UniProtKB/Swiss-Prot protein knowledgebase release 2014_03 statistics





1.  INTRODUCTION



Release 2014_03 of 19-Mar-14 of UniProtKB/Swiss-Prot contains 542782 sequence entries,

comprising 193019802 amino acids abstracted from 226896 references. 



286 sequences have been added since release 2014_02, the sequence data of

93 existing entries has been updated and the annotations of

79690 entries have been revised.



Number of fragments: 9080

Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 36011





Protein existence (PE):           entries     %



1: Evidence at protein level        82087   15.1%

2: Evidence at transcript level     62272   11.5%

3: Inferred from homology          380832   70.2%

4: Predicted                        15705    2.9%

5: Uncertain                         1886    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: 13068



   The first twenty species represent 114426 sequences:  21.1 % of the total

   number of entries.





   2.1 Table of the frequency of occurrence of species



        Species represented 1x: 5447

                            2x: 1902

                            3x:  996

                            4x:  645

                            5x:  468

                            6x:  396

                            7x:  286

                            8x:  223

                            9x:  212

                           10x:  124

                       11- 20x:  695

                       21- 50x:  419

                       51-100x:  212

                         >100x: 1043





   2.2  Table of the most represented species



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

  Number  Frequency  Species

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

       1      20263  Homo sapiens (Human)

       2      16664  Mus musculus (Mouse)

       3      12720  Arabidopsis thaliana (Mouse-ear cress)

       4       7889  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       3465  Caenorhabditis elegans

      12       3382  Xenopus laevis (African clawed frog)

      13       3220  Drosophila melanogaster (Fruit fly)

      14       3138  Oryza sativa subsp. japonica (Rice)

      15       2919  Danio rerio (Zebrafish) (Brachydanio rerio)

      16       2257  Gallus gallus (Chicken)

      17       2218  Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)

      18       2044  Mycobacterium tuberculosis

      19       2015  Escherichia coli O157:H7

      20       1787  Methanocaldococcus jannaschii  

      21       1772  Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

      22       1707  Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)

      23       1700  Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)

      24       1684  Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)

      25       1679  Shigella flexneri

      26       1413  Sus scrofa (Pig)

      27       1346  Salmonella typhi

      28       1261  Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)

      29       1242  Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)

      30       1170  Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)

      31       1045  Synechocystis sp. (strain PCC 6803 / Kazusa)

      32       1019  Yersinia pestis

      33       1017  Archaeoglobus fulgidus 

      34        955  Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

      35        930  Salmonella paratyphi A (strain ATCC 9150 / SARB42)

      36        926  Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)  

      37        925  Staphylococcus aureus (strain N315)

      38        924  Staphylococcus aureus (strain Mu50 / ATCC 700699)

      39        909  Acanthamoeba polyphaga mimivirus (APMV)

      40        905  Kluyveromyces lactis   

      41        899  Staphylococcus aureus (strain COL)

      42        895  Staphylococcus aureus (strain MW2)

      43        889  Escherichia coli O6:K15:H31 (strain 536 / UPEC)

      44        889  Staphylococcus aureus (strain MSSA476)

      45        889  Oryctolagus cuniculus (Rabbit)

      46        888  Staphylococcus aureus (strain MRSA252)

      47        882  Salmonella choleraesuis (strain SC-B67)

      48        878  Shigella sonnei (strain Ss046)

      49        870  Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)

      50        866  Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)

      51        863  Yersinia pseudotuberculosis serotype I (strain IP32953)

      52        862  Candida glabrata   

      53        841  Escherichia coli O9:H4 (strain HS)

      54        837  Neurospora crassa 

      55        834  Escherichia coli O139:H28 (strain E24377A / ETEC)

      56        829  Shigella boydii serotype 4 (strain Sb227)

      57        825  Escherichia coli (strain UTI89 / UPEC)

      58        821  Shigella dysenteriae serotype 1 (strain Sd197)

      59        819  Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)

      60        808  Canis familiaris (Dog) (Canis lupus familiaris)

      61        791  Escherichia coli (strain SMS-3-5 / SECEC)

      62        788  Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)

      63        783  Erwinia carotovora subsp. atroseptica (strain SCRI 1043 / ATCC BAA-672) 

      64        783  Aquifex aeolicus (strain VF5)

      65        782  Emericella nidulans  

      66        775  Pasteurella multocida (strain Pm70)

      67        771  Escherichia coli (strain K12 / DH10B)

      68        765  Escherichia coli O127:H6 (strain E2348/69 / EPEC)

      69        765  Escherichia coli (strain K12 / MC4100 / BW2952)

      70        765  Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)

      71        764  Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)

      72        762  Escherichia coli (strain 55989 / EAEC)

      73        761  Escherichia coli O8 (strain IAI1)

      74        760  Shigella flexneri serotype 5b (strain 8401)

      75        759  Staphylococcus epidermidis (strain ATCC 35984 / RP62A)

      76        758  Staphylococcus epidermidis (strain ATCC 12228)

      77        756  Escherichia coli (strain SE11)

      78        756  Escherichia coli O45:K1 (strain S88 / ExPEC)

      79        753  Escherichia coli O7:K1 (strain IAI39 / ExPEC)

      80        748  Escherichia coli O157:H7 (strain EC4115 / EHEC)

      81        745  Photorhabdus luminescens subsp. laumondii (strain TT01)

      82        740  Staphylococcus aureus (strain NCTC 8325)

      83        737  Bacillus halodurans 

      84        736  Bacillus anthracis

      85        735  Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)

      86        735  Zea mays (Maize)

      87        733  Vibrio vulnificus (strain CMCP6)

      88        731  Escherichia coli O81 (strain ED1a)

      89        721  Salmonella enteritidis PT4 (strain P125109)

      90        717  Vibrio vulnificus (strain YJ016)

      91        716  Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)

      92        715  Yersinia pestis bv. Antiqua (strain Nepal516)

      93        714  Salmonella paratyphi A (strain AKU_12601)

      94        713  Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)

      95        713  Enterobacter sp. (strain 638)

      96        713  Salmonella agona (strain SL483)

      97        713  Escherichia coli O1:K1 / APEC

      98        713  Salmonella newport (strain SL254)

      99        713  Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)

     100        712  Salmonella schwarzengrund (strain CVM19633)

     101        711  Yersinia pestis bv. Antiqua (strain Antiqua)

     102        710  Salmonella heidelberg (strain SL476)

     103        702  Salmonella dublin (strain CT_02021853)

     104        699  Pseudomonas putida (strain KT2440)

     105        698  Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)

     106        696  Klebsiella pneumoniae (strain 342)

     107        695  Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)

     108        691  Nostoc sp. (strain PCC 7120 / UTEX 2576)

     109        689  Pan troglodytes (Chimpanzee)

     110        687  Mycoplasma pneumoniae (strain ATCC 29342 / M129)

     111        683  Salmonella gallinarum (strain 287/91 / NCTC 13346)

     112        678  Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)

     113        675  Pseudomonas syringae pv. tomato (strain DC3000)

     114        670  Serratia proteamaculans (strain 568)

     115        668  Mycobacterium leprae (strain TN)

     116        667  Yersinia pestis (strain Pestoides F)

     117        667  Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) 

     118        666  Staphylococcus aureus (strain USA300)

     119        659  Bradyrhizobium diazoefficiens 

     120        658  Escherichia coli

     121        658  Rhizobium sp. (strain NGR234)

     122        654  Bacillus cereus (strain ATCC 14579 / DSM 31)

     123        653  Debaryomyces hansenii   

     124        650  Oryza sativa subsp. indica (Rice)

     125        644  Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)

     126        643  Staphylococcus aureus (strain bovine RF122 / ET3-1)

     127        642  Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)

     128        638  Yersinia pseudotuberculosis serotype O:3 (strain YPIII)

     129        635  Shewanella oneidensis (strain MR-1)

     130        634  Yersinia pseudotuberculosis serotype IB (strain PB1/+)

     131        634  Agrobacterium tumefaciens (strain C58 / ATCC 33970)

     132        622  Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)

     133        616  Methanothermobacter thermautotrophicus  

     134        616  Treponema pallidum (strain Nichols)

     135        613  Staphylococcus haemolyticus (strain JCSC1435)

     136        607  Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)

     137        605  Xanthomonas campestris pv. campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)

     138        604  Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)

     139        602  Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)

     140        602  Photobacterium profundum (Photobacterium sp. (strain SS9))

     141        602  Staphylococcus saprophyticus subsp. saprophyticus 

     142        601  Salmonella paratyphi C (strain RKS4594)

     143        600  Yersinia pestis bv. Antiqua (strain Angola)

     144        591  Bacillus cereus (strain ATCC 10987)

     145        591  Listeria innocua serovar 6a (strain CLIP 11262)

     146        589  Pectobacterium carotovorum subsp. carotovorum (strain PC1)

     147        587  Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)

     148        586  Rickettsia prowazekii (strain Madrid E)

     149        579  Neisseria meningitidis serogroup B (strain MC58)

     150        576  Brucella suis biovar 1 (strain 1330)

     151        573  Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)

     152        572  Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) 

     153        568  Caenorhabditis briggsae

     154        567  Bacillus thuringiensis subsp. konkukian (strain 97-27)

     155        567  Pseudomonas syringae pv. syringae (strain B728a)

     156        566  Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)

     157        565  Caulobacter crescentus (strain ATCC 19089 / CB15)

     158        564  Bacillus licheniformis (strain DSM 13 / ATCC 14580)

     159        564  Vibrio fischeri (strain ATCC 700601 / ES114)

     160        564  Pseudomonas aeruginosa (strain UCBPP-PA14)

     161        562  Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)

     162        561  Bacillus cereus (strain ZK / E33L)

     163        557  Clostridium acetobutylicum 

     164        556  Xanthomonas axonopodis pv. citri (strain 306)

     165        552  Oceanobacillus iheyensis (strain DSM 14371 / JCM 11309 / KCTC 3954 / HTE831)

     166        552  Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)

     167        552  Pseudomonas fluorescens (strain Pf0-1)

     168        546  Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477)

     169        545  Pseudomonas syringae pv. phaseolicola (strain 1448A / Race 6)

     170        534  Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)

     171        533  Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)

     172        531  Erwinia tasmaniensis (strain DSM 17950 / Et1/99)

     173        529  Sodalis glossinidius (strain morsitans)

     174        529  Listeria monocytogenes serotype 4b (strain F2365)

     175        525  Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50) 

     176        522  Xylella fastidiosa (strain 9a5c)

     177        515  Chromobacterium violaceum 

     178        515  Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

     179        513  Corynebacterium glutamicum 

     180        513  Vibrio cholerae serotype O1 (strain ATCC 39541 / Ogawa 395 / O395)

     181        512  Xylella fastidiosa (strain Temecula1 / ATCC 700964)

     182        511  Pseudomonas aeruginosa (strain PA7)

     183        510  Haemophilus ducreyi (strain 35000HP / ATCC 700724)

     184        508  Staphylococcus aureus (strain Newman)

     185        508  Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)

     186        507  Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)

     187        507  Geobacillus kaustophilus (strain HTA426)

     188        506  Streptomyces avermitilis 

     189        503  Deinococcus radiodurans 

     190        502  Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

     191        500  Pseudomonas entomophila (strain L48)

     192        499  Brucella abortus biovar 1 (strain 9-941)

     193        497  Rickettsia conorii (strain ATCC VR-613 / Malish 7)

     194        496  Bacillus clausii (strain KSM-K16)

     195        495  Burkholderia pseudomallei (strain K96243)

     196        495  Haemophilus influenzae (strain 86-028NP)

     197        494  Proteus mirabilis (strain HI4320)

     198        492  Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)

     199        492  Bacillus amyloliquefaciens (strain FZB42)

     200        491  Xanthomonas campestris pv. campestris (strain 8004)

     201        490  Vibrio campbellii (strain ATCC BAA-1116 / BB120)

     202        487  Shewanella sp. (strain MR-7)

     203        486  Mannheimia succiniciproducens (strain MBEL55E)

     204        484  Pseudomonas aeruginosa (strain LESB58)

     205        484  Staphylococcus aureus (strain Mu3 / ATCC 700698)

     206        484  Shewanella sp. (strain MR-4)

     207        483  Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)

     208        483  Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)

     209        483  Methanosarcina mazei  

     210        483  Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)

     211        482  Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)

     212        482  Thermosynechococcus elongatus (strain BP-1)

     213        479  Pyrococcus horikoshii 

     214        479  Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)

     215        477  Pseudomonas putida (strain F1 / ATCC 700007)

     216        477  Brucella abortus (strain 2308)

     217        476  Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

     218        474  Burkholderia sp. (strain 383) (Burkholderia cepacia 

     219        473  Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)

     220        470  Pyrococcus abyssi (strain GE5 / Orsay)

     221        468  Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1) 

     222        468  Clostridium perfringens (strain 13 / Type A)

     223        466  Xanthomonas campestris pv. vesicatoria (strain 85-10)

     224        466  Shewanella frigidimarina (strain NCIMB 400)

     225        466  Pseudomonas putida (strain GB-1)

     226        466  Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337) 

     227        464  Nicotiana tabacum (Common tobacco)

     228        464  Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / NCIB 9240)

     229        463  Anabaena variabilis (strain ATCC 29413 / PCC 7937)

     230        463  Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

     231        463  Shewanella sp. (strain ANA-3)

     232        462  Burkholderia mallei (strain ATCC 23344)

     233        461  Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

     234        461  Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

     235        459  Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Ralstonia eutropha 

     236        458  Enterococcus faecalis (strain ATCC 700802 / V583)

     237        456  Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168)

     238        455  Staphylococcus aureus (strain JH1)

     239        455  Ovis aries (Sheep)

     240        454  Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)

     241        454  Xanthomonas oryzae pv. oryzae (strain MAFF 311018)

     242        453  Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)

     243        453  Pseudomonas putida (strain W619)

     244        453  Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)

     245        452  Shewanella baltica (strain OS185)

     246        451  Aeromonas salmonicida (strain A449)

     247        450  Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)

     248        450  Dechloromonas aromatica (strain RCB)

     249        449  Thermoanaerobacter tengcongensis  

     250        449  Staphylococcus aureus (strain JH9)





   

   2.3  Taxonomic distribution of the sequences



   



   Kingdom        sequences (% of the database)

    Archaea           19069 (  4%)

    Bacteria         329423 ( 61%)

    Eukaryota        177837 ( 33%)

    Viruses           16453 (  3%)





   Within Eukaryota:



   



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

     Human                  20264 ( 11%)           (  4%)

     Other Mammalia         46022 ( 26%)           (  8%)

     Other Vertebrata       17636 ( 10%)           (  3%)

     Viridiplantae          34907 ( 20%)           (  6%)

     Fungi                  31099 ( 17%)           (  6%)

     Insecta                 8729 (  5%)           (  2%)

     Nematoda                4341 (  2%)           (  1%)

     Other                  14839 (  8%)           (  3%)







3.  SEQUENCE SIZE



   Repartition of the sequences by size (excluding fragments)



               From   To  Number             From   To   Number

                  1-  50    9080             1001-1100     3776

                 51- 100   41541             1101-1200     2615

                101- 150   57908             1201-1300     2034

                151- 200   57885             1301-1400     1908

                201- 250   56656             1401-1500     1527

                251- 300   50226             1501-1600      742

                301- 350   50368             1601-1700      573

                351- 400   43629             1701-1800      477

                401- 450   35721             1801-1900      433

                451- 500   28744             1901-2000      354

                501- 550   20483             2001-2100      217

                551- 600   14693             2101-2200      295

                601- 650   12329             2201-2300      300

                651- 700    8908             2301-2400      184

                701- 750    7332             2401-2500      140

                751- 800    5233             >2500         1101

                801- 850    4568

                851- 900    5053

                901- 950    3899

                951-1000    2770



   





   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: 2391





   4.1 Table of the frequency of journal citations



        Journals cited 1x:  777

                       2x:  313

                       3x:  163

                       4x:  119

                       5x:   86

                       6x:   81

                       7x:   57

                       8x:   46

                       9x:   33

                      10x:   38

                  11- 20x:  183

                  21- 50x:  195

                  51-100x:  109

                    >100x:  191





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



   Nb    Citations   Journal name

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

    1        21824   Journal of Biological Chemistry

    2         9882   Proceedings of the National Academy of Sciences of the U.S.A.

    3         5884   Journal of Bacteriology

    4         5137   Biochemical and Biophysical Research Communications

    5         4638   Nucleic Acids Research

    6         4636   Gene

    7         4606   Biochemistry

    8         4441   FEBS Letters

    9         4325   The EMBO Journal

   10         4004   Molecular and Cellular Biology

   11         3861   Nature

   12         3722   Journal of Molecular Biology

   13         3288   Biochimica et Biophysica Acta

   14         3262   European Journal of Biochemistry

   15         3146   Cell

   16         2665   Journal of Virology

   17         2570   Biochemical Journal

   18         2563   Science

   19         2516   Genomics

   20         2150   Molecular Microbiology

   21         1967   Plant Physiology

   22         1948   Journal of Cell Biology

   23         1700   The American Journal of Human Genetics

   24         1679   Plant Molecular Biology

   25         1643   Genes and Development

   26         1554   Virology

   27         1552   Nature Genetics

   28         1509   Human Molecular Genetics

   29         1463   Oncogene

   30         1417   Molecular Biology of the Cell

   31         1414   The Plant Cell

   32         1393   Development

   33         1353   Molecular and General Genetics

   34         1338   Human Mutation

   35         1275   The Plant Journal

   36         1260   Journal of Biochemistry

   37         1243   Molecular Cell

   38         1204   Journal of Immunology

   39         1132   Genetics

   40         1128   Structure

   41         1042   Journal of General Virology

   42         1009   Blood

   43          995   Journal of Cell Science

   44          992   Infection and Immunity

   45          954   Archives of Biochemistry and Biophysics

   46          919   Microbiology

   47          861   Developmental Biology

   48          848   Current Biology

   49          823   Cancer Research

   50          803   Yeast

   51          799   PLoS ONE

   52          749   FEMS Microbiology Letters

   53          718   Acta Crystallographica, Section D

   54          683   Journal of Neuroscience

   55          682   Protein Science

   56          678   Applied and Environmental Microbiology

   57          675   Toxicon

   58          636   Human Genetics

   59          630   Nature Structural Biology

   60          626   Mechanisms of Development

   61          612   Neuron

   62          588   Journal of Clinical Investigation

   63          571   American Journal of Physiology

   64          546   The Journal of Experimental Medicine

   65          543   Current Genetics

   66          521   Proteins

   67          514   Plant and Cell Physiology

   68          501   Molecular Endocrinology

   69          481   Mammalian Genome

   70          477   Journal of Neurochemistry

   71          468   Nature Cell Biology

   72          460   Immunogenetics

   73          460   Bioscience, Biotechnology, and Biochemistry

   74          454   Endocrinology

   75          452   Journal of Medical Genetics

   76          448   The Journal of Clinical Endocrinology and Metabolism

   77          435   Molecular and Biochemical Parasitology

   78          402   Journal of Molecular Evolution

   79          391   Experimental Cell Research

   80          380   Molecular Biology and Evolution

   81          377   DNA and Cell Biology

   82          367   DNA Sequence

   83          366   Nature Structural and Molecular Biology

   84          364   Peptides

   85          352   The FEBS Journal

   86          346   RNA

   87          344   Developmental Cell

   88          335   Antimicrobial Agents and Chemotherapy

   89          332   Eukaryotic Cell

   90          330   Brain Research. Molecular Brain Research

   91          326   Tissue Antigens

   92          322   Comparative Biochemistry and Physiology

   93          318   Journal of Investigative Dermatology

   94          318   Planta

   95          314   Molecular Pharmacology

   96          296   Biology of Reproduction

   97          294   Biological Chemistry Hoppe-Seyler

   98          289   Neurology

   99          280   Cytogenetics and Cell Genetics

  100          279   Developmental Dynamics

  101          273   EMBO Reports

  102          271   Biochimie

  103          270   Virus Research

  104          269   Immunity

  105          268   Genome Research

  106          266   Genes to Cells

  107          263   Journal of General Microbiology

  108          263   The FASEB Journal

  109          253   The New England Journal of Medicine

  110          250   Molecular Plant-Microbe Interactions

  111          240   Journal of the American Chemical Society

  112          236   European Journal of Human Genetics

  113          235   European Journal of Immunology

  114          233   Annals of Neurology

  115          230   Acta Crystallographica, Section F

  116          223   PLoS Genetics

  117          218   Hoppe-Seyler's Zeitschrift fur Physiologische Chemie

  118          216   DNA Research

  119          214   Journal of Human Genetics

  120          212   Investigative Ophthalmology and Visual Science

  121          209   Archives of Microbiology

  122          207   Journal of Experimental Botany

  123          205   Nature Immunology

  124          204   BMC Genomics

  125          203   Journal of Cellular Biochemistry

  126          196   American Journal of Medical Genetics. Part A

  127          195   Journal of Medicinal Chemistry

  128          193   Glycobiology

  129          192   Molecular and Cellular Endocrinology

  130          191   Archives of Virology

  131          188   Clinical Genetics

  132          187   Molecular Immunology

  133          183   Circulation Research

  134          181   Diabetes

  135          176   Insect Biochemistry and Molecular Biology

  136          175   Traffic

  137          172   Cell Cycle

  138          171   Molecular Genetics and Metabolism

  139          169   Phytochemistry

  140          169   Molecular Phylogenetics and Evolution

  141          168   American Journal of Medical Genetics

  142          166   International Journal of Cancer

  143          166   PLoS Pathogens

  144          162   Applied Microbiology and Biotechnology

  145          162   Protein Expression and Purification

  146          160   Molecular Reproduction and Development

  147          159   DNA

  148          159   Biological Chemistry

  149          157   Molecular and Cellular Neuroscience

  150          156   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)                      1070151                 1.97                                         

   Journal                            865257     423922      1.59       1                                 

   Submitted to EMBL/GenBank/DDBJ     195688     174541      0.36       2                                 

   Submitted to other databases         6953       6471      0.01       3                                 

   Book citation                         725        711     <0.01       4                                 

   Plant Gene Register                   592        580     <0.01       5                                 

   Thesis                                418        415     <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: 347809



                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Comments (CC)                        2473483                 4.56                                         

   ALLERGEN                              661        661     <0.01      25                                 

   ALTERNATIVE PRODUCTS                22633      22633      0.04      13                                 

   BIOPHYSICOCHEMICAL PROPERTIES        5503       5503      0.01      23                                 

   BIOTECHNOLOGY                         370        368     <0.01      28                                 

   CATALYTIC ACTIVITY                 247026     222908      0.46       5                                 

   CAUTION                              9766       9585      0.02      18                                 

   COFACTOR                           112508     103012      0.21       7                                 

   DEVELOPMENTAL STAGE                 10232      10232      0.02      17                                 

   DISEASE                              5546       3726      0.01      22                                 

   DISRUPTION PHENOTYPE                 6833       6833      0.01      20                                 

   DOMAIN                              41449      36117      0.08      10                                 

   ENZYME REGULATION                   12215      12215      0.02      16                                 

   FUNCTION                           429052     411402      0.79       2                                 

   INDUCTION                           15972      15972      0.03      14                                 

   INTERACTION                         12500      12500      0.02      15                                 

   MASS SPECTROMETRY                    5712       4350      0.01      21                                 

   MISCELLANEOUS                       33361      30809      0.06      12                                 

   PATHWAY                            132615     120674      0.24       6                                 

   PHARMACEUTICAL                         94         94     <0.01      29                                 

   POLYMORPHISM                         1033        979     <0.01      24                                 

   PTM                                 46127      35788      0.08       8                                 

   RNA EDITING                           627        627     <0.01      26                                 

   SEQUENCE CAUTION                    41565      41565      0.08       9                                 

   SIMILARITY                         647436     518250      1.19       1                                 

   SUBCELLULAR LOCATION               330437     324270      0.61       3                                 

   SUBUNIT                            252155     252155      0.46       4                                 

   TISSUE SPECIFICITY                  39990      39990      0.07      11                                 

   TOXIC DOSE                            573        536     <0.01      27                                 

   WEB RESOURCE                         9492       7545      0.02      19                                 



Total number of comment topics: 29





                                      Total    Number of  Average

   Line type / subtype                number   entries    per entry  Rank

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

Features (FT)                        3844596                 7.08                                         

   ACT_SITE                           146946      89896      0.27       9                                 

   BINDING                            311925      83335      0.57       4                                 

   CA_BIND                              3945       1649      0.01      35                                 

   CARBOHYD                           108634      27786      0.20      15                                 

   CHAIN                              549932     536489      1.01       1                                 

   COILED                              20571      14130      0.04      26                                 

   COMPBIAS                            55390      29457      0.10      18                                 

   CONFLICT                           129439      45351      0.24      12                                 

   CROSSLNK                             7027       4022      0.01      34                                 

   DISULFID                           112630      30789      0.21      14                                 

   DNA_BIND                            10573       9609      0.02      31                                 

   DOMAIN                             164797      98094      0.30       8                                 

   HELIX                              192323      18512      0.35       6                                 

   INIT_MET                            17561      17561      0.03      27                                 

   INTRAMEM                             2193        951     <0.01      37                                 

   LIPID                               12180       7753      0.02      30                                 

   METAL                              334178      82516      0.62       3                                 

   MOD_RES                            172688      62104      0.32       7                                 

   MOTIF                               37303      24218      0.07      24                                 

   MUTAGEN                             47498      10909      0.09      20                                 

   NON_CONS                             2063        752     <0.01      38                                 

   NON_STD                               356        281     <0.01      39                                 

   NON_TER                             12226       9344      0.02      29                                 

   NP_BIND                            125453      75517      0.23      13                                 

   PEPTIDE                             10405       7108      0.02      32                                 

   PROPEP                              12883      11093      0.02      28                                 

   REGION                             145314      73353      0.27      10                                 

   REPEAT                              96784      14279      0.18      16                                 

   SIGNAL                              38756      38746      0.07      23                                 

   SITE                                48327      26684      0.09      19                                 

   STRAND                             201754      17488      0.37       5                                 

   TOPO_DOM                           131920      27309      0.24      11                                 

   TRANSIT                              8573       8467      0.02      33                                 

   TRANSMEM                           357951      74012      0.66       2                                 

   TURN                                46899      15038      0.09      22                                 

   UNSURE                               3404        726      0.01      36                                 

   VAR_SEQ                             47003      19689      0.09      21                                 

   VARIANT                             87277      16867      0.16      17                                 

   ZN_FING                             29515      12990      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)               16510884                30.42                                                           

   Allergome                            1629       1061     <0.01     103      Protein family/group databases               

   ArachnoServer                         763        755     <0.01     115      Organism-specific databases                  

   ArrayExpress                        33313      33313      0.06      50      Gene expression databases                    

   Bgee                                38826      38826      0.07      46      Gene expression databases                    

   BindingDB                            5033       5033      0.01      88      Chemistry                                    

   BioCyc                             323220     307315      0.60      20      Enzyme and pathway databases                 

   BioGrid                             38818      38475      0.07      47      Protein-protein interaction databases        

   BRENDA                               4346       4335      0.01      93      Enzyme and pathway databases                 

   CAZy                                 7686       6919      0.01      76      Protein family/group databases               

   CGD                                   844        822     <0.01     111      Organism-specific databases                  

   ChEMBL                               5710       5710      0.01      82      Chemistry                                    

   ChiTaRS                             12552      12547      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                                 71035      70314      0.13      38      Organism-specific databases                  

   CYGD                                 5596       5593      0.01      83      Organism-specific databases                  

   dictyBase                            4203       4087      0.01      95      Organism-specific databases                  

   DIP                                 15221      15150      0.03      68      Protein-protein interaction databases        

   DisProt                               608        605     <0.01     118      3D structure databases                       

   DMDM                                16748      16745      0.03      65      Polymorphism databases                       

   DNASU                               18749      18678      0.03      60      Protocols and materials databases            

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

   DrugBank                             5319       1628      0.01      85      Chemistry                                    

   EchoBASE                             4161       4161      0.01      96      Organism-specific databases                  

   EcoGene                              4292       4290      0.01      94      Organism-specific databases                  

   eggNOG                             431692     431692      0.80      10      Phylogenomic databases                       

   EMBL                               948959     531461      1.75       3      Sequence databases                           

   Ensembl                             85096      48953      0.16      35      Genome annotation databases                  

   EnsemblBacteria                    348487     328039      0.64      18      Genome annotation databases                  

   EnsemblFungi                        18595      18295      0.03      61      Genome annotation databases                  

   EnsemblMetazoa                      12578       9361      0.02      71      Genome annotation databases                  

   EnsemblPlants                       17351      14968      0.03      64      Genome annotation databases                  

   EnsemblProtists                      4576       4449      0.01      92      Genome annotation databases                  

   euHCVdb                                55         44     <0.01     128      Organism-specific databases                  

   EuPathDB                              776        776     <0.01     112      Organism-specific databases                  

   EvolutionaryTrace                   16669      16669      0.03      66      Other                                        

   FlyBase                              5922       5548      0.01      80      Organism-specific databases                  

   Gene3D                             359683     274487      0.66      17      Family and domain databases                  

   GeneCards                           20898      19799      0.04      57      Organism-specific databases                  

   GeneFarm                             3229       3218      0.01      97      Organism-specific databases                  

   GeneID                             499051     466004      0.92       6      Genome annotation databases                  

   GeneTree                            38122      38104      0.07      48      Phylogenomic databases                       

   Genevestigator                      67904      67904      0.13      40      Gene expression databases                    

   GeneWiki                            10375      10288      0.02      74      Other                                        

   GenoList                             7071       7059      0.01      77      Organism-specific databases                  

   GenomeRNAi                          21333      21333      0.04      56      Other                                        

   GO                                2525007     513441      4.65       1      Ontologies                                   

   Gramene                              6169       6169      0.01      79      Organism-specific databases                  

   GuidetoPHARMACOLOGY                  1797       1797     <0.01     102      Chemistry                                    

   H-InvDB                              5590       4770      0.01      84      Organism-specific databases                  

   HAMAP                              322750     319854      0.59      21      Family and domain databases                  

   HGNC                                19912      19746      0.04      59      Organism-specific databases                  

   HOGENOM                            386419     386419      0.71      14      Phylogenomic databases                       

   HOVERGEN                            75647      75647      0.14      36      Phylogenomic databases                       

   HPA                                 22363      15991      0.04      55      Organism-specific databases                  

   InParanoid                          70607      70607      0.13      39      Phylogenomic databases                       

   IntAct                              41208      41208      0.08      45      Protein-protein interaction databases        

   InterPro                          1833772     520812      3.38       2      Family and domain databases                  

   KEGG                               471424     441884      0.87       7      Genome annotation databases                  

   KO                                 371610     371130      0.68      16      Phylogenomic databases                       

   LegioList                             765        763     <0.01     114      Organism-specific databases                  

   Leproma                               671        668     <0.01     117      Organism-specific databases                  

   MaizeGDB                              502        497     <0.01     121      Organism-specific databases                  

   MEROPS                              11928      11928      0.02      73      Protein family/group databases               

   MGI                                 16576      16532      0.03      67      Organism-specific databases                  

   MIM                                 18532      13891      0.03      62      Organism-specific databases                  

   MINT                                31573      31573      0.06      51      Protein-protein interaction databases        

   mycoCLAP                              281        275     <0.01     124      Protein family/group databases               

   NextBio                             71131      71131      0.13      37      Other                                        

   neXtProt                            20109      20109      0.04      58      Organism-specific databases                  

   OGP                                   377        377     <0.01     123      2D gel databases                             

   OMA                                401133     401133      0.74      12      Phylogenomic databases                       

   Orphanet                             5918       3119      0.01      81      Organism-specific databases                  

   OrthoDB                            390589     390589      0.72      13      Phylogenomic databases                       

   PANTHER                            192266     180644      0.35      25      Family and domain databases                  

   PATRIC                             309213     309181      0.57      22      Genome annotation databases                  

   PaxDb                               66737      66737      0.12      41      Proteomic databases                          

   PDB                                104653      20520      0.19      31      3D structure databases                       

   PDBsum                             104652      20519      0.19      32      3D structure databases                       

   PeptideAtlas                         5162       5162      0.01      87      Proteomic databases                          

   PeroxiBase                            772        756     <0.01     113      Protein family/group databases               

   Pfam                               726447     500274      1.34       4      Family and domain databases                  

   PharmGKB                            18386      18358      0.03      63      Organism-specific databases                  

   PhosphoSite                         33569      33569      0.06      49      PTM databases                                

   PhosSite                              699        687     <0.01     116      PTM databases                                

   PhylomeDB                           27777      27777      0.05      54      Phylogenomic databases                       

   PIR                                119310     109128      0.22      30      Sequence databases                           

   PIRSF                              101369     100409      0.19      34      Family and domain databases                  

   PMAP-CutDB                           1462       1462     <0.01     104      Other                                        

   PomBase                              5015       4968      0.01      89      Organism-specific databases                  

   PptaseDB                               40         40     <0.01     129      Protein family/group databases               

   PRIDE                              123436     123436      0.23      29      Proteomic databases                          

   PRINTS                             136853     120555      0.25      27      Family and domain databases                  

   PRO                                 57913      57913      0.11      43      Other                                        

   ProDom                              29310      29131      0.05      53      Family and domain databases                  

   ProMEX                                868        868     <0.01     110      Proteomic databases                          

   PROSITE                            433184     282288      0.80       9      Family and domain databases                  

   ProtClustDB                        344899     344899      0.64      19      Phylogenomic databases                       

   ProteinModelPortal                 436690     436690      0.80       8      3D structure databases                       

   PseudoCAP                            1269       1260     <0.01     105      Organism-specific databases                  

   Reactome                            14062       8201      0.03      69      Enzyme and pathway databases                 

   REBASE                                403        403     <0.01     122      Protein family/group databases               

   RefSeq                             561663     475105      1.03       5      Sequence databases                           

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

   RGD                                  7809       7805      0.01      75      Organism-specific databases                  

   SABIO-RK                             2823       2823      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                              168608     126304      0.31      26      Family and domain databases                  

   SMR                                223485     223485      0.41      24      3D structure databases                       

   STRING                             403787     403787      0.74      11      Protein-protein interaction databases        

   SUPFAM                             379455     293600      0.70      15      Family and domain databases                  

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

   TAIR                                12729      12673      0.02      70      Organism-specific databases                  

   TCDB                                 5215       5183      0.01      86      Protein family/group databases               

   TIGRFAMs                           290192     270131      0.53      23      Family and domain databases                  

   TreeFam                             44655      44650      0.08      44      Phylogenomic databases                       

   TubercuList                          2057       2021     <0.01     101      Organism-specific databases                  

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

   UCSC                                58351      44696      0.11      42      Genome annotation databases                  

   UniCarbKB                             272        272     <0.01     125      PTM databases                                

   UniGene                            101579      91884      0.19      33      Sequence databases                           

   UniPathway                         132459     120523      0.24      28      Enzyme and pathway databases                 

   VectorBase                            607        589     <0.01     119      Genome annotation databases                  

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

   WormBase                             5015       3995      0.01      90      Organism-specific databases                  

   Xenbase                              4758       4752      0.01      91      Organism-specific databases                  

   ZFIN                                 2759       2759      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) 8.25   Gln (Q) 3.93   Leu (L) 9.66   Ser (S) 6.57

   Arg (R) 5.53   Glu (E) 6.75   Lys (K) 5.84   Thr (T) 5.34

   Asn (N) 4.06   Gly (G) 7.07   Met (M) 2.41   Trp (W) 1.08

   Asp (D) 5.45   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) 6.86



   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 3734 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: 75528