UniProtKB/Swiss-Prot protein knowledgebase release 2014_11 statistics





1.  INTRODUCTION



Release 2014_11 of 26-Nov-14 of UniProtKB/Swiss-Prot contains 547085 sequence entries,

comprising 194742747 amino acids abstracted from 232844 references. 



307 sequences have been added since release 2014_10, the sequence data of

19 existing entries has been updated and the annotations of

203542 entries have been revised.



Number of fragments: 9122

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 38434





Protein existence (PE):           entries     %



1: Evidence at protein level        84836   15.5%

2: Evidence at transcript level     62784   11.5%

3: Inferred from homology          385983   70.6%

4: Predicted                        11518    2.1%

5: Uncertain                         1964    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: 13161



   The first twenty species represent 115526 sequences:  21.1 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5477

                            2x: 1899

                            3x: 1011

                            4x:  657

                            5x:  479

                            6x:  398

                            7x:  290

                            8x:  224

                            9x:  213

                           10x:  122

                       11- 20x:  711

                       21- 50x:  422

                       51-100x:  212

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20193  Homo sapiens (Human)

       2      16689  Mus musculus (Mouse)

       3      13414  Arabidopsis thaliana (Mouse-ear cress)

       4       7914  Rattus norvegicus (Rat)

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

       6       5988  Bos taurus (Bovine)

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

       8       4433  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4128  Dictyostelium discoideum (Slime mold)

      11       3480  Caenorhabditis elegans

      12       3390  Xenopus laevis (African clawed frog)

      13       3283  Oryza sativa subsp. japonica (Rice)

      14       3240  Drosophila melanogaster (Fruit fly)

      15       2936  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2262  Gallus gallus (Chicken)

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

      18       2037  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2027  Escherichia coli O157:H7

      20       1887  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1779  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

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

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

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

      26       1679  Shigella flexneri

      27       1415  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1273  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      30       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

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

      32       1050  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1025  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

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

      36        953  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      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        924  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      41        909  Acanthamoeba polyphaga mimivirus (APMV)

      42        905  Kluyveromyces lactis   

      43        899  Staphylococcus aureus (strain COL)

      44        895  Staphylococcus aureus (strain MW2)

      45        889  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      46        889  Staphylococcus aureus (strain MSSA476)

      47        889  Oryctolagus cuniculus (Rabbit)

      48        888  Staphylococcus aureus (strain MRSA252)

      49        882  Salmonella choleraesuis (strain SC-B67)

      50        878  Shigella sonnei (strain Ss046)

      51        875  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        841  Escherichia coli O9:H4 (strain HS)

      55        839  Neurospora crassa 

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

      57        829  Shigella boydii serotype 4 (strain Sb227)

      58        825  Escherichia coli (strain UTI89 / UPEC)

      59        822  Shigella dysenteriae serotype 1 (strain Sd197)

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

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

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

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

      64        788  Emericella nidulans  

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

      66        784  Aquifex aeolicus (strain VF5)

      67        776  Pasteurella multocida (strain Pm70)

      68        771  Escherichia coli (strain K12 / DH10B)

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

      70        770  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

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

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

      73        762  Escherichia coli (strain 55989 / EAEC)

      74        761  Escherichia coli O8 (strain IAI1)

      75        760  Shigella flexneri serotype 5b (strain 8401)

      76        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      77        758  Staphylococcus epidermidis (strain ATCC 12228)

      78        756  Escherichia coli (strain SE11)

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

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

      81        748  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        737  Bacillus halodurans 

      86        736  Bacillus anthracis

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

      88        733  Vibrio vulnificus (strain CMCP6)

      89        731  Escherichia coli O81 (strain ED1a)

      90        722  Salmonella enteritidis PT4 (strain P125109)

      91        717  Vibrio vulnificus (strain YJ016)

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

      93        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      94        715  Enterobacter sp. (strain 638)

      95        714  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        703  Pseudomonas putida (strain KT2440)

     105        702  Salmonella dublin (strain CT_02021853)

     106        698  Klebsiella pneumoniae (strain 342)

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

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

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

     110        689  Pan troglodytes (Chimpanzee)

     111        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     112        685  Oryza sativa subsp. indica (Rice)

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

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

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

     116        672  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     117        670  Serratia proteamaculans (strain 568)

     118        668  Mycobacterium leprae (strain TN)

     119        667  Yersinia pestis (strain Pestoides F)

     120        666  Staphylococcus aureus (strain USA300)

     121        665  Escherichia coli

     122        660  Bradyrhizobium diazoefficiens 

     123        659  Bacillus cereus (strain ATCC 14579 / DSM 31)

     124        658  Rhizobium sp. (strain NGR234)

     125        653  Debaryomyces hansenii   

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

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

     128        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     129        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     130        638  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     131        636  Shewanella oneidensis (strain MR-1)

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

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

     134        620  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

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

     138        607  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     139        606  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

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

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

     142        602  Staphylococcus saprophyticus subsp. saprophyticus 

     143        601  Salmonella paratyphi C (strain RKS4594)

     144        600  Yersinia pestis bv. Antiqua (strain Angola)

     145        591  Bacillus cereus (strain ATCC 10987)

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

     147        591  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

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

     149        586  Rickettsia prowazekii (strain Madrid E)

     150        579  Neisseria meningitidis serogroup B (strain MC58)

     151        576  Brucella suis biovar 1 (strain 1330)

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

     153        572  Pseudomonas aeruginosa (strain UCBPP-PA14)

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

     155        568  Caenorhabditis briggsae

     156        568  Caulobacter crescentus (strain ATCC 19089 / CB15)

     157        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     158        567  Pseudomonas syringae pv. syringae (strain B728a)

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

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

     161        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     162        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     163        561  Bacillus cereus (strain ZK / E33L)

     164        558  Clostridium acetobutylicum 

     165        556  Xanthomonas axonopodis pv. citri (strain 306)

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

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

     168        552  Pseudomonas fluorescens (strain Pf0-1)

     169        546  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

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

     171        538  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

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

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

     174        529  Sodalis glossinidius (strain morsitans)

     175        529  Listeria monocytogenes serotype 4b (strain F2365)

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

     177        522  Xylella fastidiosa (strain 9a5c)

     178        515  Chromobacterium violaceum 

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

     180        515  Corynebacterium glutamicum 

     181        514  Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)

     182        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        511  Pseudomonas aeruginosa (strain PA7)

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

     185        508  Staphylococcus aureus (strain Newman)

     186        508  Deinococcus radiodurans 

     187        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     188        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     189        507  Geobacillus kaustophilus (strain HTA426)

     190        506  Streptomyces avermitilis 

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

     192        500  Pseudomonas entomophila (strain L48)

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

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

     195        496  Bacillus clausii (strain KSM-K16)

     196        495  Burkholderia pseudomallei (strain K96243)

     197        495  Haemophilus influenzae (strain 86-028NP)

     198        494  Proteus mirabilis (strain HI4320)

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

     200        492  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     201        492  Bacillus amyloliquefaciens subsp. plantarum 

     202        491  Xanthomonas campestris pv. campestris (strain 8004)

     203        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     204        490  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

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

     206        487  Shewanella sp. (strain MR-7)

     207        486  Mannheimia succiniciproducens (strain MBEL55E)

     208        484  Pseudomonas aeruginosa (strain LESB58)

     209        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     210        484  Thermosynechococcus elongatus (strain BP-1)

     211        484  Shewanella sp. (strain MR-4)

     212        484  Methanosarcina mazei  

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

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

     215        481  Pyrococcus horikoshii 

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

     217        478  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     218        477  Pseudomonas putida (strain F1 / ATCC 700007)

     219        477  Pyrococcus abyssi (strain GE5 / Orsay)

     220        477  Brucella abortus (strain 2308)

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

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

     223        468  Clostridium perfringens (strain 13 / Type A)

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

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

     226        466  Shewanella frigidimarina (strain NCIMB 400)

     227        466  Pseudomonas putida (strain GB-1)

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

     229        464  Nicotiana tabacum (Common tobacco)

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

     231        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     232        464  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     233        463  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     234        463  Shewanella sp. (strain ANA-3)

     235        462  Burkholderia mallei (strain ATCC 23344)

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

     237        460  Enterococcus faecalis (strain ATCC 700802 / V583)

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

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

     240        456  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     241        455  Staphylococcus aureus (strain JH1)

     242        455  Ovis aries (Sheep)

     243        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     244        453  Pseudomonas putida (strain W619)

     245        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     246        452  Shewanella baltica (strain OS185)

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

     248        451  Aeromonas salmonicida (strain A449)

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

     250        450  Dechloromonas aromatica (strain RCB)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19304 (  4%)

    Bacteria         331826 ( 61%)

    Eukaryota        179476 ( 33%)

    Viruses           16479 (  3%)





   Within Eukaryota:



   



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

     Human                  20194 ( 11%)           (  4%)

     Other Mammalia         46098 ( 26%)           (  8%)

     Other Vertebrata       17768 ( 10%)           (  3%)

     Viridiplantae          35875 ( 20%)           (  7%)

     Fungi                  31426 ( 18%)           (  6%)

     Insecta                 8771 (  5%)           (  2%)

     Nematoda                4356 (  2%)           (  1%)

     Other                  14988 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9105             1001-1100     3804

                 51- 100   41836             1101-1200     2656

                101- 150   58305             1201-1300     2058

                151- 200   58175             1301-1400     1926

                201- 250   57036             1401-1500     1537

                251- 300   50621             1501-1600      751

                301- 350   50814             1601-1700      578

                351- 400   44031             1701-1800      485

                401- 450   36104             1801-1900      441

                451- 500   28998             1901-2000      357

                501- 550   20686             2001-2100      218

                551- 600   14835             2101-2200      297

                601- 650   12424             2201-2300      301

                651- 700    8987             2301-2400      186

                701- 750    7414             2401-2500      142

                751- 800    5312             >2500         1112

                801- 850    4618

                851- 900    5088

                901- 950    3928

                951-1000    2797



   





   The average sequence length in UniProtKB/Swiss-Prot is 355 amino acids.



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

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





4.  JOURNAL CITATIONS



   Note: the following citation statistics reflect the number of distinct

         journal citations.



   Total number of journals cited in this release of UniProtKB/Swiss-Prot: 2453





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  799

                       2x:  321

                       3x:  166

                       4x:  119

                       5x:   92

                       6x:   78

                       7x:   58

                       8x:   48

                       9x:   33

                      10x:   36

                  11- 20x:  198

                  21- 50x:  196

                  51-100x:  113

                    >100x:  196





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



   Nb    Citations   Journal name

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

    1        22342   Journal of Biological Chemistry

    2        10123   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6080   Journal of Bacteriology

    4         5227   Biochemical and Biophysical Research Communications

    5         4775   Biochemistry

    6         4717   Nucleic Acids Research

    7         4679   Gene

    8         4529   FEBS Letters

    9         4387   The EMBO Journal

   10         4068   Molecular and Cellular Biology

   11         3954   Nature

   12         3841   Journal of Molecular Biology

   13         3348   Biochimica et Biophysica Acta

   14         3300   European Journal of Biochemistry

   15         3207   Cell

   16         2718   Journal of Virology

   17         2648   Science

   18         2625   Biochemical Journal

   19         2517   Genomics

   20         2223   Molecular Microbiology

   21         2064   Plant Physiology

   22         1982   Journal of Cell Biology

   23         1776   The American Journal of Human Genetics

   24         1715   Plant Molecular Biology

   25         1685   Genes and Development

   26         1588   Nature Genetics

   27         1585   Virology

   28         1558   Human Molecular Genetics

   29         1517   The Plant Cell

   30         1475   Oncogene

   31         1439   Molecular Biology of the Cell

   32         1426   Development

   33         1375   The Plant Journal

   34         1372   Human Mutation

   35         1364   Molecular and General Genetics

   36         1287   Molecular Cell

   37         1279   Journal of Biochemistry

   38         1224   Journal of Immunology

   39         1165   Structure

   40         1157   Genetics

   41         1046   Journal of General Virology

   42         1032   Blood

   43         1025   Journal of Cell Science

   44         1017   Infection and Immunity

   45          970   Archives of Biochemistry and Biophysics

   46          963   PLoS ONE

   47          951   Microbiology

   48          879   Developmental Biology

   49          869   Current Biology

   50          832   Cancer Research

   51          815   Yeast

   52          771   FEMS Microbiology Letters

   53          749   Acta Crystallographica, Section D

   54          725   Applied and Environmental Microbiology

   55          703   Protein Science

   56          703   Journal of Neuroscience

   57          697   Toxicon

   58          644   Human Genetics

   59          635   Nature Structural Biology

   60          629   Mechanisms of Development

   61          627   Neuron

   62          611   Journal of Clinical Investigation

   63          594   American Journal of Physiology

   64          557   The Journal of Experimental Medicine

   65          550   Current Genetics

   66          540   Proteins

   67          537   Plant and Cell Physiology

   68          505   Molecular Endocrinology

   69          489   Journal of Neurochemistry

   70          483   Mammalian Genome

   71          482   Nature Cell Biology

   72          476   Journal of Medical Genetics

   73          473   Bioscience, Biotechnology, and Biochemistry

   74          463   Endocrinology

   75          460   Immunogenetics

   76          452   The Journal of Clinical Endocrinology and Metabolism

   77          442   Molecular and Biochemical Parasitology

   78          403   Journal of Molecular Evolution

   79          402   Experimental Cell Research

   80          390   Nature Structural and Molecular Biology

   81          382   Molecular Biology and Evolution

   82          379   DNA and Cell Biology

   83          377   Peptides

   84          373   The FEBS Journal

   85          368   DNA Sequence

   86          364   Developmental Cell

   87          361   RNA

   88          349   Antimicrobial Agents and Chemotherapy

   89          346   Eukaryotic Cell

   90          335   Planta

   91          332   Journal of Investigative Dermatology

   92          331   Brain Research. Molecular Brain Research

   93          328   Comparative Biochemistry and Physiology

   94          325   Tissue Antigens

   95          324   Molecular Pharmacology

   96          302   Neurology

   97          300   Biology of Reproduction

   98          294   Biological Chemistry Hoppe-Seyler

   99          286   EMBO Reports

  100          284   Developmental Dynamics

  101          281   Cytogenetics and Cell Genetics

  102          279   The FASEB Journal

  103          277   Biochimie

  104          277   Immunity

  105          273   Genes to Cells

  106          271   Genome Research

  107          271   Virus Research

  108          269   The New England Journal of Medicine

  109          263   Journal of General Microbiology

  110          263   Molecular Plant-Microbe Interactions

  111          263   PLoS Genetics

  112          263   Journal of the American Chemical Society

  113          248   Acta Crystallographica, Section F

  114          246   European Journal of Human Genetics

  115          239   Annals of Neurology

  116          238   European Journal of Immunology

  117          228   Journal of Experimental Botany

  118          224   Investigative Ophthalmology and Visual Science

  119          220   DNA Research

  120          219   BMC Genomics

  121          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  122          218   Nature Immunology

  123          218   Journal of Human Genetics

  124          217   Archives of Microbiology

  125          208   American Journal of Medical Genetics. Part A

  126          206   Journal of Cellular Biochemistry

  127          200   Glycobiology

  128          199   Journal of Medicinal Chemistry

  129          196   Molecular and Cellular Endocrinology

  130          196   Clinical Genetics

  131          195   Archives of Virology

  132          192   Molecular Immunology

  133          188   Diabetes

  134          187   Circulation Research

  135          185   Cell Cycle

  136          183   PLoS Pathogens

  137          180   Applied Microbiology and Biotechnology

  138          180   Traffic

  139          177   Molecular Genetics and Metabolism

  140          176   Insect Biochemistry and Molecular Biology

  141          175   Phytochemistry

  142          172   Protein Expression and Purification

  143          170   International Journal of Cancer

  144          169   Molecular Phylogenetics and Evolution

  145          168   American Journal of Medical Genetics

  146          164   PLoS Biology

  147          162   Proteomics

  148          162   Biological Chemistry

  149          161   Journal of Lipid Research

  150          160   Molecular Reproduction and Development





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)                      1090567                 1.99                                         

   Journal                            896769     434626      1.64       1                                 

   Submitted to EMBL/GenBank/DDBJ     183742     162671      0.34       2                                 

   Submitted to other databases         7039       6536      0.01       3                                 

   Book citation                        1467       1453     <0.01       4                                 

   Plant Gene Register                   594        582     <0.01       5                                 

   Thesis                                424        421     <0.01       6                                 

   Unpublished observations              335        331     <0.01       7                                 

   Patent                                191        188     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 356767



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2523325                 4.61                                         

   ALLERGEN                              664        664     <0.01      25                                 

   ALTERNATIVE PRODUCTS                24029      24029      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        6166       6166      0.01      21                                 

   BIOTECHNOLOGY                         426        424     <0.01      28                                 

   CATALYTIC ACTIVITY                 252554     227520      0.46       5                                 

   CAUTION                             10055       9864      0.02      18                                 

   COFACTOR                           116296     106425      0.21       7                                 

   DEVELOPMENTAL STAGE                 10394      10394      0.02      17                                 

   DISEASE                              5801       3916      0.01      23                                 

   DISRUPTION PHENOTYPE                 7929       7929      0.01      20                                 

   DOMAIN                              42450      36950      0.08       9                                 

   ENZYME REGULATION                   12954      12954      0.02      16                                 

   FUNCTION                           437941     419905      0.80       2                                 

   INDUCTION                           16876      16876      0.03      14                                 

   INTERACTION                         13151      13151      0.02      15                                 

   MASS SPECTROMETRY                    5846       4447      0.01      22                                 

   MISCELLANEOUS                       34019      31421      0.06      12                                 

   PATHWAY                            134128     121601      0.25       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1040        983     <0.01      24                                 

   PTM                                 47599      36716      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    42149      42149      0.08      10                                 

   SIMILARITY                         658823     522194      1.20       1                                 

   SUBCELLULAR LOCATION               334872     328455      0.61       3                                 

   SUBUNIT                            256674     256674      0.47       4                                 

   TISSUE SPECIFICITY                  40939      40939      0.07      11                                 

   TOXIC DOSE                            596        554     <0.01      27                                 

   WEB RESOURCE                         8229       6885      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3967384                 7.25                                         

   ACT_SITE                           151250      92546      0.28      10                                 

   BINDING                            334912      88550      0.61       4                                 

   CA_BIND                              3974       1671      0.01      35                                 

   CARBOHYD                           109479      28101      0.20      15                                 

   CHAIN                              554513     540730      1.01       1                                 

   COILED                              20868      14370      0.04      26                                 

   COMPBIAS                            56251      29995      0.10      18                                 

   CONFLICT                           130489      45656      0.24      13                                 

   CROSSLNK                             7176       4093      0.01      34                                 

   DISULFID                           115338      31457      0.21      14                                 

   DNA_BIND                            10745       9759      0.02      31                                 

   DOMAIN                             172971     105244      0.32       8                                 

   HELIX                              200686      19153      0.37       6                                 

   INIT_MET                            17757      17757      0.03      27                                 

   INTRAMEM                             2257        990     <0.01      37                                 

   LIPID                               12237       7851      0.02      30                                 

   METAL                              345525      85687      0.63       3                                 

   MOD_RES                            174002      62682      0.32       7                                 

   MOTIF                               37962      24636      0.07      24                                 

   MUTAGEN                             50740      11612      0.09      19                                 

   NON_CONS                             2069        758     <0.01      38                                 

   NON_STD                               358        283     <0.01      39                                 

   NON_TER                             12281       9387      0.02      29                                 

   NP_BIND                            133969      78541      0.24      11                                 

   PEPTIDE                             10503       7184      0.02      32                                 

   PROPEP                              13032      11227      0.02      28                                 

   REGION                             163918      78475      0.30       9                                 

   REPEAT                              98144      14406      0.18      16                                 

   SIGNAL                              39437      39427      0.07      23                                 

   SITE                                49737      27869      0.09      21                                 

   STRAND                             210154      18073      0.38       5                                 

   TOPO_DOM                           133617      27727      0.24      12                                 

   TRANSIT                              8768       8655      0.02      33                                 

   TRANSMEM                           361697      74807      0.66       2                                 

   TURN                                48539      15506      0.09      22                                 

   UNSURE                               3642        733      0.01      36                                 

   VAR_SEQ                             50131      21068      0.09      20                                 

   VARIANT                             88521      16928      0.16      17                                 

   ZN_FING                             29735      13143      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)               16892566                30.88                                                           

   Allergome                            1636       1063     <0.01     104      Protein family/group databases               

   ArachnoServer                         789        781     <0.01     114      Organism-specific databases                  

   Bgee                                38842      38842      0.07      50      Gene expression databases                    

   BindingDB                            5242       5242      0.01      88      Chemistry                                    

   BioCyc                             324578     307383      0.59      19      Enzyme and pathway databases                 

   BioGrid                             40237      39875      0.07      49      Protein-protein interaction databases        

   BRENDA                               4370       4358      0.01      94      Enzyme and pathway databases                 

   CAZy                                 7768       6990      0.01      78      Protein family/group databases               

   CCDS                                45485      33384      0.08      46      Sequence databases                           

   CGD                                   930        908     <0.01     111      Organism-specific databases                  

   ChEMBL                               6007       6007      0.01      83      Chemistry                                    

   ChiTaRS                             16446      16437      0.03      69      Other                                        

   CleanEx                             30067      29428      0.05      55      Gene expression databases                    

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

   ConoServer                            949        866     <0.01     110      Organism-specific databases                  

   CTD                                 72292      71593      0.13      39      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      85      Organism-specific databases                  

   dictyBase                            4204       4089      0.01      96      Organism-specific databases                  

   DIP                                 15791      15726      0.03      71      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     120      3D structure databases                       

   DMDM                                16404      16404      0.03      70      Polymorphism databases                       

   DNASU                               18764      18694      0.03      65      Protocols and materials databases            

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

   DrugBank                            11195       1762      0.02      75      Chemistry                                    

   EchoBASE                             4161       4161      0.01      97      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      95      Organism-specific databases                  

   eggNOG                             430955     430955      0.79      12      Phylogenomic databases                       

   EMBL                               960266     535866      1.76       3      Sequence databases                           

   Ensembl                             84413      49182      0.15      37      Genome annotation databases                  

   EnsemblBacteria                    349536     330909      0.64      18      Genome annotation databases                  

   EnsemblFungi                        19093      18751      0.03      63      Genome annotation databases                  

   EnsemblMetazoa                      12188       9459      0.02      74      Genome annotation databases                  

   EnsemblPlants                       19109      16301      0.03      62      Genome annotation databases                  

   EnsemblProtists                      4460       4335      0.01      93      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     130      Organism-specific databases                  

   EuPathDB                              811        811     <0.01     113      Organism-specific databases                  

   EvolutionaryTrace                   16496      16495      0.03      68      Other                                        

   ExpressionAtlas                     32090      32090      0.06      52      Gene expression databases                    

   FlyBase                              5942       5568      0.01      84      Organism-specific databases                  

   Gene3D                             466768     344275      0.85       8      Family and domain databases                  

   GeneCards                           20872      19797      0.04      59      Organism-specific databases                  

   GeneFarm                             3325       3313      0.01      98      Organism-specific databases                  

   GeneID                             497905     469819      0.91       6      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     109      Organism-specific databases                  

   GeneTree                            56440      56409      0.10      45      Phylogenomic databases                       

   Genevestigator                      68394      68394      0.13      41      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      76      Other                                        

   GenoList                             7074       7062      0.01      79      Organism-specific databases                  

   GenomeRNAi                          21686      21686      0.04      58      Other                                        

   GO                                2551931     518358      4.66       1      Ontologies                                   

   Gramene                              6235       6235      0.01      81      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2012       2012     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      86      Organism-specific databases                  

   HAMAP                              324284     321336      0.59      20      Family and domain databases                  

   HGNC                                19999      19837      0.04      61      Organism-specific databases                  

   HOGENOM                            385801     385801      0.71      16      Phylogenomic databases                       

   HOVERGEN                            75660      75660      0.14      38      Phylogenomic databases                       

   HPA                                 22351      15981      0.04      57      Organism-specific databases                  

   InParanoid                         134882     134882      0.25      27      Phylogenomic databases                       

   IntAct                              42432      42432      0.08      48      Protein-protein interaction databases        

   InterPro                          1903081     526256      3.48       2      Family and domain databases                  

   KEGG                               473403     448547      0.87       7      Genome annotation databases                  

   KO                                 377642     377157      0.69      17      Phylogenomic databases                       

   LegioList                             765        763     <0.01     116      Organism-specific databases                  

   Leproma                               671        668     <0.01     117      Organism-specific databases                  

   MaizeGDB                              503        498     <0.01     122      Organism-specific databases                  

   MaxQB                               31218      31218      0.06      54      Proteomic databases                          

   MEROPS                              12719      12719      0.02      73      Protein family/group databases               

   MGI                                 16605      16561      0.03      67      Organism-specific databases                  

   MIM                                 18941      14064      0.03      64      Organism-specific databases                  

   MINT                                31592      31592      0.06      53      Protein-protein interaction databases        

   mycoCLAP                              323        317     <0.01     126      Protein family/group databases               

   NextBio                             71243      71243      0.13      40      Other                                        

   neXtProt                            20039      20039      0.04      60      Organism-specific databases                  

   OGP                                   376        376     <0.01     125      2D gel databases                             

   OMA                                403577     403577      0.74      13      Phylogenomic databases                       

   Orphanet                             6201       3262      0.01      82      Organism-specific databases                  

   OrthoDB                            389328     389328      0.71      15      Phylogenomic databases                       

   PANTHER                            172772     166779      0.32      24      Family and domain databases                  

   PATRIC                             307723     307692      0.56      21      Genome annotation databases                  

   PaxDb                               66624      66623      0.12      42      Proteomic databases                          

   PDB                                114222      21478      0.21      32      3D structure databases                       

   PDBsum                             114222      21478      0.21      31      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      89      Proteomic databases                          

   PeroxiBase                            770        754     <0.01     115      Protein family/group databases               

   Pfam                               739892     507435      1.35       4      Family and domain databases                  

   PharmGKB                            18384      18356      0.03      66      Organism-specific databases                  

   PhosphoSite                         33561      33561      0.06      51      PTM databases                                

   PhosSite                              606        597     <0.01     119      PTM databases                                

   PhylomeDB                           93513      93513      0.17      35      Phylogenomic databases                       

   PIR                                121800     111582      0.22      30      Sequence databases                           

   PIRSF                              102233     101271      0.19      34      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     105      Other                                        

   PomBase                              5134       5098      0.01      90      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     131      Protein family/group databases               

   PRIDE                              122348     122348      0.22      29      Proteomic databases                          

   PRINTS                             136746     120440      0.25      26      Family and domain databases                  

   PRO                                 58050      58050      0.11      44      Other                                        

   ProDom                              29238      29059      0.05      56      Family and domain databases                  

   ProMEX                                382        382     <0.01     124      Proteomic databases                          

   PROSITE                            445750     287422      0.81       9      Family and domain databases                  

   ProteinModelPortal                 441081     441081      0.81      11      3D structure databases                       

   PseudoCAP                            1281       1272     <0.01     106      Organism-specific databases                  

   Reactome                            87649      26663      0.16      36      Enzyme and pathway databases                 

   REBASE                                406        406     <0.01     123      Protein family/group databases               

   RefSeq                             646353     479079      1.18       5      Sequence databases                           

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

   RGD                                  7835       7831      0.01      77      Organism-specific databases                  

   SABIO-RK                             2997       2997      0.01      99      Enzyme and pathway databases                 

   SGD                                  6737       6732      0.01      80      Organism-specific databases                  

   SignaLink                            2969       2961      0.01     100      Enzyme and pathway databases                 

   SMART                              170024     127341      0.31      25      Family and domain databases                  

   SMR                                224114     224114      0.41      23      3D structure databases                       

   STRING                             402810     402809      0.74      14      Protein-protein interaction databases        

   SUPFAM                             442177     339990      0.81      10      Family and domain databases                  

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

   TAIR                                13402      13346      0.02      72      Organism-specific databases                  

   TCDB                                 5364       5343      0.01      87      Protein family/group databases               

   TIGRFAMs                           291301     271129      0.53      22      Family and domain databases                  

   TreeFam                             44774      44769      0.08      47      Phylogenomic databases                       

   TubercuList                          2062       2026     <0.01     102      Organism-specific databases                  

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

   UCSC                                59025      44762      0.11      43      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     127      PTM databases                                

   UniGene                            102597      92526      0.19      33      Sequence databases                           

   UniPathway                         133930     121409      0.24      28      Enzyme and pathway databases                 

   VectorBase                            613        595     <0.01     118      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     112      2D gel databases                             

   WormBase                             5049       4010      0.01      91      Organism-specific databases                  

   Xenbase                              4768       4762      0.01      92      Organism-specific databases                  

   ZFIN                                 2773       2773      0.01     101      Organism-specific databases                  



Total number of cross-referenced databases: 131



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



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

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

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

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

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



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



   



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

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





   6.2  Classification of the amino acids by their frequency



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

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4464 entries are encoded on a mitochondrion, and 3797 are encoded on a plasmid.



12188 entries are encoded on a plastid, 

of which 21 are encoded on apicoplasts, 

11623 on chloroplasts, 

51 on organellar chromatophores,

145 on cyanelles, 

149 on non-photosynthetic plastids and 

199 on unspecified types of plastid.



Number of entries with at least one sequence correction: 76255