UniProtKB/Swiss-Prot protein knowledgebase release 2014_04 statistics





1.  INTRODUCTION



Release 2014_04 of 16-Apr-14 of UniProtKB/Swiss-Prot contains 544996 sequence entries,

comprising 193815432 amino acids abstracted from 227703 references. 



4088 sequences have been added since release 2014_03, the sequence data of

58 existing entries has been updated and the annotations of

199857 entries have been revised.



Number of fragments: 9092

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 36305





Protein existence (PE):           entries     %



1: Evidence at protein level        82375   15.1%

2: Evidence at transcript level     62379   11.4%

3: Inferred from homology          382367   70.2%

4: Predicted                        15987    2.9%

5: Uncertain                         1888    0.3%



The growth of the database is summarized below.



   





2.  TAXONOMIC ORIGIN



   Total number of species represented in this release of UniProtKB/Swiss-Prot: 13076



   The first twenty species represent 114623 sequences:    21 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5447

                            2x: 1904

                            3x:  994

                            4x:  645

                            5x:  470

                            6x:  397

                            7x:  287

                            8x:  223

                            9x:  211

                           10x:  121

                       11- 20x:  702

                       21- 50x:  419

                       51-100x:  210

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20265  Homo sapiens (Human)

       2      16669  Mus musculus (Mouse)

       3      12788  Arabidopsis thaliana (Mouse-ear cress)

       4       7895  Rattus norvegicus (Rat)

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

       6       5984  Bos taurus (Bovine)

       7       5097  Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)

       8       4431  Escherichia coli (strain K12)

       9       4185  Bacillus subtilis (strain 168)

      10       4127  Dictyostelium discoideum (Slime mold)

      11       3466  Caenorhabditis elegans

      12       3383  Xenopus laevis (African clawed frog)

      13       3224  Drosophila melanogaster (Fruit fly)

      14       3166  Oryza sativa subsp. japonica (Rice)

      15       2921  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2258  Gallus gallus (Chicken)

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

      18       2024  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2015  Escherichia coli O157:H7

      20       1885  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1772  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

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

      24       1700  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      25       1684  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      26       1679  Shigella flexneri

      27       1413  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1261  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       1045  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1019  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

      35        955  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      36        930  Salmonella paratyphi A (strain ATCC 9150 / SARB42)

      37        926  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      38        925  Staphylococcus aureus (strain N315)

      39        924  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      40        921  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      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        870  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      52        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      53        862  Candida glabrata   

      54        841  Escherichia coli O9:H4 (strain HS)

      55        837  Neurospora crassa 

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

      57        829  Shigella boydii serotype 4 (strain Sb227)

      58        825  Escherichia coli (strain UTI89 / UPEC)

      59        821  Shigella dysenteriae serotype 1 (strain Sd197)

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

      61        809  Canis familiaris (Dog) (Canis lupus familiaris)

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

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

      64        784  Emericella nidulans  

      65        783  Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672) 

      66        783  Aquifex aeolicus (strain VF5)

      67        775  Pasteurella multocida (strain Pm70)

      68        771  Escherichia coli (strain K12 / DH10B)

      69        767  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      70        765  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        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      82        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      83        740  Staphylococcus aureus (strain NCTC 8325)

      84        737  Bacillus halodurans 

      85        736  Bacillus anthracis

      86        735  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      87        735  Zea mays (Maize)

      88        733  Vibrio vulnificus (strain CMCP6)

      89        731  Escherichia coli O81 (strain ED1a)

      90        721  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        714  Salmonella paratyphi A (strain AKU_12601)

      95        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      96        713  Enterobacter sp. (strain 638)

      97        713  Salmonella agona (strain SL483)

      98        713  Escherichia coli O1:K1 / APEC

      99        713  Salmonella newport (strain SL254)

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

     101        712  Salmonella schwarzengrund (strain CVM19633)

     102        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     103        710  Salmonella heidelberg (strain SL476)

     104        702  Salmonella dublin (strain CT_02021853)

     105        699  Pseudomonas putida (strain KT2440)

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

     107        696  Klebsiella pneumoniae (strain 342)

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

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

     110        689  Pan troglodytes (Chimpanzee)

     111        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     112        683  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     113        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     114        675  Pseudomonas syringae pv. tomato (strain DC3000)

     115        670  Serratia proteamaculans (strain 568)

     116        668  Oryza sativa subsp. indica (Rice)

     117        668  Mycobacterium leprae (strain TN)

     118        667  Yersinia pestis (strain Pestoides F)

     119        667  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     120        666  Staphylococcus aureus (strain USA300)

     121        659  Bradyrhizobium diazoefficiens 

     122        658  Escherichia coli

     123        658  Rhizobium sp. (strain NGR234)

     124        654  Bacillus cereus (strain ATCC 14579 / DSM 31)

     125        653  Debaryomyces hansenii   

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

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

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

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

     130        635  Shewanella oneidensis (strain MR-1)

     131        634  Yersinia pseudotuberculosis serotype IB (strain PB1/+)

     132        634  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

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

     134        616  Methanothermobacter thermautotrophicus  

     135        616  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

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

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

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

     140        602  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

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

     142        602  Staphylococcus saprophyticus subsp. saprophyticus 

     143        601  Salmonella paratyphi C (strain RKS4594)

     144        600  Yersinia pestis bv. Antiqua (strain Angola)

     145        591  Bacillus cereus (strain ATCC 10987)

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

     147        589  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     148        588  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     149        586  Rickettsia prowazekii (strain Madrid E)

     150        579  Neisseria meningitidis serogroup B (strain MC58)

     151        576  Brucella suis biovar 1 (strain 1330)

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

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

     154        568  Caenorhabditis briggsae

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

     156        567  Pseudomonas syringae pv. syringae (strain B728a)

     157        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     158        565  Caulobacter crescentus (strain ATCC 19089 / CB15)

     159        564  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     160        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     161        564  Pseudomonas aeruginosa (strain UCBPP-PA14)

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

     163        561  Bacillus cereus (strain ZK / E33L)

     164        557  Clostridium acetobutylicum 

     165        556  Xanthomonas axonopodis pv. citri (strain 306)

     166        552  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     167        552  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     168        552  Pseudomonas fluorescens (strain Pf0-1)

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

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

     171        535  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     172        533  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

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

     174        529  Sodalis glossinidius (strain morsitans)

     175        529  Listeria monocytogenes serotype 4b (strain F2365)

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

     177        522  Xylella fastidiosa (strain 9a5c)

     178        515  Chromobacterium violaceum 

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

     180        514  Corynebacterium glutamicum 

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

     182        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     183        511  Pseudomonas aeruginosa (strain PA7)

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

     185        508  Staphylococcus aureus (strain Newman)

     186        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

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

     188        507  Geobacillus kaustophilus (strain HTA426)

     189        506  Streptomyces avermitilis 

     190        503  Deinococcus radiodurans 

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

     200        492  Bacillus amyloliquefaciens subsp. plantarum 

     201        491  Xanthomonas campestris pv. campestris (strain 8004)

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

     203        487  Shewanella sp. (strain MR-7)

     204        486  Mannheimia succiniciproducens (strain MBEL55E)

     205        484  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     206        484  Pseudomonas aeruginosa (strain LESB58)

     207        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     208        484  Shewanella sp. (strain MR-4)

     209        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     210        483  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     211        483  Methanosarcina mazei  

     212        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     213        482  Thermosynechococcus elongatus (strain BP-1)

     214        479  Pyrococcus horikoshii 

     215        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     216        477  Pseudomonas putida (strain F1 / ATCC 700007)

     217        477  Brucella abortus (strain 2308)

     218        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     219        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     220        473  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     221        472  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     222        470  Pyrococcus abyssi (strain GE5 / Orsay)

     223        468  Clostridium perfringens (strain 13 / Type A)

     224        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     225        466  Shewanella frigidimarina (strain NCIMB 400)

     226        466  Pseudomonas putida (strain GB-1)

     227        466  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     228        464  Nicotiana tabacum (Common tobacco)

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

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

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

     232        463  Shewanella sp. (strain ANA-3)

     233        462  Burkholderia mallei (strain ATCC 23344)

     234        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     235        461  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     236        459  Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Ralstonia eutropha 

     237        458  Enterococcus faecalis (strain ATCC 700802 / V583)

     238        456  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     239        455  Staphylococcus aureus (strain JH1)

     240        455  Ovis aries (Sheep)

     241        454  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     242        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     243        453  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     244        453  Pseudomonas putida (strain W619)

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

     246        452  Shewanella baltica (strain OS185)

     247        451  Aeromonas salmonicida (strain A449)

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

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

     250        450  Dechloromonas aromatica (strain RCB)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19110 (  4%)

    Bacteria         331317 ( 61%)

    Eukaryota        178110 ( 33%)

    Viruses           16459 (  3%)





   Within Eukaryota:



   



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

     Human                  20266 ( 11%)           (  4%)

     Other Mammalia         46036 ( 26%)           (  8%)

     Other Vertebrata       17653 ( 10%)           (  3%)

     Viridiplantae          35044 ( 20%)           (  6%)

     Fungi                  31166 ( 17%)           (  6%)

     Insecta                 8736 (  5%)           (  2%)

     Nematoda                4342 (  2%)           (  1%)

     Other                  14867 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9086             1001-1100     3787

                 51- 100   41702             1101-1200     2628

                101- 150   58142             1201-1300     2041

                151- 200   58061             1301-1400     1912

                201- 250   56874             1401-1500     1531

                251- 300   50455             1501-1600      745

                301- 350   50602             1601-1700      574

                351- 400   43815             1701-1800      478

                401- 450   35892             1801-1900      435

                451- 500   28871             1901-2000      354

                501- 550   20590             2001-2100      217

                551- 600   14770             2101-2200      296

                601- 650   12382             2201-2300      300

                651- 700    8955             2301-2400      184

                701- 750    7366             2401-2500      140

                751- 800    5263             >2500         1101

                801- 850    4587

                851- 900    5068

                901- 950    3916

                951-1000    2784



   





   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: 2402





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  783

                       2x:  313

                       3x:  165

                       4x:  118

                       5x:   86

                       6x:   79

                       7x:   57

                       8x:   50

                       9x:   30

                      10x:   41

                  11- 20x:  183

                  21- 50x:  197

                  51-100x:  108

                    >100x:  192





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



   Nb    Citations   Journal name

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

    1        21892   Journal of Biological Chemistry

    2         9916   Proceedings of the National Academy of Sciences of the U.S.A.

    3         5898   Journal of Bacteriology

    4         5145   Biochemical and Biophysical Research Communications

    5         4655   Nucleic Acids Research

    6         4643   Gene

    7         4629   Biochemistry

    8         4448   FEBS Letters

    9         4331   The EMBO Journal

   10         4016   Molecular and Cellular Biology

   11         3876   Nature

   12         3732   Journal of Molecular Biology

   13         3292   Biochimica et Biophysica Acta

   14         3265   European Journal of Biochemistry

   15         3154   Cell

   16         2670   Journal of Virology

   17         2579   Science

   18         2575   Biochemical Journal

   19         2517   Genomics

   20         2163   Molecular Microbiology

   21         1977   Plant Physiology

   22         1951   Journal of Cell Biology

   23         1712   The American Journal of Human Genetics

   24         1686   Plant Molecular Biology

   25         1646   Genes and Development

   26         1558   Virology

   27         1557   Nature Genetics

   28         1519   Human Molecular Genetics

   29         1466   Oncogene

   30         1426   The Plant Cell

   31         1418   Molecular Biology of the Cell

   32         1393   Development

   33         1353   Molecular and General Genetics

   34         1346   Human Mutation

   35         1288   The Plant Journal

   36         1262   Journal of Biochemistry

   37         1249   Molecular Cell

   38         1211   Journal of Immunology

   39         1135   Genetics

   40         1133   Structure

   41         1042   Journal of General Virology

   42         1014   Blood

   43         1003   Infection and Immunity

   44          999   Journal of Cell Science

   45          955   Archives of Biochemistry and Biophysics

   46          923   Microbiology

   47          863   Developmental Biology

   48          854   Current Biology

   49          826   PLoS ONE

   50          823   Cancer Research

   51          806   Yeast

   52          753   FEMS Microbiology Letters

   53          720   Acta Crystallographica, Section D

   54          684   Protein Science

   55          684   Journal of Neuroscience

   56          680   Applied and Environmental Microbiology

   57          675   Toxicon

   58          636   Human Genetics

   59          630   Nature Structural Biology

   60          626   Mechanisms of Development

   61          613   Neuron

   62          591   Journal of Clinical Investigation

   63          573   American Journal of Physiology

   64          546   The Journal of Experimental Medicine

   65          544   Current Genetics

   66          524   Proteins

   67          517   Plant and Cell Physiology

   68          504   Molecular Endocrinology

   69          482   Mammalian Genome

   70          478   Journal of Neurochemistry

   71          469   Nature Cell Biology

   72          460   Immunogenetics

   73          460   Bioscience, Biotechnology, and Biochemistry

   74          457   Journal of Medical Genetics

   75          454   Endocrinology

   76          448   The Journal of Clinical Endocrinology and Metabolism

   77          435   Molecular and Biochemical Parasitology

   78          402   Journal of Molecular Evolution

   79          392   Experimental Cell Research

   80          381   Molecular Biology and Evolution

   81          377   DNA and Cell Biology

   82          369   Nature Structural and Molecular Biology

   83          368   Peptides

   84          367   DNA Sequence

   85          353   The FEBS Journal

   86          350   RNA

   87          347   Developmental Cell

   88          339   Eukaryotic Cell

   89          336   Antimicrobial Agents and Chemotherapy

   90          330   Brain Research. Molecular Brain Research

   91          326   Tissue Antigens

   92          323   Comparative Biochemistry and Physiology

   93          321   Journal of Investigative Dermatology

   94          321   Planta

   95          315   Molecular Pharmacology

   96          299   Biology of Reproduction

   97          294   Biological Chemistry Hoppe-Seyler

   98          290   Neurology

   99          281   Cytogenetics and Cell Genetics

  100          279   Developmental Dynamics

  101          277   EMBO Reports

  102          274   Immunity

  103          272   Biochimie

  104          270   Virus Research

  105          268   Genome Research

  106          266   Genes to Cells

  107          265   The FASEB Journal

  108          263   Journal of General Microbiology

  109          254   The New England Journal of Medicine

  110          252   Molecular Plant-Microbe Interactions

  111          242   Journal of the American Chemical Society

  112          237   European Journal of Human Genetics

  113          236   Annals of Neurology

  114          235   European Journal of Immunology

  115          230   Acta Crystallographica, Section F

  116          227   PLoS Genetics

  117          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  118          218   Investigative Ophthalmology and Visual Science

  119          216   DNA Research

  120          214   Journal of Human Genetics

  121          212   Nature Immunology

  122          209   Archives of Microbiology

  123          208   Journal of Experimental Botany

  124          205   BMC Genomics

  125          203   Journal of Cellular Biochemistry

  126          197   American Journal of Medical Genetics. Part A

  127          196   Glycobiology

  128          195   Journal of Medicinal Chemistry

  129          192   Molecular and Cellular Endocrinology

  130          192   Archives of Virology

  131          189   Molecular Immunology

  132          188   Clinical Genetics

  133          183   Circulation Research

  134          181   Diabetes

  135          176   Insect Biochemistry and Molecular Biology

  136          175   Traffic

  137          174   Cell Cycle

  138          171   Phytochemistry

  139          171   Molecular Genetics and Metabolism

  140          169   PLoS Pathogens

  141          169   Molecular Phylogenetics and Evolution

  142          168   American Journal of Medical Genetics

  143          166   International Journal of Cancer

  144          163   Protein Expression and Purification

  145          162   Applied Microbiology and Biotechnology

  146          160   Molecular Reproduction and Development

  147          159   DNA

  148          159   Biological Chemistry

  149          158   PLoS Biology

  150          157   Molecular and Cellular Neuroscience





5.  STATISTICS FOR SOME LINE TYPES



The following table summarizes the total number of some UniProtKB/Swiss-Prot lines,

as well as the number of entries with at least one such line, and the

frequency of the lines.



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry

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



References (RL)                      1072735                 1.97                                         

   Journal                            867587     426145      1.59       1                                 

   Submitted to EMBL/GenBank/DDBJ     195932     174702      0.36       2                                 

   Submitted to other databases         6960       6476      0.01       3                                 

   Book citation                         725        711     <0.01       4                                 

   Plant Gene Register                   592        580     <0.01       5                                 

   Thesis                                421        418     <0.01       6                                 

   Unpublished observations              322        318     <0.01       7                                 

   Patent                                190        187     <0.01       8                                 

   Worm Breeder's Gazette                  6          6     <0.01       9                                 



Total number of distinct authors cited in UniProtKB/Swiss-Prot: 348992



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2484144                 4.56                                         

   ALLERGEN                              661        661     <0.01      25                                 

   ALTERNATIVE PRODUCTS                22756      22756      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5560       5560      0.01      23                                 

   BIOTECHNOLOGY                         370        368     <0.01      28                                 

   CATALYTIC ACTIVITY                 247899     223680      0.45       5                                 

   CAUTION                              9800       9619      0.02      18                                 

   COFACTOR                           113298     103751      0.21       7                                 

   DEVELOPMENTAL STAGE                 10255      10255      0.02      17                                 

   DISEASE                              5585       3747      0.01      22                                 

   DISRUPTION PHENOTYPE                 7024       7024      0.01      20                                 

   DOMAIN                              41643      36285      0.08      10                                 

   ENZYME REGULATION                   12309      12309      0.02      16                                 

   FUNCTION                           430677     412857      0.79       2                                 

   INDUCTION                           16133      16133      0.03      14                                 

   INTERACTION                         12729      12729      0.02      15                                 

   MASS SPECTROMETRY                    5719       4357      0.01      21                                 

   MISCELLANEOUS                       33450      30897      0.06      12                                 

   PATHWAY                            133119     121125      0.24       6                                 

   PHARMACEUTICAL                         94         94     <0.01      29                                 

   POLYMORPHISM                         1034        979     <0.01      24                                 

   PTM                                 46531      35942      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    41686      41686      0.08       9                                 

   SIMILARITY                         649914     520189      1.19       1                                 

   SUBCELLULAR LOCATION               331827     325472      0.61       3                                 

   SUBUNIT                            253209     253209      0.46       4                                 

   TISSUE SPECIFICITY                  40164      40164      0.07      11                                 

   TOXIC DOSE                            575        537     <0.01      27                                 

   WEB RESOURCE                         9496       7548      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3861729                 7.09                                         

   ACT_SITE                           147686      90290      0.27       9                                 

   BINDING                            313681      83868      0.58       4                                 

   CA_BIND                              3948       1652      0.01      35                                 

   CARBOHYD                           108772      27832      0.20      15                                 

   CHAIN                              552394     538681      1.01       1                                 

   COILED                              20628      14180      0.04      26                                 

   COMPBIAS                            55773      29658      0.10      18                                 

   CONFLICT                           129391      45262      0.24      12                                 

   CROSSLNK                             7063       4038      0.01      34                                 

   DISULFID                           112778      30880      0.21      14                                 

   DNA_BIND                            10669       9695      0.02      31                                 

   DOMAIN                             165473      98590      0.30       8                                 

   HELIX                              193377      18581      0.35       6                                 

   INIT_MET                            17612      17612      0.03      27                                 

   INTRAMEM                             2206        963     <0.01      37                                 

   LIPID                               12255       7788      0.02      29                                 

   METAL                              336462      83180      0.62       3                                 

   MOD_RES                            173085      62253      0.32       7                                 

   MOTIF                               37475      24347      0.07      24                                 

   MUTAGEN                             47936      11009      0.09      20                                 

   NON_CONS                             2063        752     <0.01      38                                 

   NON_STD                               356        281     <0.01      39                                 

   NON_TER                             12240       9356      0.02      30                                 

   NP_BIND                            125998      75808      0.23      13                                 

   PEPTIDE                             10428       7131      0.02      32                                 

   PROPEP                              12912      11122      0.02      28                                 

   REGION                             146058      73878      0.27      10                                 

   REPEAT                              96978      14308      0.18      16                                 

   SIGNAL                              38921      38911      0.07      23                                 

   SITE                                48651      26969      0.09      19                                 

   STRAND                             202733      17556      0.37       5                                 

   TOPO_DOM                           132165      27391      0.24      11                                 

   TRANSIT                              8606       8500      0.02      33                                 

   TRANSMEM                           359936      74405      0.66       2                                 

   TURN                                47165      15097      0.09      22                                 

   UNSURE                               3404        726      0.01      36                                 

   VAR_SEQ                             47353      19815      0.09      21                                 

   VARIANT                             87482      16859      0.16      17                                 

   ZN_FING                             29616      13069      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)               16548164                30.36                                                           

   Allergome                            1629       1060     <0.01     103      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     115      Organism-specific databases                  

   ArrayExpress                        21858      21858      0.04      55      Gene expression databases                    

   Bgee                                38831      38831      0.07      47      Gene expression databases                    

   BindingDB                            4991       4991      0.01      90      Chemistry                                    

   BioCyc                             319970     305571      0.59      21      Enzyme and pathway databases                 

   BioGrid                             38818      38475      0.07      48      Protein-protein interaction databases        

   BRENDA                               4322       4311      0.01      93      Enzyme and pathway databases                 

   CAZy                                 7663       6898      0.01      76      Protein family/group databases               

   CGD                                   898        876     <0.01     110      Organism-specific databases                  

   ChEMBL                               5586       5586      0.01      84      Chemistry                                    

   ChiTaRS                             12554      12549      0.02      72      Other                                        

   CleanEx                             30070      29430      0.06      52      Gene expression databases                    

   COMPLUYEAST-2DPAGE                     99         98     <0.01     127      2D gel databases                             

   ConoServer                            948        866     <0.01     108      Organism-specific databases                  

   CTD                                 71846      71122      0.13      38      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      82      Organism-specific databases                  

   dictyBase                            4203       4087      0.01      95      Organism-specific databases                  

   DIP                                 15195      15124      0.03      68      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     118      3D structure databases                       

   DMDM                                16431      16431      0.03      66      Polymorphism databases                       

   DNASU                               18727      18656      0.03      61      Protocols and materials databases            

   DOSAC-COBS-2DPAGE                     149        147     <0.01     126      2D gel databases                             

   DrugBank                             5305       1617      0.01      85      Chemistry                                    

   EchoBASE                             4161       4161      0.01      96      Organism-specific databases                  

   EcoGene                              4292       4290      0.01      94      Organism-specific databases                  

   eggNOG                             430122     430122      0.79      10      Phylogenomic databases                       

   EMBL                               950659     533831      1.74       3      Sequence databases                           

   Ensembl                             85488      49131      0.16      35      Genome annotation databases                  

   EnsemblBacteria                    344815     326229      0.63      18      Genome annotation databases                  

   EnsemblFungi                        18888      18571      0.03      60      Genome annotation databases                  

   EnsemblMetazoa                      12763       9371      0.02      71      Genome annotation databases                  

   EnsemblPlants                       17532      15067      0.03      64      Genome annotation databases                  

   EnsemblProtists                      4594       4461      0.01      92      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     128      Organism-specific databases                  

   EuPathDB                              800        800     <0.01     112      Organism-specific databases                  

   EvolutionaryTrace                   16400      16399      0.03      67      Other                                        

   FlyBase                              5926       5552      0.01      80      Organism-specific databases                  

   Gene3D                             414352     306764      0.76      11      Family and domain databases                  

   GeneCards                           20898      19799      0.04      57      Organism-specific databases                  

   GeneFarm                             3229       3218      0.01      97      Organism-specific databases                  

   GeneID                             489125     459993      0.90       6      Genome annotation databases                  

   GeneTree                            35269      35255      0.06      49      Phylogenomic databases                       

   Genevestigator                      67972      67972      0.12      41      Gene expression databases                    

   GeneWiki                            10375      10288      0.02      74      Other                                        

   GenoList                             7071       7059      0.01      77      Organism-specific databases                  

   GenomeRNAi                          21387      21387      0.04      56      Other                                        

   GO                                2508637     512151      4.60       1      Ontologies                                   

   Gramene                              6174       6174      0.01      79      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  1797       1797     <0.01     102      Chemistry                                    

   H-InvDB                              5590       4770      0.01      83      Organism-specific databases                  

   HAMAP                              323409     320503      0.59      20      Family and domain databases                  

   HGNC                                19914      19748      0.04      59      Organism-specific databases                  

   HOGENOM                            384806     384806      0.71      16      Phylogenomic databases                       

   HOVERGEN                            75658      75658      0.14      37      Phylogenomic databases                       

   HPA                                 22363      15991      0.04      54      Organism-specific databases                  

   InParanoid                          70676      70676      0.13      40      Phylogenomic databases                       

   IntAct                              41624      41624      0.08      46      Protein-protein interaction databases        

   InterPro                          1831255     519443      3.36       2      Family and domain databases                  

   KEGG                               467059     441193      0.86       7      Genome annotation databases                  

   KO                                 372229     371758      0.68      17      Phylogenomic databases                       

   LegioList                             765        763     <0.01     114      Organism-specific databases                  

   Leproma                               671        668     <0.01     116      Organism-specific databases                  

   MaizeGDB                              502        497     <0.01     121      Organism-specific databases                  

   MEROPS                              11904      11904      0.02      73      Protein family/group databases               

   MGI                                 16581      16537      0.03      65      Organism-specific databases                  

   MIM                                 18582      13907      0.03      62      Organism-specific databases                  

   MINT                                31566      31566      0.06      51      Protein-protein interaction databases        

   mycoCLAP                              281        275     <0.01     124      Protein family/group databases               

   NextBio                             71154      71154      0.13      39      Other                                        

   neXtProt                            20109      20109      0.04      58      Organism-specific databases                  

   OGP                                   377        377     <0.01     123      2D gel databases                             

   OMA                                399558     399558      0.73      13      Phylogenomic databases                       

   Orphanet                             5918       3119      0.01      81      Organism-specific databases                  

   OrthoDB                            388861     388861      0.71      14      Phylogenomic databases                       

   PANTHER                            191941     180343      0.35      25      Family and domain databases                  

   PATRIC                             307400     307372      0.56      22      Genome annotation databases                  

   PaxDb                               66590      66590      0.12      42      Proteomic databases                          

   PDB                                105490      20629      0.19      32      3D structure databases                       

   PDBsum                             105490      20629      0.19      31      3D structure databases                       

   PeptideAtlas                         5162       5162      0.01      87      Proteomic databases                          

   PeroxiBase                            768        752     <0.01     113      Protein family/group databases               

   Pfam                               726820     500598      1.33       4      Family and domain databases                  

   PharmGKB                            18387      18359      0.03      63      Organism-specific databases                  

   PhosphoSite                         33572      33572      0.06      50      PTM databases                                

   PhosSite                              592        583     <0.01     119      PTM databases                                

   PhylomeDB                           75979      75979      0.14      36      Phylogenomic databases                       

   PIR                                121199     111010      0.22      30      Sequence databases                           

   PIRSF                              101439     100481      0.19      34      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     104      Other                                        

   PomBase                              5015       4968      0.01      89      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     129      Protein family/group databases               

   PRIDE                              122212     122212      0.22      29      Proteomic databases                          

   PRINTS                             136605     120339      0.25      27      Family and domain databases                  

   PRO                                 57918      57918      0.11      44      Other                                        

   ProDom                              29285      29106      0.05      53      Family and domain databases                  

   ProMEX                                870        870     <0.01     111      Proteomic databases                          

   PROSITE                            435966     283937      0.80       8      Family and domain databases                  

   ProtClustDB                        343139     343139      0.63      19      Phylogenomic databases                       

   ProteinModelPortal                 434941     434941      0.80       9      3D structure databases                       

   PseudoCAP                            1269       1260     <0.01     105      Organism-specific databases                  

   Reactome                            14004       8144      0.03      69      Enzyme and pathway databases                 

   REBASE                                402        402     <0.01     122      Protein family/group databases               

   RefSeq                             547974     469103      1.01       5      Sequence databases                           

   REPRODUCTION-2DPAGE                  1258       1037     <0.01     106      2D gel databases                             

   RGD                                  7816       7812      0.01      75      Organism-specific databases                  

   SABIO-RK                             2852       2852      0.01      99      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      78      Organism-specific databases                  

   SignaLink                            2960       2959      0.01      98      Enzyme and pathway databases                 

   SMART                              168308     126091      0.31      26      Family and domain databases                  

   SMR                                222110     222110      0.41      24      3D structure databases                       

   STRING                             402046     402046      0.74      12      Protein-protein interaction databases        

   SUPFAM                             387723     298142      0.71      15      Family and domain databases                  

   SWISS-2DPAGE                         1182       1181     <0.01     107      2D gel databases                             

   TAIR                                12797      12741      0.02      70      Organism-specific databases                  

   TCDB                                 5162       5132      0.01      86      Protein family/group databases               

   TIGRFAMs                           289465     269441      0.53      23      Family and domain databases                  

   TreeFam                             44693      44688      0.08      45      Phylogenomic databases                       

   TubercuList                          2057       2021     <0.01     101      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     120      2D gel databases                             

   UCSC                                58363      44706      0.11      43      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     125      PTM databases                                

   UniGene                            101771      91956      0.19      33      Sequence databases                           

   UniPathway                         132964     120975      0.24      28      Enzyme and pathway databases                 

   VectorBase                            607        589     <0.01     117      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     109      2D gel databases                             

   WormBase                             5019       3996      0.01      88      Organism-specific databases                  

   Xenbase                              4732       4726      0.01      91      Organism-specific databases                  

   ZFIN                                 2760       2760      0.01     100      Organism-specific databases                  



Total number of cross-referenced databases: 129



6.  AMINO ACID COMPOSITION



   6.1  Composition in percent for the complete database



   Ala (A) 8.26   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.57

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

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

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

   Cys (C) 1.37   Ile (I) 5.95   Pro (P) 4.71   Val (V) 6.87



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



   



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

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





   6.2  Classification of the amino acids by their frequency



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

   Phe, Tyr, Met, His, Cys, Trp





7.  MISCELLANEOUS STATISTICS



4465 entries are encoded on a mitochondrion, and 3740 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: 75568