222   Journal of Human Genetics

  121          220   DNA Research

  122          219   Archives of Microbiology

  123          219   Nature Immunology

  124          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  125          214   American Journal of Medical Genetics. Part A

  126          208   Journal of Cellular Biochemistry

  127          207   Clinical Genetics

  128          203   Glycobiology

  129          202   Journal of Medicinal Chemistry

  130          201   PLoS Pathogens

  131          196   Molecular and Cellular Endocrinology

  132          195   Archives of Virology

  133          194   Circulation Research

  134          192   Molecular Immunology

  135          191   Traffic

  136          189   Diabetes

  137          189   Cell Cycle

  138          186   Applied Microbiology and Biotechnology

  139          182   Molecular Genetics and Metabolism

  140          176   Insect Biochemistry and Molecular Biology

  141          176   Protein Expression and Purification

  142          176   Phytochemistry

  143          171   International Journal of Cancer

  144          170   PLoS Biology

  145          170   Molecular Phylogenetics and Evolution

  146          168   American Journal of Medical Genetics

  147          165   Journal of Lipid Research

  148          165   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)                      1102938                 2.01                                         

   Journal                            908895     436484      1.66       1                                 

   Submitted to EMBL/GenBank/DDBJ     183917     162489      0.34       2                                 

   Submitted to other databases         7081       6568      0.01       3                                 

   Book citation                        1483       1469     <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: 361899



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2539094                 4.63                                         

   ALLERGEN                              664        664     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24178      24178      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6430       6430      0.01      21                                 

   BIOTECHNOLOGY                         438        436     <0.01      28                                 

   CATALYTIC ACTIVITY                 253931     228930      0.46       5                                 

   CAUTION                             10128       9936      0.02      18                                 

   COFACTOR                           117068     107172      0.21       7                                 

   DEVELOPMENTAL STAGE                 10503      10503      0.02      17                                 

   DISEASE                              5948       4002      0.01      22                                 

   DISRUPTION PHENOTYPE                 8482       8482      0.02      19                                 

   DOMAIN                              42929      37255      0.08       9                                 

   ENZYME REGULATION                   13102      13102      0.02      16                                 

   FUNCTION                           440379     422392      0.80       2                                 

   INDUCTION                           17179      17179      0.03      14                                 

   INTERACTION                         13307      13307      0.02      15                                 

   MASS SPECTROMETRY                    5908       4479      0.01      23                                 

   MISCELLANEOUS                       34450      31660      0.06      12                                 

   PATHWAY                            134661     122099      0.25       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1045        987     <0.01      24                                 

   PTM                                 48632      37201      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42462      42462      0.08      10                                 

   SIMILARITY                         661245     523313      1.21       1                                 

   SUBCELLULAR LOCATION               336126     329563      0.61       3                                 

   SUBUNIT                            258944     258944      0.47       4                                 

   TISSUE SPECIFICITY                  41338      41338      0.08      11                                 

   TOXIC DOSE                            605        559     <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)                        4016930                 7.33                                         

   ACT_SITE                           152224      93242      0.28      10                                 

   BINDING                            341230      90114      0.62       4                                 

   CA_BIND                              3985       1678      0.01      35                                 

   CARBOHYD                           109819      28209      0.20      15                                 

   CHAIN                              555684     541841      1.01       1                                 

   COILED                              21015      14489      0.04      26                                 

   COMPBIAS                            56653      30234      0.10      18                                 

   CONFLICT                           131028      45853      0.24      13                                 

   CROSSLNK                             7600       4164      0.01      34                                 

   DISULFID                           115789      31601      0.21      14                                 

   DNA_BIND                            10811       9815      0.02      31                                 

   DOMAIN                             175469     106361      0.32       8                                 

   HELIX                              205682      19540      0.38       6                                 

   INIT_MET                            17960      17960      0.03      27                                 

   INTRAMEM                             2340       1021     <0.01      37                                 

   LIPID                               12280       7884      0.02      29                                 

   METAL                              347314      86203      0.63       3                                 

   MOD_RES                            185555      64071      0.34       7                                 

   MOTIF                               38725      25017      0.07      24                                 

   MUTAGEN                             52125      11904      0.10      19                                 

   NON_CONS                             2051        757     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12274       9383      0.02      30                                 

   NP_BIND                            134831      78793      0.25      11                                 

   PEPTIDE                             10574       7209      0.02      32                                 

   PROPEP                              13075      11267      0.02      28                                 

   REGION                             167632      80297      0.31       9                                 

   REPEAT                              99198      14355      0.18      16                                 

   SIGNAL                              39619      39609      0.07      23                                 

   SITE                                50405      28051      0.09      21                                 

   STRAND                             214926      18433      0.39       5                                 

   TOPO_DOM                           134405      27607      0.25      12                                 

   TRANSIT                              8858       8745      0.02      33                                 

   TRANSMEM                           362424      75116      0.66       2                                 

   TURN                                49736      15845      0.09      22                                 

   UNSURE                               3643        734      0.01      36                                 

   VAR_SEQ                             50411      21174      0.09      20                                 

   VARIANT                             89387      16964      0.16      17                                 

   ZN_FING                             29835      13180      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)               17287071                31.53                                                           

   Allergome                            1639       1065     <0.01     105      Protein family/group databases               

   ArachnoServer                         789        781     <0.01     115      Organism-specific databases                  

   Bgee                                38840      38840      0.07      51      Gene expression databases                    

   BindingDB                            5472       5472      0.01      89      Chemistry                                    

   BioCyc                             324897     307663      0.59      19      Enzyme and pathway databases                 

   BioGrid                             40739      40371      0.07      50      Protein-protein interaction databases        

   BRENDA                              12674      11907      0.02      75      Enzyme and pathway databases                 

   CAZy                                 7801       7020      0.01      80      Protein family/group databases               

   CCDS                                45685      33432      0.08      47      Sequence databases                           

   CGD                                   965        935     <0.01     111      Organism-specific databases                  

   ChEMBL                               6158       6158      0.01      84      Chemistry                                    

   ChiTaRS                             16452      16443      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                                 72448      71755      0.13      40      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      87      Organism-specific databases                  

   DEPOD                                 239        239     <0.01     128      PTM databases                                

   dictyBase                            4207       4091      0.01      97      Organism-specific databases                  

   DIP                                 15989      15929      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                               18800      18730      0.03      66      Protocols and materials databases            

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

   DrugBank                            11213       1762      0.02      77      Chemistry                                    

   EchoBASE                             4161       4161      0.01      98      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      96      Organism-specific databases                  

   eggNOG                             431530     431530      0.79      11      Phylogenomic databases                       

   EMBL                               963956     536980      1.76       3      Sequence databases                           

   Ensembl                             82909      48348      0.15      38      Genome annotation databases                  

   EnsemblBacteria                    343315     325101      0.63      18      Genome annotation databases                  

   EnsemblFungi                        19328      18990      0.04      64      Genome annotation databases                  

   EnsemblMetazoa                      12670       9497      0.02      76      Genome annotation databases                  

   EnsemblPlants                       20453      17459      0.04      61      Genome annotation databases                  

   EnsemblProtists                      4440       4315      0.01      95      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     132      Organism-specific databases                  

   EuPathDB                              820        820     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16507      16507      0.03      69      Other                                        

   ExpressionAtlas                     33846      33846      0.06      52      Gene expression databases                    

   FlyBase                              5947       5573      0.01      86      Organism-specific databases                  

   Gene3D                             463713     341784      0.85       8      Family and domain databases                  

   GeneCards                           20869      19793      0.04      60      Organism-specific databases                  

   GeneFarm                             3373       3361      0.01      99      Organism-specific databases                  

   GeneID                             306177     287671      0.56      22      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     110      Organism-specific databases                  

   GeneTree                            55196      55172      0.10      46      Phylogenomic databases                       

   Genevestigator                      68755      68755      0.13      42      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      78      Other                                        

   GenoList                             7075       7063      0.01      81      Organism-specific databases                  

   GenomeRNAi                          21692      21692      0.04      59      Other                                        

   GO                                2644203     519638      4.82       1      Ontologies                                   

   Gramene                              6265       6265      0.01      83      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2068       2067     <0.01     104      Chemistry                                    

   H-InvDB                              5590       4770      0.01      88      Organism-specific databases                  

   HAMAP                              324414     321460      0.59      20      Family and domain databases                  

   HGNC                                20012      19850      0.04      63      Organism-specific databases                  

   HOGENOM                            387297     387297      0.71      15      Phylogenomic databases                       

   HOVERGEN                            75690      75690      0.14      39      Phylogenomic databases                       

   HPA                                 24721      16225      0.05      58      Organism-specific databases                  

   InParanoid                         135165     135165      0.25      28      Phylogenomic databases                       

   IntAct                              43299      43299      0.08      49      Protein-protein interaction databases        

   InterPro                          1910680     527259      3.49       2      Family and domain databases                  

   KEGG                               485414     458052      0.89       7      Genome annotation databases                  

   KO                                 380060     379570      0.69      16      Phylogenomic databases                       

   LegioList                             765        763     <0.01     117      Organism-specific databases                  

   Leproma                               671        668     <0.01     118      Organism-specific databases                  

   MaizeGDB                              505        500     <0.01     122      Organism-specific databases                  

   MaxQB                               31649      31649      0.06      54      Proteomic databases                          

   MEROPS                              12867      12867      0.02      74      Protein family/group databases               

   MGI                                 16623      16579      0.03      68      Organism-specific databases                  

   MIM                                 19220      14197      0.04      65      Organism-specific databases                  

   MINT                                31616      31616      0.06      55      Protein-protein interaction databases        

   MoonProt                               63         63     <0.01     131      Protein family/group databases               

   mycoCLAP                              322        317     <0.01     126      Protein family/group databases               

   NextBio                             71324      71324      0.13      41      Other                                        

   neXtProt                            20056      20056      0.04      62      Organism-specific databases                  

   OGP                                   376        376     <0.01     125      2D gel databases                             

   OMA                                408330     408330      0.74      12      Phylogenomic databases                       

   Orphanet                             6148       3289      0.01      85      Organism-specific databases                  

   OrthoDB                            390025     390025      0.71      14      Phylogenomic databases                       

   PANTHER                            180987     173976      0.33      25      Family and domain databases                  

   PATRIC                             307902     307867      0.56      21      Genome annotation databases                  

   PaxDb                               66681      66680      0.12      43      Proteomic databases                          

   PDB                                112335      21835      0.20      33      3D structure databases                       

   PDBsum                             112335      21835      0.20      32      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      91      Proteomic databases                          

   PeroxiBase                            770        754     <0.01     116      Protein family/group databases               

   Pfam                               740304     507872      1.35       4      Family and domain databases                  

   PharmGKB                            18391      18359      0.03      67      Organism-specific databases                  

   PhosphoSite                         33556      33556      0.06      53      PTM databases                                

   PhylomeDB                           93935      93935      0.17      36      Phylogenomic databases                       

   PIR                                122155     111916      0.22      31      Sequence databases                           

   PIRSF                              104173     103144      0.19      34      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     106      Other                                        

   PomBase                              5139       5103      0.01      92      Organism-specific databases                  

   PRIDE                              123356     123356      0.23      30      Proteomic databases                          

   PRINTS                             136825     120545      0.25      27      Family and domain databases                  

   PRO                                 58146      58146      0.11      45      Other                                        

   ProDom                              29261      29082      0.05      57      Family and domain databases                  

   ProMEX                                402        402     <0.01     124      Proteomic databases                          

   PROSITE                            447910     288558      0.82       9      Family and domain databases                  

   ProteinModelPortal                 373374     373374      0.68      17      3D structure databases                       

   Proteomes                          507417     481798      0.93       6      Other                                        

   PseudoCAP                            1291       1282     <0.01     107      Organism-specific databases                  

   Reactome                            87903      26447      0.16      37      Enzyme and pathway databases                 

   REBASE                                407        407     <0.01     123      Protein family/group databases               

   RefSeq                             645632     480646      1.18       5      Sequence databases                           

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

   RGD                                  7844       7840      0.01      79      Organism-specific databases                  

   SABIO-RK                             3003       3003      0.01     100      Enzyme and pathway databases                 

   SGD                                  6737       6732      0.01      82      Organism-specific databases                  

   SignaLink                            2985       2970      0.01     101      Enzyme and pathway databases                 

   SMART                              170366     127612      0.31      26      Family and domain databases                  

   SMR                                224338     224338      0.41      24      3D structure databases                       

   STRING                             403759     403759      0.74      13      Protein-protein interaction databases        

   SUPFAM                             441789     340685      0.81      10      Family and domain databases                  

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

   TAIR                                13805      13749      0.03      73      Organism-specific databases                  

   TCDB                                 5395       5374      0.01      90      Protein family/group databases               

   TIGRFAMs                           291412     271233      0.53      23      Family and domain databases                  

   TreeFam                             44810      44805      0.08      48      Phylogenomic databases                       

   TubercuList                          2078       2042     <0.01     103      Organism-specific databases                  

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

   UCSC                                59387      44822      0.11      44      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     127      PTM databases                                

   UniGene                            103367      93083      0.19      35      Sequence databases                           

   UniPathway                         134450     121897      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                             5124       4050      0.01      93      Organism-specific databases                  

   Xenbase                              4769       4763      0.01      94      Organism-specific databases                  

   ZFIN                                 2780       2780      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 3815 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: 76674