UniProtKB/Swiss-Prot protein knowledgebase release 2018_09 statistics
1. INTRODUCTION
Release 2018_09 of 10-Oct-18 of UniProtKB/Swiss-Prot contains 558590 sequence entries,
comprising 200544181 amino acids abstracted from 262369 references.
468 sequences have been added since release 2018_08, the sequence data of
52 existing entries has been updated and the annotations of
335311 entries have been revised.
Number of fragments: 9161
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 39968
Protein existence (PE): entries %
1: Evidence at protein level 99454 17.8%
2: Evidence at transcript level 57213 10.2%
3: Inferred from homology 386612 69.2%
4: Predicted 13447 2.4%
5: Uncertain 1864 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: 13674
The first twenty species represent 120651 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5664
2x: 1953
3x: 1062
4x: 693
5x: 511
6x: 407
7x: 296
8x: 248
9x: 229
10x: 138
11- 20x: 748
21- 50x: 457
51-100x: 218
>100x: 1050
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20410 Homo sapiens (Human)
2 17001 Mus musculus (Mouse)
3 15814 Arabidopsis thaliana (Mouse-ear cress)
4 8050 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 4139 Dictyostelium discoideum (Slime mold)
11 4034 Caenorhabditis elegans
12 3999 Oryza sativa subsp. japonica (Rice)
13 3538 Drosophila melanogaster (Fruit fly)
14 3443 Xenopus laevis (African clawed frog)
15 3079 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2290 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2172 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2036 Escherichia coli O157:H7
20 1898 Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
21 1795 Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
22 1787 Methanocaldococcus jannaschii
23 1707 Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
24 1705 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
25 1694 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1683 Shigella flexneri
27 1424 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 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
38 930 Staphylococcus aureus (strain Mu50 / ATCC 700699)
39 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
40 926 Staphylococcus aureus (strain N315)
41 914 Kluyveromyces lactis
42 914 Emericella nidulans
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 Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
51 882 Salmonella choleraesuis (strain SC-B67)
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 Escherichia coli O139:H28 (strain E24377A / ETEC)
58 829 Shigella boydii serotype 4 (strain Sb227)
59 825 Escherichia coli (strain UTI89 / UPEC)
60 823 Oryza sativa subsp. indica (Rice)
61 822 Shigella dysenteriae serotype 1 (strain Sd197)
62 821 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
63 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
64 819 Canis lupus familiaris (Dog) (Canis familiaris)
65 806 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 O127:H6 (strain E2348/69 / EPEC)
73 771 Escherichia coli (strain K12 / DH10B)
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 O45:K1 (strain S88 / ExPEC)
83 756 Escherichia coli (strain SE11)
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 Escherichia coli O1:K1 / APEC
100 714 Salmonella paratyphi A (strain AKU_12601)
101 713 Salmonella agona (strain SL483)
102 713 Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)
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 Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
124 664 Bradyrhizobium diazoefficiens
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 Treponema pallidum (strain Nichols)
134 622 Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)
135 620 Methanothermobacter thermautotrophicus
136 614 Staphylococcus haemolyticus (strain JCSC1435)
137 611 Mesorhizobium japonicum (Mesorhizobium loti
138 610 Xanthomonas campestris pv. campestris
139 608 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
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 Listeria monocytogenes serotype 4b (strain F2365)
176 529 Corynebacterium glutamicum
177 529 Sodalis glossinidius (strain morsitans)
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 Deinococcus radiodurans
186 513 Staphylococcus aureus (strain Newman)
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 Streptomyces avermitilis
192 508 Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)
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 Shewanella sp. (strain MR-4)
215 484 Pseudomonas aeruginosa (strain LESB58)
216 483 Brucella abortus (strain 2308)
217 483 Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)
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 Pseudomonas putida (strain GB-1)
232 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
233 466 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
234 466 Shewanella sp. (strain ANA-3)
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)
241 457 Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
242 457 Ovis aries (Sheep)
243 455 Staphylococcus aureus (strain JH1)
244 454 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
245 453 Pseudomonas putida (strain W619)
246 452 Aeromonas salmonicida (strain A449)
247 452 Shewanella baltica (strain OS185)
248 452 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
249 450 Caldanaerobacter subterraneus subsp. tengcongensis
250 450 Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)
2.3 Taxonomic distribution of the sequences
Kingdom sequences (% of the database)
Archaea 19544 ( 3%)
Bacteria 333708 ( 60%)
Eukaryota 188529 ( 34%)
Viruses 16809 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20411 ( 11%) ( 4%)
Other Mammalia 46680 ( 25%) ( 8%)
Other Vertebrata 18334 ( 10%) ( 3%)
Viridiplantae 39669 ( 21%) ( 7%)
Fungi 33712 ( 18%) ( 6%)
Insecta 9210 ( 5%) ( 2%)
Nematoda 4936 ( 3%) ( 1%)
Other 15577 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9576 1001-1100 3984
51- 100 42544 1101-1200 2798
101- 150 58994 1201-1300 2143
151- 200 58869 1301-1400 2001
201- 250 57712 1401-1500 1621
251- 300 51434 1501-1600 792
301- 350 51808 1601-1700 616
351- 400 44951 1701-1800 552
401- 450 36940 1801-1900 470
451- 500 29770 1901-2000 375
501- 550 21491 2001-2100 248
551- 600 15332 2101-2200 326
601- 650 12796 2201-2300 313
651- 700 9215 2301-2400 210
701- 750 7649 2401-2500 159
751- 800 5520 >2500 1278
801- 850 4769
851- 900 5205
901- 950 4049
951-1000 2919
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: 2750
4.1 Table of the frequency of journal citations
Journals cited 1x: 866
2x: 389
3x: 162
4x: 137
5x: 110
6x: 98
7x: 68
8x: 56
9x: 37
10x: 34
11- 20x: 220
21- 50x: 224
51-100x: 119
>100x: 230
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24411 Journal of Biological Chemistry
2 11304 Proceedings of the National Academy of Sciences of the U.S.A.
3 6601 Journal of Bacteriology
4 5612 Biochemical and Biophysical Research Communications
5 5304 Biochemistry
6 4982 Nucleic Acids Research
7 4816 FEBS Letters
8 4805 Gene
9 4674 The EMBO Journal
10 4496 Nature
11 4332 Molecular and Cellular Biology
12 4244 Journal of Molecular Biology
13 3614 Biochimica et Biophysica Acta
14 3544 Cell
15 3391 European Journal of Biochemistry
16 3198 Journal of Virology
17 2987 Science
18 2841 Biochemical Journal
19 2539 Plant Physiology
20 2534 Genomics
21 2513 Molecular Microbiology
22 2183 Journal of Cell Biology
23 2125 The American Journal of Human Genetics
24 1978 The Plant Cell
25 1869 PLoS ONE
26 1850 Plant Molecular Biology
27 1832 Genes and Development
28 1817 The Plant Journal
29 1794 Human Molecular Genetics
30 1767 Virology
31 1742 Nature Genetics
32 1659 Development
33 1655 Molecular Biology of the Cell
34 1565 Human Mutation
35 1539 Oncogene
36 1526 Molecular Cell
37 1416 Journal of Immunology
38 1394 Molecular and General Genetics
39 1333 Journal of Biochemistry
40 1325 Structure
41 1310 Genetics
42 1238 Journal of Cell Science
43 1143 Blood
44 1131 Journal of General Virology
45 1106 Infection and Immunity
46 1051 Microbiology
47 1043 Developmental Biology
48 1042 Current Biology
49 1041 Archives of Biochemistry and Biophysics
50 899 Applied and Environmental Microbiology
51 884 Journal of Neuroscience
52 882 Cancer Research
53 871 Acta Crystallographica, Section D
54 838 Yeast
55 836 FEMS Microbiology Letters
56 769 Protein Science
57 766 Toxicon
58 737 Neuron
59 719 Journal of Clinical Investigation
60 688 Human Genetics
61 672 American Journal of Physiology
62 667 Plant and Cell Physiology
63 647 Mechanisms of Development
64 645 Nature Structural Biology
65 627 PLoS Genetics
66 626 The Journal of Experimental Medicine
67 614 Proteins
68 599 Journal of Medical Genetics
69 574 Current Genetics
70 568 Nature Cell Biology
71 549 Bioscience, Biotechnology, and Biochemistry
72 532 Molecular Endocrinology
73 530 Journal of Neurochemistry
74 526 Nature Structural and Molecular Biology
75 517 The Journal of Clinical Endocrinology and Metabolism
76 505 Developmental Cell
77 502 Endocrinology
78 501 The FEBS Journal
79 488 Mammalian Genome
80 472 Immunogenetics
81 464 Antimicrobial Agents and Chemotherapy
82 455 Experimental Cell Research
83 448 Molecular and Biochemical Parasitology
84 431 Eukaryotic Cell
85 422 Planta
86 416 RNA
87 410 Peptides
88 407 Journal of Molecular Evolution
89 397 Molecular Biology and Evolution
90 386 DNA and Cell Biology
91 384 Nature Communications
92 374 Journal of Experimental Botany
93 374 DNA Sequence
94 372 Journal of the American Chemical Society
95 372 Molecular Pharmacology
96 359 EMBO Reports
97 358 Neurology
98 357 Journal of Investigative Dermatology
99 353 PLoS Pathogens
100 350 The FASEB Journal
101 349 Comparative Biochemistry and Physiology
102 347 Biology of Reproduction
103 343 Acta Crystallographica, Section F
104 339 Brain Research. Molecular Brain Research
105 339 Molecular Plant-Microbe Interactions
106 334 American Journal of Medical Genetics. Part A
107 331 European Journal of Human Genetics
108 326 Tissue Antigens
109 323 Immunity
110 317 Biochimie
111 316 Genes to Cells
112 315 Scientific Reports
113 315 The New England Journal of Medicine
114 312 Virus Research
115 311 Developmental Dynamics
116 296 Biological Chemistry Hoppe-Seyler
117 296 Genome Research
118 292 Clinical Genetics
119 286 Annals of Neurology
120 282 Cytogenetics and Cell Genetics
121 271 Journal of General Microbiology
122 270 European Journal of Immunology
123 269 BMC Genomics
124 265 Nature Immunology
125 265 Investigative Ophthalmology and Visual Science
126 259 Applied Microbiology and Biotechnology
127 253 Journal of Human Genetics
128 246 Journal of Medicinal Chemistry
129 244 PLoS Biology
130 240 Archives of Microbiology
131 231 Glycobiology
132 231 DNA Research
133 229 Journal of Cellular Biochemistry
134 223 Traffic
135 219 Cell Cycle
136 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
137 218 Molecular Genetics and Metabolism
138 216 Journal of Lipid Research
139 215 Circulation Research
140 212 Molecular Immunology
141 209 Archives of Virology
142 208 Diabetes
143 207 Molecular and Cellular Endocrinology
144 204 Protein Expression and Purification
145 202 Phytochemistry
146 198 Fungal Genetics and Biology
147 196 Nature Medicine
148 196 Molecular Genetics and Genomics
149 185 Cell Reports
150 183 Insect Biochemistry and Molecular 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) 1215846 2.18
Journal 1038510 454345 1.86 1
Submitted to EMBL/GenBank/DDBJ 166540 150910 0.30 2
Submitted to other databases 7374 6809 0.01 3
Book citation 1757 1734 <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 207 202 <0.01 8
Worm Breeder's Gazette 6 6 <0.01 9
Total number of distinct authors cited in UniProtKB/Swiss-Prot: 405296
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2511754 4.50
ACTIVITY REGULATION 14691 14691 0.03 16
ALLERGEN 722 722 <0.01 26
ALTERNATIVE PRODUCTS 25230 25230 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8137 8137 0.01 20
BIOTECHNOLOGY 941 927 <0.01 25
CATALYTIC ACTIVITY 267532 235907 0.48 5
CAUTION 12810 12573 0.02 18
COFACTOR 122995 112607 0.22 7
DEVELOPMENTAL STAGE 12056 12055 0.02 19
DISEASE 6953 4662 0.01 21
DISRUPTION PHENOTYPE 14053 14052 0.03 17
DOMAIN 48482 41759 0.09 9
FUNCTION 465052 444653 0.83 2
INDUCTION 20769 20757 0.04 14
INTERACTION 19107 19107 0.03 15
MASS SPECTROMETRY 6916 5210 0.01 23
MISCELLANEOUS 38426 35383 0.07 12
PATHWAY 137937 125135 0.25 6
PHARMACEUTICAL 114 111 <0.01 29
POLYMORPHISM 1306 1250 <0.01 24
PTM 56066 41571 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44000 44000 0.08 11
SIMILARITY 507302 503155 0.91 1
SUBCELLULAR LOCATION 348405 341139 0.62 3
SUBUNIT 277937 277160 0.50 4
TISSUE SPECIFICITY 45578 45577 0.08 10
TOXIC DOSE 666 609 <0.01 27
WEB RESOURCE 6944 5784 0.01 22
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4471332 8.00
ACT_SITE 163498 99216 0.29 10
BINDING 404030 106386 0.72 2
CA_BIND 4176 1729 0.01 36
CARBOHYD 115705 29742 0.21 15
CHAIN 566390 551519 1.01 1
COILED 21994 15214 0.04 27
COMPBIAS 58977 31734 0.11 20
CONFLICT 135082 47305 0.24 13
CROSSLNK 23537 8448 0.04 26
DISULFID 124543 33619 0.22 14
DNA_BIND 11630 10522 0.02 32
DOMAIN 194182 119695 0.35 9
HELIX 251288 23297 0.45 6
INIT_MET 17150 17150 0.03 28
INTRAMEM 2651 1198 <0.01 37
LIPID 13007 8398 0.02 30
METAL 378771 93983 0.68 3
MOD_RES 248386 71777 0.44 7
MOTIF 42868 28010 0.08 23
MUTAGEN 68958 15173 0.12 18
NON_CONS 2257 787 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12397 9511 0.02 31
NP_BIND 156662 85141 0.28 11
PEPTIDE 11566 7965 0.02 33
PROPEP 14198 12108 0.03 29
REGION 197131 93402 0.35 8
REPEAT 105360 14727 0.19 16
SIGNAL 41607 41605 0.07 24
SITE 57166 31702 0.10 21
STRAND 262002 21922 0.47 5
TOPO_DOM 140221 28747 0.25 12
TRANSIT 9085 8969 0.02 34
TRANSMEM 370417 77289 0.66 4
TURN 60539 18880 0.11 19
UNSURE 4455 797 0.01 35
VAR_SEQ 51949 21996 0.09 22
VARIANT 96651 17071 0.17 17
ZN_FING 30489 13398 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) 18848749 33.74
Allergome 1757 1148 <0.01 121 Protein family/group databases
ArachnoServer 1145 1136 <0.01 130 Organism-specific databases
Araport 15835 15739 0.03 83 Organism-specific databases
Bgee 56433 56433 0.10 45 Gene expression databases
BindingDB 4999 4999 0.01 104 Chemistry
BioCyc 158119 154054 0.28 29 Enzyme and pathway databases
BioGrid 50875 50375 0.09 50 Protein-protein interaction databases
BioMuta 17236 17227 0.03 79 Polymorphism and mutation databases
BRENDA 12908 12134 0.02 87 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 128 PTM databases
CAZy 9482 8547 0.02 90 Protein family/group databases
CCDS 48096 34096 0.09 52 Sequence databases
CDD 184485 168568 0.33 26 Family and domain databases
CGD 1997 1980 <0.01 118 Organism-specific databases
ChEMBL 6867 6867 0.01 94 Chemistry
ChiTaRS 20474 20463 0.04 69 Other
CleanEx 30014 29383 0.05 59 Gene expression databases
CollecTF 133 133 <0.01 152 Gene expression databases
ComplexPortal 8435 4415 0.02 91 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 153 2D gel databases
ConoServer 951 868 <0.01 131 Organism-specific databases
CORUM 5168 5168 0.01 101 Protein-protein interaction databases
CTD 74911 74030 0.13 43 Organism-specific databases
DEPOD 239 239 <0.01 148 PTM databases
dictyBase 4215 4100 0.01 108 Organism-specific databases
DIP 17349 17317 0.03 77 Protein-protein interaction databases
DisGeNET 14841 14607 0.03 84 Organism-specific databases
DisProt 708 703 <0.01 135 3D structure databases
DMDM 16280 16280 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 664679 331625 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 120 Protein-protein interaction databases
EMBL 983858 546874 1.76 3 Sequence databases
Ensembl 90199 50311 0.16 41 Genome annotation databases
EnsemblBacteria 354628 335501 0.63 17 Genome annotation databases
EnsemblFungi 30821 28977 0.06 58 Genome annotation databases
EnsemblMetazoa 17312 10139 0.03 78 Genome annotation databases
EnsemblPlants 27396 20449 0.05 63 Genome annotation databases
EnsemblProtists 5014 4830 0.01 103 Genome annotation databases
EPD 21825 21825 0.04 66 Proteomic databases
ESTHER 2503 2503 <0.01 116 Protein family/group databases
euHCVdb 55 44 <0.01 154 Organism-specific databases
EuPathDB 37952 37758 0.07 55 Organism-specific databases
EvolutionaryTrace 16626 16626 0.03 81 Other
ExpressionAtlas 51714 51714 0.09 48 Gene expression databases
FlyBase 6166 5870 0.01 97 Organism-specific databases
Gene3D 365944 292564 0.66 16 Family and domain databases
GeneCards 20338 20171 0.04 71 Organism-specific databases
GeneDB 575 519 <0.01 139 Genome annotation databases
GeneID 290388 280087 0.52 22 Genome annotation databases
GeneReviews 1154 1151 <0.01 129 Organism-specific databases
GeneTree 59353 59329 0.11 44 Phylogenomic databases
Genevisible 55235 55235 0.10 46 Gene expression databases
GeneWiki 10356 10273 0.02 89 Other
GenomeRNAi 22041 22041 0.04 65 Other
GlyConnect 1437 1353 <0.01 122 PTM databases
GO 2896974 532310 5.19 1 Ontologies
Gramene 27396 20449 0.05 64 Genome annotation databases
GuidetoPHARMACOLOGY 1948 1948 <0.01 119 Chemistry
H-InvDB 5628 4802 0.01 100 Organism-specific databases
HAMAP 329828 326952 0.59 19 Family and domain databases
HGNC 20349 20209 0.04 70 Organism-specific databases
HOGENOM 391685 391685 0.70 15 Phylogenomic databases
HOVERGEN 76119 76119 0.14 42 Phylogenomic databases
HPA 27402 16829 0.05 62 Organism-specific databases
IMGT_GENE-DB 142 142 <0.01 151 Protein family/group databases
InParanoid 139547 139547 0.25 30 Phylogenomic databases
IntAct 52710 52710 0.09 47 Protein-protein interaction databases
InterPro 2235115 539798 4.00 2 Family and domain databases
iPTMnet 51307 51307 0.09 49 PTM databases
KEGG 502715 475354 0.90 7 Genome annotation databases
KO 405013 404569 0.73 14 Phylogenomic databases
LegioList 765 763 <0.01 134 Organism-specific databases
Leproma 672 669 <0.01 136 Organism-specific databases
MaizeGDB 509 505 <0.01 140 Organism-specific databases
MalaCards 4438 4435 0.01 106 Organism-specific databases
MaxQB 29710 29710 0.05 60 Proteomic databases
MEROPS 11396 11396 0.02 88 Protein family/group databases
MGI 16905 16865 0.03 80 Organism-specific databases
MIM 20985 15059 0.04 68 Organism-specific databases
MINT 21794 21794 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 20181 20178 0.04 72 Organism-specific databases
OGP 373 373 <0.01 144 2D gel databases
OMA 416791 416791 0.75 13 Phylogenomic databases
OpenTargets 18370 18209 0.03 75 Organism-specific databases
Orphanet 6144 3286 0.01 98 Organism-specific databases
OrthoDB 293508 293508 0.53 20 Phylogenomic databases
PANTHER 283612 270620 0.51 23 Family and domain databases
PATRIC 91857 91857 0.16 40 Genome annotation databases
PaxDb 124653 124653 0.22 33 Proteomic databases
PDB 167430 26834 0.30 27 3D structure databases
PDBsum 167430 26834 0.30 28 3D structure databases
PeptideAtlas 32131 32131 0.06 57 Proteomic databases
PeroxiBase 773 755 <0.01 133 Protein family/group databases
Pfam 762063 518628 1.36 4 Family and domain databases
PharmGKB 18360 18318 0.03 76 Organism-specific databases
PhosphoSitePlus 39022 39022 0.07 54 PTM databases
PhylomeDB 96327 96327 0.17 38 Phylogenomic databases
PIR 124185 113735 0.22 34 Sequence databases
PIRSF 108750 107721 0.19 37 Family and domain databases
PMAP-CutDB 1401 1401 <0.01 123 Other
PomBase 5133 5129 0.01 102 Organism-specific databases
PRIDE 225011 225011 0.40 24 Proteomic databases
PRINTS 132904 117386 0.24 32 Family and domain databases
PRO 95987 95987 0.17 39 Other
ProDom 29146 28963 0.05 61 Family and domain databases
ProMEX 456 456 <0.01 142 Proteomic databases
PROSITE 467283 298841 0.84 10 Family and domain databases
ProteinModelPortal 449101 449101 0.80 11 3D structure databases
Proteomes 479260 455133 0.86 9 Other
ProteomicsDB 36388 19835 0.07 56 Proteomic databases
PseudoCAP 1334 1325 <0.01 125 Organism-specific databases
Reactome 123603 36718 0.22 35 Enzyme and pathway databases
REBASE 395 395 <0.01 143 Protein family/group databases
RefSeq 608326 463394 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 126 2D gel databases
RGD 7974 7973 0.01 92 Organism-specific databases
SABIO-RK 3963 3963 0.01 111 Enzyme and pathway databases
SFLD 14139 6513 0.03 86 Family and domain databases
SGD 6739 6734 0.01 96 Organism-specific databases
SignaLink 3065 3065 0.01 114 Enzyme and pathway databases
SIGNOR 4081 4081 0.01 110 Enzyme and pathway databases
SMART 192101 141790 0.34 25 Family and domain databases
SMR 444075 444075 0.79 12 3D structure databases
STRING 332666 332666 0.60 18 Protein-protein interaction databases
SUPFAM 496981 376889 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 127 2D gel databases
SwissLipids 1359 1272 <0.01 124 Chemistry
SwissPalm 7256 7256 0.01 93 PTM databases
TAIR 14623 14567 0.03 85 Organism-specific databases
TCDB 6793 6751 0.01 95 Protein family/group databases
TIGRFAMs 292622 272599 0.52 21 Family and domain databases
TopDownProteomics 3241 2964 0.01 113 Proteomic databases
TreeFam 45474 45464 0.08 53 Phylogenomic databases
TubercuList 2190 2154 <0.01 117 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 141 2D gel databases
UCSC 49894 45591 0.09 51 Genome annotation databases
UniCarbKB 584 584 <0.01 138 PTM databases
UniGene 109746 96207 0.20 36 Sequence databases
UniLectin 237 237 <0.01 149 Protein family/group databases
UniPathway 136299 123518 0.24 31 Enzyme and pathway databases
VectorBase 597 517 <0.01 137 Genome annotation databases
VGNC 3875 3875 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 6017 4593 0.01 99 Organism-specific databases
Xenbase 4557 4551 0.01 105 Organism-specific databases
ZFIN 3060 3055 0.01 115 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 3882 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: 79217