UniProtKB/Swiss-Prot protein knowledgebase release 2018_11 statistics
1. INTRODUCTION
Release 2018_11 of 05-Dec-18 of UniProtKB/Swiss-Prot contains 558898 sequence entries,
comprising 200750628 amino acids abstracted from 263453 references.
219 sequences have been added since release 2018_10, the sequence data of
28 existing entries has been updated and the annotations of
337657 entries have been revised.
Number of fragments: 9154
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40004
Protein existence (PE): entries %
1: Evidence at protein level 99780 17.9%
2: Evidence at transcript level 57193 10.2%
3: Inferred from homology 386593 69.2%
4: Predicted 13493 2.4%
5: Uncertain 1839 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: 13696
The first twenty species represent 120727 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5664
2x: 1957
3x: 1066
4x: 695
5x: 515
6x: 407
7x: 298
8x: 248
9x: 230
10x: 140
11- 20x: 751
21- 50x: 457
51-100x: 218
>100x: 1050
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20412 Homo sapiens (Human)
2 17001 Mus musculus (Mouse)
3 15823 Arabidopsis thaliana (Mouse-ear cress)
4 8054 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6003 Bos taurus (Bovine)
7 5141 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4477 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4146 Dictyostelium discoideum (Slime mold)
11 4036 Caenorhabditis elegans
12 4029 Oryza sativa subsp. japonica (Rice)
13 3549 Drosophila melanogaster (Fruit fly)
14 3444 Xenopus laevis (African clawed frog)
15 3086 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2291 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2173 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2037 Escherichia coli O157:H7
20 1898 Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
21 1796 Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
22 1787 Methanocaldococcus jannaschii
23 1707 Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
24 1706 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
25 1694 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1683 Shigella flexneri
27 1427 Sus scrofa (Pig)
28 1347 Salmonella typhi
29 1326 Pseudomonas aeruginosa
30 1244 Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
31 1173 Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
32 1064 Synechocystis sp. (strain PCC 6803 / Kazusa)
33 1034 Archaeoglobus fulgidus
34 1022 Yersinia pestis
35 1009 Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
36 975 Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
37 930 Staphylococcus aureus (strain Mu50 / ATCC 700699)
38 930 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
39 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
40 926 Staphylococcus aureus (strain N315)
41 924 Emericella nidulans
42 918 Kluyveromyces lactis
43 909 Acanthamoeba polyphaga mimivirus (APMV)
44 899 Staphylococcus aureus (strain COL)
45 895 Staphylococcus aureus (strain MW2)
46 893 Oryctolagus cuniculus (Rabbit)
47 892 Escherichia coli O6:K15:H31 (strain 536 / UPEC)
48 889 Staphylococcus aureus (strain MSSA476)
49 888 Staphylococcus aureus (strain MRSA252)
50 882 Salmonella choleraesuis (strain SC-B67)
51 882 Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
52 879 Shigella sonnei (strain Ss046)
53 878 Candida glabrata
54 863 Yersinia pseudotuberculosis serotype I (strain IP32953)
55 855 Neurospora crassa
56 841 Escherichia coli O9:H4 (strain HS)
57 834 Oryza sativa subsp. indica (Rice)
58 834 Escherichia coli O139:H28 (strain E24377A / ETEC)
59 829 Shigella boydii serotype 4 (strain Sb227)
60 825 Escherichia coli (strain UTI89 / UPEC)
61 822 Canis lupus familiaris (Dog) (Canis familiaris)
62 822 Shigella dysenteriae serotype 1 (strain Sd197)
63 821 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
64 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
65 810 Zea mays (Maize)
66 796 Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
67 793 Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
68 792 Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
69 791 Escherichia coli (strain SMS-3-5 / SECEC)
70 784 Aquifex aeolicus (strain VF5)
71 776 Pasteurella multocida (strain Pm70)
72 771 Escherichia coli (strain K12 / DH10B)
73 771 Escherichia coli O127:H6 (strain E2348/69 / EPEC)
74 766 Staphylococcus aureus (strain NCTC 8325)
75 765 Escherichia coli (strain K12 / MC4100 / BW2952)
76 765 Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)
77 762 Escherichia coli (strain 55989 / EAEC)
78 761 Escherichia coli O8 (strain IAI1)
79 760 Staphylococcus epidermidis (strain ATCC 35984 / RP62A)
80 760 Shigella flexneri serotype 5b (strain 8401)
81 759 Staphylococcus epidermidis (strain ATCC 12228)
82 756 Escherichia coli (strain SE11)
83 756 Escherichia coli O45:K1 (strain S88 / ExPEC)
84 753 Escherichia coli O7:K1 (strain IAI39 / ExPEC)
85 751 Bacillus anthracis
86 748 Escherichia coli O157:H7 (strain EC4115 / EHEC)
87 746 Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
88 741 Bacillus halodurans
89 737 Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
90 733 Vibrio vulnificus (strain CMCP6)
91 731 Escherichia coli O81 (strain ED1a)
92 722 Salmonella enteritidis PT4 (strain P125109)
93 718 Vibrio vulnificus (strain YJ016)
94 718 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
95 716 Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)
96 715 Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
97 715 Yersinia pestis bv. Antiqua (strain Nepal516)
98 715 Enterobacter sp. (strain 638)
99 714 Salmonella paratyphi A (strain AKU_12601)
100 714 Escherichia coli O1:K1 / APEC
101 713 Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)
102 713 Salmonella agona (strain SL483)
103 713 Salmonella newport (strain SL254)
104 712 Salmonella schwarzengrund (strain CVM19633)
105 711 Yersinia pestis bv. Antiqua (strain Antiqua)
106 710 Salmonella heidelberg (strain SL476)
107 702 Salmonella dublin (strain CT_02021853)
108 698 Klebsiella pneumoniae (strain 342)
109 698 Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)
110 695 Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)
111 693 Pan troglodytes (Chimpanzee)
112 692 Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
113 687 Mycoplasma pneumoniae (strain ATCC 29342 / M129)
114 684 Salmonella gallinarum (strain 287/91 / NCTC 13346)
115 680 Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)
116 678 Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)
117 673 Escherichia coli
118 673 Staphylococcus aureus (strain USA300)
119 670 Serratia proteamaculans (strain 568)
120 669 Mycobacterium leprae (strain TN)
121 667 Yersinia pestis (strain Pestoides F)
122 665 Bacillus cereus
123 664 Bradyrhizobium diazoefficiens
124 664 Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
125 658 Sinorhizobium fredii (strain NBRC 101917 / NGR234)
126 653 Debaryomyces hansenii
127 646 Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
128 645 Shewanella oneidensis (strain MR-1)
129 643 Staphylococcus aureus (strain bovine RF122 / ET3-1)
130 642 Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)
131 638 Yersinia pseudotuberculosis serotype O:3 (strain YPIII)
132 634 Yersinia pseudotuberculosis serotype IB (strain PB1/+)
133 622 Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)
134 622 Treponema pallidum (strain Nichols)
135 620 Methanothermobacter thermautotrophicus
136 615 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
137 614 Staphylococcus haemolyticus (strain JCSC1435)
138 611 Mesorhizobium japonicum (Mesorhizobium loti
139 610 Xanthomonas campestris pv. campestris
140 603 Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)
141 603 Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
142 602 Staphylococcus saprophyticus subsp. saprophyticus
143 602 Photobacterium profundum (strain SS9)
144 601 Salmonella paratyphi C (strain RKS4594)
145 600 Yersinia pestis bv. Antiqua (strain Angola)
146 594 Pseudomonas aeruginosa (strain UCBPP-PA14)
147 594 Bacillus cereus (strain ATCC 10987 / NRS 248)
148 594 Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
149 591 Pectobacterium carotovorum subsp. carotovorum (strain PC1)
150 586 Rickettsia prowazekii (strain Madrid E)
151 582 Neisseria meningitidis serogroup B (strain MC58)
152 580 Caenorhabditis briggsae
153 579 Brucella suis biovar 1 (strain 1330)
154 574 Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
155 573 Aliivibrio fischeri (strain ATCC 700601 / ES114) (Vibrio fischeri)
156 572 Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS)
157 571 Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus)
158 569 Bacillus thuringiensis subsp. konkukian (strain 97-27)
159 568 Helicobacter pylori (strain J99 / ATCC 700824) (Campylobacter pylori J99)
160 567 Pseudomonas syringae pv. syringae (strain B728a)
161 564 Bacillus licheniformis
162 562 Bacillus cereus (strain ZK / E33L)
163 562 Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)
164 559 Clostridium acetobutylicum
165 557 Xanthomonas axonopodis pv. citri (strain 306)
166 555 Pseudomonas fluorescens (strain Pf0-1)
167 555 Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
168 554 Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)
169 553 Oceanobacillus iheyensis
170 551 Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
171 550 Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
172 547 Pseudomonas savastanoi pv. phaseolicola (Pseudomonas syringae pv. phaseolicola
173 537 Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)
174 531 Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99)
175 529 Corynebacterium glutamicum
176 529 Sodalis glossinidius (strain morsitans)
177 529 Listeria monocytogenes serotype 4b (strain F2365)
178 527 Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)
179 522 Xylella fastidiosa (strain 9a5c)
180 520 Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
181 517 Chromobacterium violaceum
182 516 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
183 515 Xylella fastidiosa (strain Temecula1 / ATCC 700964)
184 514 Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)
185 513 Staphylococcus aureus (strain Newman)
186 513 Deinococcus radiodurans
187 512 Pseudomonas aeruginosa (strain PA7)
188 511 Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
189 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
190 510 Geobacillus kaustophilus (strain HTA426)
191 508 Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)
192 508 Streptomyces avermitilis
193 507 Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
194 502 Pseudomonas entomophila (strain L48)
195 501 Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
196 501 Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
197 499 Brucella abortus biovar 1 (strain 9-941)
198 498 Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
199 497 Haemophilus influenzae (strain 86-028NP)
200 497 Rickettsia conorii (strain ATCC VR-613 / Malish 7)
201 496 Bacillus clausii (strain KSM-K16)
202 496 Burkholderia pseudomallei (strain K96243)
203 494 Proteus mirabilis (strain HI4320)
204 493 Xanthomonas campestris pv. campestris (strain 8004)
205 492 Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / FZB42)
206 491 Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
207 490 Vibrio campbellii (strain ATCC BAA-1116 / BB120)
208 488 Methanosarcina mazei
209 487 Shewanella sp. (strain MR-7)
210 487 Pyrococcus horikoshii
211 486 Mannheimia succiniciproducens (strain MBEL55E)
212 485 Thermosynechococcus elongatus (strain BP-1)
213 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
214 484 Pseudomonas aeruginosa (strain LESB58)
215 484 Shewanella sp. (strain MR-4)
216 483 Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)
217 483 Brucella abortus (strain 2308)
218 480 Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
219 479 Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
220 478 Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
221 478 Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
222 477 Pyrococcus abyssi (strain GE5 / Orsay)
223 475 Nicotiana tabacum (Common tobacco)
224 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
225 475 Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
226 474 Burkholderia lata
227 472 Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
228 468 Clostridium perfringens (strain 13 / Type A)
229 467 Shewanella frigidimarina (strain NCIMB 400)
230 467 Campylobacter jejuni subsp. jejuni serotype O:2
231 466 Shewanella sp. (strain ANA-3)
232 466 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
233 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
234 466 Pseudomonas putida (strain GB-1)
235 465 Anabaena variabilis (strain ATCC 29413 / PCC 7937)
236 464 Aeromonas hydrophila subsp. hydrophila
237 463 Enterococcus faecalis (strain ATCC 700802 / V583)
238 462 Burkholderia mallei (strain ATCC 23344)
239 459 Cupriavidus necator (strain JMP 134 / LMG 1197) (Ralstonia eutropha
240 458 Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
241 458 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
242 457 Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
243 457 Ovis aries (Sheep)
244 455 Staphylococcus aureus (strain JH1)
245 454 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
246 453 Pseudomonas putida (strain W619)
247 452 Aeromonas salmonicida (strain A449)
248 452 Shewanella baltica (strain OS185)
249 452 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
250 450 Caldanaerobacter subterraneus subsp. tengcongensis
2.3 Taxonomic distribution of the sequences
Kingdom sequences (% of the database)
Archaea 19544 ( 3%)
Bacteria 333732 ( 60%)
Eukaryota 188781 ( 34%)
Viruses 16841 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20413 ( 11%) ( 4%)
Other Mammalia 46690 ( 25%) ( 8%)
Other Vertebrata 18347 ( 10%) ( 3%)
Viridiplantae 39754 ( 21%) ( 7%)
Fungi 33823 ( 18%) ( 6%)
Insecta 9221 ( 5%) ( 2%)
Nematoda 4941 ( 3%) ( 1%)
Other 15592 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9581 1001-1100 3990
51- 100 42549 1101-1200 2801
101- 150 59007 1201-1300 2141
151- 200 58891 1301-1400 2005
201- 250 57734 1401-1500 1623
251- 300 51461 1501-1600 791
301- 350 51827 1601-1700 616
351- 400 44973 1701-1800 557
401- 450 36957 1801-1900 474
451- 500 29796 1901-2000 377
501- 550 21507 2001-2100 248
551- 600 15350 2101-2200 338
601- 650 12824 2201-2300 314
651- 700 9221 2301-2400 212
701- 750 7653 2401-2500 161
751- 800 5530 >2500 1283
801- 850 4771
851- 900 5208
901- 950 4049
951-1000 2924
The average sequence length in UniProtKB/Swiss-Prot is 359 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: 2759
4.1 Table of the frequency of journal citations
Journals cited 1x: 872
2x: 389
3x: 165
4x: 133
5x: 110
6x: 99
7x: 67
8x: 57
9x: 38
10x: 32
11- 20x: 220
21- 50x: 226
51-100x: 120
>100x: 231
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24497 Journal of Biological Chemistry
2 11358 Proceedings of the National Academy of Sciences of the U.S.A.
3 6610 Journal of Bacteriology
4 5625 Biochemical and Biophysical Research Communications
5 5319 Biochemistry
6 4986 Nucleic Acids Research
7 4819 FEBS Letters
8 4805 Gene
9 4685 The EMBO Journal
10 4509 Nature
11 4336 Molecular and Cellular Biology
12 4256 Journal of Molecular Biology
13 3619 Biochimica et Biophysica Acta
14 3560 Cell
15 3393 European Journal of Biochemistry
16 3234 Journal of Virology
17 2997 Science
18 2848 Biochemical Journal
19 2554 Plant Physiology
20 2534 Genomics
21 2524 Molecular Microbiology
22 2191 Journal of Cell Biology
23 2138 The American Journal of Human Genetics
24 1989 The Plant Cell
25 1882 PLoS ONE
26 1855 Plant Molecular Biology
27 1833 Genes and Development
28 1827 The Plant Journal
29 1800 Human Molecular Genetics
30 1795 Virology
31 1746 Nature Genetics
32 1666 Development
33 1659 Molecular Biology of the Cell
34 1570 Human Mutation
35 1540 Oncogene
36 1533 Molecular Cell
37 1424 Journal of Immunology
38 1394 Molecular and General Genetics
39 1338 Journal of Biochemistry
40 1332 Structure
41 1311 Genetics
42 1247 Journal of Cell Science
43 1154 Blood
44 1144 Journal of General Virology
45 1109 Infection and Immunity
46 1053 Microbiology
47 1047 Current Biology
48 1045 Developmental Biology
49 1042 Archives of Biochemistry and Biophysics
50 900 Applied and Environmental Microbiology
51 893 Journal of Neuroscience
52 882 Cancer Research
53 875 Acta Crystallographica, Section D
54 838 Yeast
55 836 FEMS Microbiology Letters
56 769 Protein Science
57 767 Toxicon
58 743 Neuron
59 723 Journal of Clinical Investigation
60 688 Human Genetics
61 675 Plant and Cell Physiology
62 673 American Journal of Physiology
63 648 Mechanisms of Development
64 645 Nature Structural Biology
65 636 PLoS Genetics
66 629 The Journal of Experimental Medicine
67 617 Proteins
68 600 Journal of Medical Genetics
69 574 Current Genetics
70 571 Nature Cell Biology
71 551 Bioscience, Biotechnology, and Biochemistry
72 532 Molecular Endocrinology
73 531 Journal of Neurochemistry
74 529 Nature Structural and Molecular Biology
75 518 The Journal of Clinical Endocrinology and Metabolism
76 509 Developmental Cell
77 504 The FEBS Journal
78 503 Endocrinology
79 488 Mammalian Genome
80 472 Immunogenetics
81 466 Antimicrobial Agents and Chemotherapy
82 457 Experimental Cell Research
83 448 Molecular and Biochemical Parasitology
84 431 Eukaryotic Cell
85 425 Planta
86 416 RNA
87 411 Peptides
88 407 Journal of Molecular Evolution
89 402 Nature Communications
90 397 Molecular Biology and Evolution
91 386 DNA and Cell Biology
92 383 Journal of Experimental Botany
93 375 Molecular Pharmacology
94 375 Journal of the American Chemical Society
95 374 DNA Sequence
96 362 EMBO Reports
97 360 PLoS Pathogens
98 360 Neurology
99 359 Journal of Investigative Dermatology
100 352 The FASEB Journal
101 349 Comparative Biochemistry and Physiology
102 347 Biology of Reproduction
103 347 Acta Crystallographica, Section F
104 342 Molecular Plant-Microbe Interactions
105 340 Scientific Reports
106 339 Brain Research. Molecular Brain Research
107 336 American Journal of Medical Genetics. Part A
108 333 European Journal of Human Genetics
109 328 Immunity
110 326 Tissue Antigens
111 321 Virus Research
112 318 Biochimie
113 318 The New England Journal of Medicine
114 317 Genes to Cells
115 313 Developmental Dynamics
116 296 Biological Chemistry Hoppe-Seyler
117 296 Genome Research
118 294 Clinical Genetics
119 287 Annals of Neurology
120 282 Cytogenetics and Cell Genetics
121 273 European Journal of Immunology
122 271 Journal of General Microbiology
123 269 BMC Genomics
124 268 Nature Immunology
125 266 Investigative Ophthalmology and Visual Science
126 260 Applied Microbiology and Biotechnology
127 254 Journal of Human Genetics
128 250 Journal of Medicinal Chemistry
129 245 PLoS Biology
130 241 Archives of Microbiology
131 233 Glycobiology
132 231 DNA Research
133 229 Journal of Cellular Biochemistry
134 228 Journal of Lipid Research
135 224 Traffic
136 220 Cell Cycle
137 218 Molecular Genetics and Metabolism
138 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
139 215 Circulation Research
140 213 Archives of Virology
141 213 Molecular Immunology
142 208 Diabetes
143 207 Molecular and Cellular Endocrinology
144 204 Protein Expression and Purification
145 203 Phytochemistry
146 202 Fungal Genetics and Biology
147 198 Nature Medicine
148 197 Cell Reports
149 196 Molecular Genetics and Genomics
150 185 Chemistry and Biology
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) 1218938 2.18
Journal 1041539 454671 1.86 1
Submitted to EMBL/GenBank/DDBJ 166597 150958 0.30 2
Submitted to other databases 7369 6804 0.01 3
Book citation 1766 1743 <0.01 4
Plant Gene Register 611 598 <0.01 5
Thesis 433 430 <0.01 6
Unpublished observations 408 404 <0.01 7
Patent 209 203 <0.01 8
Worm Breeder's Gazette 6 6 <0.01 9
Total number of distinct authors cited in UniProtKB/Swiss-Prot: 407031
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2528661 4.52
ACTIVITY REGULATION 14758 14758 0.03 16
ALLERGEN 732 732 <0.01 26
ALTERNATIVE PRODUCTS 25255 25255 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8196 8196 0.01 20
BIOTECHNOLOGY 965 951 <0.01 25
CATALYTIC ACTIVITY 280857 236553 0.50 4
CAUTION 12836 12591 0.02 18
COFACTOR 123073 112694 0.22 7
DEVELOPMENTAL STAGE 12114 12113 0.02 19
DISEASE 6998 4693 0.01 21
DISRUPTION PHENOTYPE 14241 14240 0.03 17
DOMAIN 48790 41994 0.09 9
FUNCTION 465638 445143 0.83 2
INDUCTION 20930 20918 0.04 14
INTERACTION 19158 19158 0.03 15
MASS SPECTROMETRY 6928 5219 0.01 22
MISCELLANEOUS 38524 35464 0.07 12
PATHWAY 138080 125263 0.25 6
PHARMACEUTICAL 116 112 <0.01 29
POLYMORPHISM 1319 1263 <0.01 24
PTM 56375 41678 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44037 44037 0.08 11
SIMILARITY 507792 503644 0.91 1
SUBCELLULAR LOCATION 348787 341461 0.62 3
SUBUNIT 278381 277583 0.50 5
TISSUE SPECIFICITY 45732 45731 0.08 10
TOXIC DOSE 666 609 <0.01 27
WEB RESOURCE 6756 5595 0.01 23
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4485822 8.03
ACT_SITE 163657 99346 0.29 10
BINDING 403952 106515 0.72 2
CA_BIND 4177 1730 0.01 36
CARBOHYD 115834 29778 0.21 15
CHAIN 566776 551826 1.01 1
COILED 22022 15224 0.04 27
COMPBIAS 59023 31760 0.11 20
CONFLICT 135211 47345 0.24 13
CROSSLNK 23597 8464 0.04 26
DISULFID 124995 33668 0.22 14
DNA_BIND 11646 10535 0.02 32
DOMAIN 194480 119878 0.35 9
HELIX 254370 23521 0.46 6
INIT_MET 17163 17163 0.03 28
INTRAMEM 2656 1199 <0.01 37
LIPID 13035 8420 0.02 30
METAL 380886 94160 0.68 3
MOD_RES 248588 71846 0.44 7
MOTIF 43083 28086 0.08 23
MUTAGEN 69887 15311 0.13 18
NON_CONS 2257 787 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12393 9508 0.02 31
NP_BIND 156863 85217 0.28 11
PEPTIDE 11578 7968 0.02 33
PROPEP 14215 12127 0.03 29
REGION 197903 93670 0.35 8
REPEAT 105498 14748 0.19 16
SIGNAL 41665 41663 0.07 24
SITE 57874 31744 0.10 21
STRAND 264910 22134 0.47 5
TOPO_DOM 140360 28766 0.25 12
TRANSIT 9093 8977 0.02 34
TRANSMEM 370755 77358 0.66 4
TURN 61239 19060 0.11 19
UNSURE 4454 796 0.01 35
VAR_SEQ 51990 22021 0.09 22
VARIANT 96845 17086 0.17 17
ZN_FING 30535 13409 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) 18980779 33.96
Allergome 1770 1157 <0.01 121 Protein family/group databases
ArachnoServer 1145 1136 <0.01 130 Organism-specific databases
Araport 15844 15748 0.03 83 Organism-specific databases
Bgee 56478 56478 0.10 45 Gene expression databases
BindingDB 5000 5000 0.01 104 Chemistry
BioCyc 237341 232844 0.42 24 Enzyme and pathway databases
BioGrid 51009 50508 0.09 50 Protein-protein interaction databases
BioMuta 17236 17227 0.03 79 Polymorphism and mutation databases
BRENDA 12911 12137 0.02 86 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 129 PTM databases
CAZy 9490 8555 0.02 89 Protein family/group databases
CCDS 48182 34160 0.09 52 Sequence databases
CDD 185133 169158 0.33 27 Family and domain databases
CGD 1997 1980 <0.01 118 Organism-specific databases
ChEMBL 6868 6868 0.01 96 Chemistry
ChiTaRS 20480 20469 0.04 69 Other
CleanEx 30012 29381 0.05 58 Gene expression databases
CollecTF 133 133 <0.01 152 Gene expression databases
ComplexPortal 8550 4498 0.02 90 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 153 2D gel databases
ConoServer 951 868 <0.01 131 Organism-specific databases
CORUM 5803 5803 0.01 100 Protein-protein interaction databases
CTD 74980 74083 0.13 43 Organism-specific databases
DEPOD 239 239 <0.01 148 PTM databases
dictyBase 4221 4106 0.01 108 Organism-specific databases
DIP 17358 17326 0.03 77 Protein-protein interaction databases
DisGeNET 14839 14605 0.03 84 Organism-specific databases
DisProt 708 703 <0.01 135 3D structure databases
DMDM 16276 16276 0.03 82 Polymorphism and mutation databases
DNASU 18993 18926 0.03 73 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 150 2D gel databases
DrugBank 18747 3637 0.03 74 Chemistry
EchoBASE 4159 4159 0.01 109 Organism-specific databases
EcoGene 4293 4293 0.01 107 Organism-specific databases
eggNOG 664897 331735 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 120 Protein-protein interaction databases
EMBL 984602 547172 1.76 3 Sequence databases
Ensembl 90923 50603 0.16 41 Genome annotation databases
EnsemblBacteria 355414 336285 0.64 17 Genome annotation databases
EnsemblFungi 29304 27806 0.05 60 Genome annotation databases
EnsemblMetazoa 17355 10154 0.03 78 Genome annotation databases
EnsemblPlants 27539 20564 0.05 62 Genome annotation databases
EnsemblProtists 5017 4831 0.01 103 Genome annotation databases
EPD 21827 21827 0.04 66 Proteomic databases
ESTHER 2504 2504 <0.01 116 Protein family/group databases
euHCVdb 55 44 <0.01 154 Organism-specific databases
EuPathDB 31161 30969 0.06 57 Organism-specific databases
EvolutionaryTrace 16627 16627 0.03 81 Other
ExpressionAtlas 51764 51764 0.09 48 Gene expression databases
FlyBase 6177 5881 0.01 98 Organism-specific databases
Gene3D 366895 292791 0.66 16 Family and domain databases
GeneCards 20364 20193 0.04 71 Organism-specific databases
GeneDB 575 519 <0.01 139 Genome annotation databases
GeneID 290368 280087 0.52 23 Genome annotation databases
GeneReviews 1479 1475 <0.01 122 Organism-specific databases
GeneTree 59094 59019 0.11 44 Phylogenomic databases
Genevisible 55240 55240 0.10 46 Gene expression databases
GeneWiki 10356 10273 0.02 88 Other
GenomeRNAi 22107 22107 0.04 65 Other
GlyConnect 1439 1353 <0.01 123 PTM databases
GO 2930845 532701 5.24 1 Ontologies
Gramene 27539 20564 0.05 63 Genome annotation databases
GuidetoPHARMACOLOGY 1957 1957 <0.01 119 Chemistry
H-InvDB 5627 4801 0.01 101 Organism-specific databases
HAMAP 329842 326966 0.59 19 Family and domain databases
HGNC 20350 20211 0.04 72 Organism-specific databases
HOGENOM 391734 391734 0.70 15 Phylogenomic databases
HOVERGEN 76122 76122 0.14 42 Phylogenomic databases
HPA 27400 16828 0.05 64 Organism-specific databases
IMGT_GENE-DB 142 142 <0.01 151 Protein family/group databases
InParanoid 139591 139591 0.25 30 Phylogenomic databases
IntAct 52784 52784 0.09 47 Protein-protein interaction databases
InterPro 2245755 540571 4.02 2 Family and domain databases
iPTMnet 51310 51310 0.09 49 PTM databases
KEGG 502331 474869 0.90 7 Genome annotation databases
KO 405035 404594 0.72 14 Phylogenomic databases
LegioList 765 763 <0.01 134 Organism-specific databases
Leproma 672 669 <0.01 136 Organism-specific databases
MaizeGDB 510 506 <0.01 140 Organism-specific databases
MalaCards 4499 4496 0.01 106 Organism-specific databases
MaxQB 29708 29708 0.05 59 Proteomic databases
MEROPS 11400 11400 0.02 87 Protein family/group databases
MGI 16909 16869 0.03 80 Organism-specific databases
MIM 21056 15089 0.04 68 Organism-specific databases
MINT 21795 21795 0.04 67 Protein-protein interaction databases
MoonDB 348 348 <0.01 146 Protein family/group databases
MoonProt 279 279 <0.01 147 Protein family/group databases
mycoCLAP 355 352 <0.01 145 Protein family/group databases
neXtProt 20369 20369 0.04 70 Organism-specific databases
OGP 373 373 <0.01 144 2D gel databases
OMA 408686 408686 0.73 13 Phylogenomic databases
OpenTargets 18383 18224 0.03 75 Organism-specific databases
Orphanet 7438 3920 0.01 93 Organism-specific databases
OrthoDB 293639 293639 0.53 21 Phylogenomic databases
PANTHER 295222 281230 0.53 20 Family and domain databases
PATRIC 91877 91877 0.16 40 Genome annotation databases
PaxDb 124699 124699 0.22 33 Proteomic databases
PDB 169808 27053 0.30 29 3D structure databases
PDBsum 169808 27053 0.30 28 3D structure databases
PeptideAtlas 32143 32143 0.06 56 Proteomic databases
PeroxiBase 780 758 <0.01 133 Protein family/group databases
Pfam 760029 517792 1.36 4 Family and domain databases
PharmGKB 18358 18316 0.03 76 Organism-specific databases
PhosphoSitePlus 39020 39020 0.07 54 PTM databases
PhylomeDB 96351 96351 0.17 38 Phylogenomic databases
PIR 124198 113748 0.22 34 Sequence databases
PIRSF 108924 107895 0.19 37 Family and domain databases
PMAP-CutDB 1401 1401 <0.01 124 Other
PomBase 5133 5129 0.01 102 Organism-specific databases
PRIDE 230710 230710 0.41 25 Proteomic databases
PRINTS 132681 117146 0.24 32 Family and domain databases
PRO 95984 95984 0.17 39 Other
ProDom 29172 28989 0.05 61 Family and domain databases
ProMEX 457 457 <0.01 142 Proteomic databases
PROSITE 467632 298998 0.84 10 Family and domain databases
ProteinModelPortal 449158 449158 0.80 11 3D structure databases
Proteomes 479587 455433 0.86 9 Other
ProteomicsDB 36380 19829 0.07 55 Proteomic databases
PseudoCAP 1334 1325 <0.01 126 Organism-specific databases
Reactome 123242 36345 0.22 35 Enzyme and pathway databases
REBASE 392 392 <0.01 143 Protein family/group databases
RefSeq 608650 463566 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 127 2D gel databases
RGD 7978 7977 0.01 92 Organism-specific databases
SABIO-RK 4098 4098 0.01 110 Enzyme and pathway databases
SFLD 8062 5976 0.01 91 Family and domain databases
SGD 6739 6734 0.01 97 Organism-specific databases
SignaLink 3065 3065 0.01 115 Enzyme and pathway databases
SIGNOR 4083 4083 0.01 111 Enzyme and pathway databases
SMART 192382 141901 0.34 26 Family and domain databases
SMR 444705 444705 0.80 12 3D structure databases
STRING 332762 332762 0.60 18 Protein-protein interaction databases
SUPFAM 498252 377829 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 128 2D gel databases
SwissLipids 1360 1273 <0.01 125 Chemistry
SwissPalm 7301 7301 0.01 94 PTM databases
TAIR 14631 14575 0.03 85 Organism-specific databases
TCDB 6918 6867 0.01 95 Protein family/group databases
TIGRFAMs 292371 272384 0.52 22 Family and domain databases
TopDownProteomics 3241 2964 0.01 113 Proteomic databases
TreeFam 45491 45481 0.08 53 Phylogenomic databases
TubercuList 2191 2155 <0.01 117 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 141 2D gel databases
UCSC 49936 45616 0.09 51 Genome annotation databases
UniCarbKB 584 584 <0.01 138 PTM databases
UniGene 109894 96298 0.20 36 Sequence databases
UniLectin 238 238 <0.01 149 Protein family/group databases
UniPathway 136320 123530 0.24 31 Enzyme and pathway databases
VectorBase 597 517 <0.01 137 Genome annotation databases
VGNC 3916 3916 0.01 112 Organism-specific databases
WBParaSite 34 34 <0.01 155 Genome annotation databases
World-2DPAGE 930 919 <0.01 132 2D gel databases
WormBase 6024 4595 0.01 99 Organism-specific databases
Xenbase 4561 4555 0.01 105 Organism-specific databases
ZFIN 3066 3061 0.01 114 Organism-specific databases
Total number of cross-referenced databases: 155
6. AMINO ACID COMPOSITION
6.1 Composition in percent for the complete database
Ala (A) 8.25 Gln (Q) 3.93 Leu (L) 9.65 Ser (S) 6.62
Arg (R) 5.53 Glu (E) 6.73 Lys (K) 5.81 Thr (T) 5.35
Asn (N) 4.05 Gly (G) 7.07 Met (M) 2.41 Trp (W) 1.09
Asp (D) 5.46 His (H) 2.27 Phe (F) 3.86 Tyr (Y) 2.91
Cys (C) 1.38 Ile (I) 5.92 Pro (P) 4.73 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
4464 entries are encoded on a mitochondrion, and 3883 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: 79284