UniProtKB/Swiss-Prot protein knowledgebase release 2014_08 statistics





1.  INTRODUCTION



Release 2014_08 of 03-Sep-14 of UniProtKB/Swiss-Prot contains 546238 sequence entries,

comprising 194363168 amino acids abstracted from 230490 references. 



258 sequences have been added since release 2014_07, the sequence data of

45 existing entries has been updated and the annotations of

141222 entries have been revised.



Number of fragments: 9120

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 37527





Protein existence (PE):           entries     %



1: Evidence at protein level        84435   15.5%

2: Evidence at transcript level     62535   11.4%

3: Inferred from homology          381759   69.9%

4: Predicted                        15627    2.9%

5: Uncertain                         1882    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: 13118



   The first twenty species represent 115027 sequences:  21.1 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5454

                            2x: 1893

                            3x: 1005

                            4x:  656

                            5x:  479

                            6x:  395

                            7x:  292

                            8x:  222

                            9x:  215

                           10x:  121

                       11- 20x:  707

                       21- 50x:  423

                       51-100x:  210

                         >100x: 1046





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20193  Homo sapiens (Human)

       2      16676  Mus musculus (Mouse)

       3      13100  Arabidopsis thaliana (Mouse-ear cress)

       4       7908  Rattus norvegicus (Rat)

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

       6       5986  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       4127  Dictyostelium discoideum (Slime mold)

      11       3468  Caenorhabditis elegans

      12       3385  Xenopus laevis (African clawed frog)

      13       3261  Oryza sativa subsp. japonica (Rice)

      14       3232  Drosophila melanogaster (Fruit fly)

      15       2929  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2261  Gallus gallus (Chicken)

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

      18       2030  Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

      19       2025  Escherichia coli O157:H7

      20       1885  Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

      21       1787  Methanocaldococcus jannaschii  

      22       1778  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       1414  Sus scrofa (Pig)

      28       1346  Salmonella typhi

      29       1271  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       1048  Synechocystis sp. (strain PCC 6803 / Kazusa)

      33       1021  Archaeoglobus fulgidus 

      34       1019  Yersinia pestis

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

      36        939  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        838  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        810  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  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      65        786  Emericella nidulans  

      66        783  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        767  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  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      82        747  Zea mays (Maize)

      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  Salmonella paratyphi A (strain AKU_12601)

      96        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      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  Pseudomonas putida (strain KT2440)

     105        702  Salmonella dublin (strain CT_02021853)

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

     113        680  Oryza sativa subsp. indica (Rice)

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

     115        677  Pseudomonas syringae pv. tomato (strain DC3000)

     116        671  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        659  Bradyrhizobium diazoefficiens 

     122        659  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        658  Escherichia coli

     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        619  Methanothermobacter thermautotrophicus  

     135        618  Treponema pallidum (strain Nichols)

     136        613  Staphylococcus haemolyticus (strain JCSC1435)

     137        608  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        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        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  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     154        568  Caenorhabditis briggsae

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

     156        567  Caulobacter crescentus (strain ATCC 19089 / CB15)

     157        567  Pseudomonas syringae pv. syringae (strain B728a)

     158        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     159        565  Pseudomonas aeruginosa (strain UCBPP-PA14)

     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        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  Deinococcus radiodurans 

     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  Bacillus amyloliquefaciens subsp. plantarum 

     201        491  Xanthomonas campestris pv. campestris (strain 8004)

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

     203        490  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     204        488  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     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  Shewanella sp. (strain MR-4)

     211        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     212        483  Methanosarcina mazei  

     213        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     214        482  Thermosynechococcus elongatus (strain BP-1)

     215        481  Pyrococcus horikoshii 

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

     217        477  Pseudomonas putida (strain F1 / ATCC 700007)

     218        477  Brucella abortus (strain 2308)

     219        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     220        476  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     221        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     222        472  Pyrococcus abyssi (strain GE5 / Orsay)

     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        464  Nicotiana tabacum (Common tobacco)

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

     230        464  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     231        463  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     232        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     233        463  Shewanella sp. (strain ANA-3)

     234        462  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     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           19272 (  4%)

    Bacteria         331627 ( 61%)

    Eukaryota        178860 ( 33%)

    Viruses           16479 (  3%)





   Within Eukaryota:



   



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

     Human                  20194 ( 11%)           (  4%)

     Other Mammalia         46068 ( 26%)           (  8%)

     Other Vertebrata       17742 ( 10%)           (  3%)

     Viridiplantae          35503 ( 20%)           (  6%)

     Fungi                  31290 ( 17%)           (  6%)

     Insecta                 8755 (  5%)           (  2%)

     Nematoda                4344 (  2%)           (  1%)

     Other                  14964 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9101             1001-1100     3797

                 51- 100   41801             1101-1200     2644

                101- 150   58212             1201-1300     2045

                151- 200   58121             1301-1400     1918

                201- 250   56981             1401-1500     1533

                251- 300   50564             1501-1600      751

                301- 350   50729             1601-1700      577

                351- 400   43957             1701-1800      481

                401- 450   36034             1801-1900      439

                451- 500   28932             1901-2000      356

                501- 550   20639             2001-2100      217

                551- 600   14805             2101-2200      297

                601- 650   12392             2201-2300      299

                651- 700    8969             2301-2400      185

                701- 750    7394             2401-2500      140

                751- 800    5288             >2500         1111

                801- 850    4610

                851- 900    5084

                901- 950    3924

                951-1000    2791



   





   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: 2434





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  796

                       2x:  320

                       3x:  161

                       4x:  119

                       5x:   91

                       6x:   79

                       7x:   57

                       8x:   47

                       9x:   31

                      10x:   43

                  11- 20x:  190

                  21- 50x:  196

                  51-100x:  110

                    >100x:  194





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



   Nb    Citations   Journal name

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

    1        22119   Journal of Biological Chemistry

    2        10049   Proceedings of the National Academy of Sciences of the U.S.A.

    3         6013   Journal of Bacteriology

    4         5191   Biochemical and Biophysical Research Communications

    5         4701   Biochemistry

    6         4696   Nucleic Acids Research

    7         4663   Gene

    8         4492   FEBS Letters

    9         4372   The EMBO Journal

   10         4047   Molecular and Cellular Biology

   11         3916   Nature

   12         3823   Journal of Molecular Biology

   13         3321   Biochimica et Biophysica Acta

   14         3288   European Journal of Biochemistry

   15         3186   Cell

   16         2707   Journal of Virology

   17         2617   Science

   18         2599   Biochemical Journal

   19         2517   Genomics

   20         2201   Molecular Microbiology

   21         2016   Plant Physiology

   22         1962   Journal of Cell Biology

   23         1740   The American Journal of Human Genetics

   24         1699   Plant Molecular Biology

   25         1670   Genes and Development

   26         1584   Virology

   27         1567   Nature Genetics

   28         1542   Human Molecular Genetics

   29         1475   The Plant Cell

   30         1471   Oncogene

   31         1427   Molecular Biology of the Cell

   32         1406   Development

   33         1358   Molecular and General Genetics

   34         1355   Human Mutation

   35         1326   The Plant Journal

   36         1273   Journal of Biochemistry

   37         1271   Molecular Cell

   38         1219   Journal of Immunology

   39         1153   Structure

   40         1146   Genetics

   41         1043   Journal of General Virology

   42         1022   Blood

   43         1014   Journal of Cell Science

   44         1007   Infection and Immunity

   45          961   Archives of Biochemistry and Biophysics

   46          936   Microbiology

   47          902   PLoS ONE

   48          865   Developmental Biology

   49          863   Current Biology

   50          823   Cancer Research

   51          810   Yeast

   52          766   FEMS Microbiology Letters

   53          734   Acta Crystallographica, Section D

   54          703   Applied and Environmental Microbiology

   55          697   Protein Science

   56          692   Journal of Neuroscience

   57          692   Toxicon

   58          639   Human Genetics

   59          634   Nature Structural Biology

   60          628   Mechanisms of Development

   61          625   Neuron

   62          596   Journal of Clinical Investigation

   63          587   American Journal of Physiology

   64          552   The Journal of Experimental Medicine

   65          549   Current Genetics

   66          537   Proteins

   67          525   Plant and Cell Physiology

   68          504   Molecular Endocrinology

   69          483   Mammalian Genome

   70          483   Journal of Neurochemistry

   71          478   Nature Cell Biology

   72          470   Bioscience, Biotechnology, and Biochemistry

   73          467   Journal of Medical Genetics

   74          461   Endocrinology

   75          460   Immunogenetics

   76          449   The Journal of Clinical Endocrinology and Metabolism

   77          441   Molecular and Biochemical Parasitology

   78          403   Journal of Molecular Evolution

   79          397   Experimental Cell Research

   80          385   Nature Structural and Molecular Biology

   81          382   Molecular Biology and Evolution

   82          378   DNA and Cell Biology

   83          377   Peptides

   84          368   DNA Sequence

   85          360   The FEBS Journal

   86          357   RNA

   87          353   Developmental Cell

   88          340   Eukaryotic Cell

   89          340   Antimicrobial Agents and Chemotherapy

   90          331   Brain Research. Molecular Brain Research

   91          327   Planta

   92          326   Comparative Biochemistry and Physiology

   93          325   Tissue Antigens

   94          323   Journal of Investigative Dermatology

   95          318   Molecular Pharmacology

   96          299   Biology of Reproduction

   97          294   Biological Chemistry Hoppe-Seyler

   98          293   Neurology

   99          283   Developmental Dynamics

  100          281   Cytogenetics and Cell Genetics

  101          281   EMBO Reports

  102          276   Biochimie

  103          276   Immunity

  104          275   The FASEB Journal

  105          270   Genome Research

  106          270   Virus Research

  107          270   Genes to Cells

  108          263   Journal of General Microbiology

  109          260   The New England Journal of Medicine

  110          257   Molecular Plant-Microbe Interactions

  111          249   PLoS Genetics

  112          246   Journal of the American Chemical Society

  113          240   European Journal of Human Genetics

  114          237   Annals of Neurology

  115          237   Acta Crystallographica, Section F

  116          235   European Journal of Immunology

  117          219   DNA Research

  118          219   Investigative Ophthalmology and Visual Science

  119          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  120          217   Journal of Experimental Botany

  121          215   Nature Immunology

  122          214   BMC Genomics

  123          214   Journal of Human Genetics

  124          213   Archives of Microbiology

  125          204   Journal of Cellular Biochemistry

  126          201   American Journal of Medical Genetics. Part A

  127          198   Journal of Medicinal Chemistry

  128          196   Glycobiology

  129          195   Molecular and Cellular Endocrinology

  130          193   Clinical Genetics

  131          193   Archives of Virology

  132          191   Molecular Immunology

  133          185   Diabetes

  134          183   Circulation Research

  135          181   Cell Cycle

  136          176   Insect Biochemistry and Molecular Biology

  137          175   Traffic

  138          174   PLoS Pathogens

  139          173   Applied Microbiology and Biotechnology

  140          173   Phytochemistry

  141          173   Molecular Genetics and Metabolism

  142          170   International Journal of Cancer

  143          170   Protein Expression and Purification

  144          169   Molecular Phylogenetics and Evolution

  145          168   American Journal of Medical Genetics

  146          162   PLoS Biology

  147          161   Biological Chemistry

  148          160   Molecular Reproduction and Development

  149          159   DNA

  150          158   Molecular Genetics and Genomics





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)                      1083211                 1.98                                         

   Journal                            889235     432801      1.63       1                                 

   Submitted to EMBL/GenBank/DDBJ     183962     163141      0.34       2                                 

   Submitted to other databases         7009       6518      0.01       3                                 

   Book citation                        1466       1452     <0.01       4                                 

   Plant Gene Register                   593        581     <0.01       5                                 

   Thesis                                422        419     <0.01       6                                 

   Unpublished observations              328        324     <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: 353074



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2509634                 4.59                                         

   ALLERGEN                              662        662     <0.01      25                                 

   ALTERNATIVE PRODUCTS                23277      23277      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5922       5922      0.01      21                                 

   BIOTECHNOLOGY                         407        405     <0.01      28                                 

   CATALYTIC ACTIVITY                 250989     226325      0.46       5                                 

   CAUTION                              9878       9695      0.02      18                                 

   COFACTOR                           115234     105551      0.21       7                                 

   DEVELOPMENTAL STAGE                 10325      10325      0.02      17                                 

   DISEASE                              5679       3821      0.01      23                                 

   DISRUPTION PHENOTYPE                 7567       7567      0.01      20                                 

   DOMAIN                              42105      36650      0.08       9                                 

   ENZYME REGULATION                   12815      12815      0.02      16                                 

   FUNCTION                           434873     417010      0.80       2                                 

   INDUCTION                           16650      16650      0.03      14                                 

   INTERACTION                         12938      12938      0.02      15                                 

   MASS SPECTROMETRY                    5771       4397      0.01      22                                 

   MISCELLANEOUS                       34287      31699      0.06      12                                 

   PATHWAY                            133428     121417      0.24       6                                 

   PHARMACEUTICAL                         98         98     <0.01      29                                 

   POLYMORPHISM                         1038        981     <0.01      24                                 

   PTM                                 47091      36346      0.09       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    41967      41967      0.08      10                                 

   SIMILARITY                         656621     521391      1.20       1                                 

   SUBCELLULAR LOCATION               334003     327615      0.61       3                                 

   SUBUNIT                            255855     255855      0.47       4                                 

   TISSUE SPECIFICITY                  40656      40656      0.07      11                                 

   TOXIC DOSE                            587        545     <0.01      27                                 

   WEB RESOURCE                         8284       6940      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3929882                 7.19                                         

   ACT_SITE                           149777      91757      0.27      10                                 

   BINDING                            325309      86419      0.60       4                                 

   CA_BIND                              3972       1669      0.01      35                                 

   CARBOHYD                           109224      28035      0.20      15                                 

   CHAIN                              553629     539892      1.01       1                                 

   COILED                              20733      14278      0.04      26                                 

   COMPBIAS                            56068      29861      0.10      18                                 

   CONFLICT                           130129      45509      0.24      13                                 

   CROSSLNK                             7146       4086      0.01      34                                 

   DISULFID                           115031      31347      0.21      14                                 

   DNA_BIND                            10717       9736      0.02      31                                 

   DOMAIN                             170960     103543      0.31       8                                 

   HELIX                              197759      18950      0.36       6                                 

   INIT_MET                            17739      17739      0.03      27                                 

   INTRAMEM                             2247        980     <0.01      37                                 

   LIPID                               12222       7842      0.02      30                                 

   METAL                              343448      85079      0.63       3                                 

   MOD_RES                            173712      62659      0.32       7                                 

   MOTIF                               37671      24462      0.07      24                                 

   MUTAGEN                             49610      11361      0.09      20                                 

   NON_CONS                             2069        759     <0.01      38                                 

   NON_STD                               357        282     <0.01      39                                 

   NON_TER                             12278       9385      0.02      29                                 

   NP_BIND                            130144      77075      0.24      12                                 

   PEPTIDE                             10487       7171      0.02      32                                 

   PROPEP                              12986      11182      0.02      28                                 

   REGION                             160624      77128      0.29       9                                 

   REPEAT                              97347      14341      0.18      16                                 

   SIGNAL                              39257      39247      0.07      23                                 

   SITE                                49721      27677      0.09      19                                 

   STRAND                             207220      17884      0.38       5                                 

   TOPO_DOM                           132851      27555      0.24      11                                 

   TRANSIT                              8692       8579      0.02      33                                 

   TRANSMEM                           360899      74598      0.66       2                                 

   TURN                                48115      15363      0.09      22                                 

   UNSURE                               3427        731      0.01      36                                 

   VAR_SEQ                             48821      20330      0.09      21                                 

   VARIANT                             87812      16893      0.16      17                                 

   ZN_FING                             29672      13111      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)               16710528                30.59                                                           

   Allergome                            1633       1061     <0.01     104      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     117      Organism-specific databases                  

   ArrayExpress                        21900      21900      0.04      57      Gene expression databases                    

   Bgee                                38828      38828      0.07      49      Gene expression databases                    

   BindingDB                            4993       4993      0.01      91      Chemistry                                    

   BioCyc                             324335     307180      0.59      19      Enzyme and pathway databases                 

   BioGrid                             39300      38955      0.07      48      Protein-protein interaction databases        

   BRENDA                               4343       4331      0.01      94      Enzyme and pathway databases                 

   CAZy                                 7737       6961      0.01      77      Protein family/group databases               

   CCDS                                44683      33293      0.08      46      Sequence databases                           

   CGD                                   916        894     <0.01     112      Organism-specific databases                  

   ChEMBL                               5684       5684      0.01      83      Chemistry                                    

   ChiTaRS                             12556      12552      0.02      72      Other                                        

   CleanEx                             30068      29429      0.06      53      Gene expression databases                    

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

   ConoServer                            949        866     <0.01     110      Organism-specific databases                  

   CTD                                 72095      71394      0.13      37      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      84      Organism-specific databases                  

   dictyBase                            4203       4088      0.01      96      Organism-specific databases                  

   DIP                                 15441      15371      0.03      70      Protein-protein interaction databases        

   DisProt                               605        602     <0.01     121      3D structure databases                       

   DMDM                                16408      16408      0.03      69      Polymorphism databases                       

   DNASU                               18747      18677      0.03      63      Protocols and materials databases            

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

   DrugBank                             5305       1617      0.01      87      Chemistry                                    

   EchoBASE                             4161       4161      0.01      97      Organism-specific databases                  

   EcoGene                              4294       4292      0.01      95      Organism-specific databases                  

   eggNOG                             430606     430606      0.79      12      Phylogenomic databases                       

   EMBL                               956195     535035      1.75       3      Sequence databases                           

   Ensembl                             86489      49139      0.16      35      Genome annotation databases                  

   EnsemblBacteria                    349028     330417      0.64      18      Genome annotation databases                  

   EnsemblFungi                        19027      18687      0.03      62      Genome annotation databases                  

   EnsemblMetazoa                      12141       9428      0.02      73      Genome annotation databases                  

   EnsemblPlants                       18596      15893      0.03      65      Genome annotation databases                  

   EnsemblProtists                      4477       4355      0.01      93      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     130      Organism-specific databases                  

   EuPathDB                              808        808     <0.01     114      Organism-specific databases                  

   EvolutionaryTrace                   16453      16453      0.03      68      Other                                        

   FlyBase                              5934       5560      0.01      82      Organism-specific databases                  

   Gene3D                             466231     343845      0.85       8      Family and domain databases                  

   GeneCards                           20887      19790      0.04      59      Organism-specific databases                  

   GeneFarm                             3312       3300      0.01      98      Organism-specific databases                  

   GeneID                             496548     469132      0.91       6      Genome annotation databases                  

   GeneReviews                          1156       1153     <0.01     109      Organism-specific databases                  

   GeneTree                            38234      38220      0.07      50      Phylogenomic databases                       

   Genevestigator                      68141      68141      0.12      40      Gene expression databases                    

   GeneWiki                            10367      10281      0.02      75      Other                                        

   GenoList                             7074       7062      0.01      78      Organism-specific databases                  

   GenomeRNAi                          21393      21393      0.04      58      Other                                        

   GO                                2548088     516955      4.66       1      Ontologies                                   

   Gramene                              6222       6222      0.01      80      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  2012       2012     <0.01     103      Chemistry                                    

   H-InvDB                              5590       4770      0.01      85      Organism-specific databases                  

   HAMAP                              323754     320835      0.59      20      Family and domain databases                  

   HGNC                                19934      19770      0.04      61      Organism-specific databases                  

   HOGENOM                            385397     385397      0.71      16      Phylogenomic databases                       

   HOVERGEN                            75638      75638      0.14      36      Phylogenomic databases                       

   HPA                                 22352      15982      0.04      56      Organism-specific databases                  

   InParanoid                          70873      70873      0.13      39      Phylogenomic databases                       

   IntAct                              41984      41984      0.08      47      Protein-protein interaction databases        

   InterPro                          1900026     525445      3.48       2      Family and domain databases                  

   KEGG                               476357     447571      0.87       7      Genome annotation databases                  

   KO                                 376524     376030      0.69      17      Phylogenomic databases                       

   LegioList                             765        763     <0.01     116      Organism-specific databases                  

   Leproma                               671        668     <0.01     118      Organism-specific databases                  

   MaizeGDB                              503        498     <0.01     123      Organism-specific databases                  

   MaxQB                               27057      27057      0.05      55      Proteomic databases                          

   MEROPS                              11916      11916      0.02      74      Protein family/group databases               

   MGI                                 16591      16547      0.03      67      Organism-specific databases                  

   MIM                                 18736      13979      0.03      64      Organism-specific databases                  

   MINT                                31577      31577      0.06      52      Protein-protein interaction databases        

   mycoCLAP                              328        320     <0.01     126      Protein family/group databases               

   NextBio                             71190      71190      0.13      38      Other                                        

   neXtProt                            20049      20049      0.04      60      Organism-specific databases                  

   OGP                                   376        376     <0.01     125      2D gel databases                             

   OMA                                403079     403079      0.74      13      Phylogenomic databases                       

   Orphanet                             6018       3167      0.01      81      Organism-specific databases                  

   OrthoDB                            389170     389170      0.71      15      Phylogenomic databases                       

   PANTHER                            172017     166148      0.31      24      Family and domain databases                  

   PATRIC                             307636     307607      0.56      21      Genome annotation databases                  

   PaxDb                               66584      66584      0.12      41      Proteomic databases                          

   PDB                                109074      21093      0.20      31      3D structure databases                       

   PDBsum                             109074      21093      0.20      30      3D structure databases                       

   PeptideAtlas                         5160       5160      0.01      88      Proteomic databases                          

   PeroxiBase                            769        753     <0.01     115      Protein family/group databases               

   Pfam                               738568     506792      1.35       4      Family and domain databases                  

   PharmGKB                            18385      18357      0.03      66      Organism-specific databases                  

   PhosphoSite                         33560      33560      0.06      51      PTM databases                                

   PhosSite                              605        596     <0.01     120      PTM databases                                

   PhylomeDB                           93247      93247      0.17      34      Phylogenomic databases                       

   PIR                                121530     111323      0.22      29      Sequence databases                           

   PIRSF                              102163     101201      0.19      33      Family and domain databases                  

   PMAP-CutDB                           1461       1461     <0.01     105      Other                                        

   PomBase                              5139       5103      0.01      89      Organism-specific databases                  

   PptaseDB                               37         37     <0.01     131      Protein family/group databases               

   PRIDE                              122255     122255      0.22      28      Proteomic databases                          

   PRINTS                             136726     120428      0.25      26      Family and domain databases                  

   PRO                                 57971      57971      0.11      43      Other                                        

   ProDom                              28667      28488      0.05      54      Family and domain databases                  

   ProMEX                                873        873     <0.01     113      Proteomic databases                          

   PROSITE                            443743     286609      0.81       9      Family and domain databases                  

   ProteinModelPortal                 440089     440089      0.81      11      3D structure databases                       

   PseudoCAP                            1279       1270     <0.01     106      Organism-specific databases                  

   Reactome                            56801      19932      0.10      44      Enzyme and pathway databases                 

   REBASE                                408        408     <0.01     124      Protein family/group databases               

   RefSeq                             644690     478238      1.18       5      Sequence databases                           

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

   RGD                                  7829       7825      0.01      76      Organism-specific databases                  

   SABIO-RK                             2896       2896      0.01     100      Enzyme and pathway databases                 

   SGD                                  6640       6635      0.01      79      Organism-specific databases                  

   SignaLink                            2964       2960      0.01      99      Enzyme and pathway databases                 

   SMART                              169676     127062      0.31      25      Family and domain databases                  

   SMR                                218329     218329      0.40      23      3D structure databases                       

   STRING                             402528     402527      0.74      14      Protein-protein interaction databases        

   SUPFAM                             441649     339536      0.81      10      Family and domain databases                  

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

   TAIR                                13099      13043      0.02      71      Organism-specific databases                  

   TCDB                                 5311       5291      0.01      86      Protein family/group databases               

   TIGRFAMs                           291074     270899      0.53      22      Family and domain databases                  

   TreeFam                             44738      44733      0.08      45      Phylogenomic databases                       

   TubercuList                          2058       2022     <0.01     102      Organism-specific databases                  

   UCD-2DPAGE                            509        500     <0.01     122      2D gel databases                             

   UCSC                                58646      44721      0.11      42      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     127      PTM databases                                

   UniGene                            102285      92329      0.19      32      Sequence databases                           

   UniPathway                         133266     121260      0.24      27      Enzyme and pathway databases                 

   VectorBase                            607        589     <0.01     119      Genome annotation databases                  

   World-2DPAGE                          921        910     <0.01     111      2D gel databases                             

   WormBase                             5030       3998      0.01      90      Organism-specific databases                  

   Xenbase                              4764       4758      0.01      92      Organism-specific databases                  

   ZFIN                                 2766       2766      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) 6.57

   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 3774 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: 75978