UniProtKB/Swiss-Prot protein knowledgebase release 2020_03 statistics
1. INTRODUCTION
Release 2020_03 of 17-Jun-20 of UniProtKB/Swiss-Prot contains 562755 sequence entries,
comprising 202599198 amino acids abstracted from 272950 references.
521 sequences have been added since release 2020_02, the sequence data of
44 existing entries has been updated and the annotations of
217472 entries have been revised.
Number of fragments: 9224
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40291
Protein existence (PE): entries %
1: Evidence at protein level 104267 18.5%
2: Evidence at transcript level 56474 10%
3: Inferred from homology 386822 68.7%
4: Predicted 13339 2.4%
5: Uncertain 1853 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: 13919
The first twenty species represent 121314 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5705
2x: 2005
3x: 1088
4x: 707
5x: 517
6x: 409
7x: 318
8x: 253
9x: 229
10x: 146
11- 20x: 800
21- 50x: 467
51-100x: 221
>100x: 1054
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20368 Homo sapiens (Human)
2 17042 Mus musculus (Mouse)
3 15983 Arabidopsis thaliana (Mouse-ear cress)
4 8106 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6012 Bos taurus (Bovine)
7 5140 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4518 Escherichia coli (strain K12)
9 4191 Bacillus subtilis (strain 168)
10 4149 Dictyostelium discoideum (Slime mold)
11 4129 Caenorhabditis elegans
12 4081 Oryza sativa subsp. japonica (Rice)
13 3608 Drosophila melanogaster (Fruit fly)
14 3451 Xenopus laevis (African clawed frog)
15 3158 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2295 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2204 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2042 Escherichia coli O157:H7
20 1898 Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
21 1801 Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
22 1787 Methanocaldococcus jannaschii
23 1707 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
24 1706 Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
25 1697 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1685 Shigella flexneri
27 1436 Sus scrofa (Pig)
28 1383 Pseudomonas aeruginosa
29 1347 Salmonella typhi
30 1244 Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
31 1175 Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
32 1073 Synechocystis sp. (strain PCC 6803 / Kazusa)
33 1035 Archaeoglobus fulgidus
34 1025 Yersinia pestis
35 1012 Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
36 986 Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
37 948 Emericella nidulans
38 941 Staphylococcus aureus (strain Mu50 / ATCC 700699)
39 930 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
40 929 Staphylococcus aureus (strain N315)
41 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
42 919 Kluyveromyces lactis
43 909 Acanthamoeba polyphaga mimivirus (APMV)
44 903 Staphylococcus aureus (strain COL)
45 896 Staphylococcus aureus (strain MW2)
46 894 Oryctolagus cuniculus (Rabbit)
47 894 Escherichia coli O6:K15:H31 (strain 536 / UPEC)
48 890 Staphylococcus aureus (strain MSSA476)
49 888 Staphylococcus aureus (strain MRSA252)
50 883 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
54 874 Neurospora crassa
55 863 Yersinia pseudotuberculosis serotype I (strain IP32953)
56 846 Oryza sativa subsp. indica (Rice)
57 841 Escherichia coli O9:H4 (strain HS)
58 834 Escherichia coli O139:H28 (strain E24377A / ETEC)
59 833 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
60 831 Zea mays (Maize)
61 829 Shigella boydii serotype 4 (strain Sb227)
62 827 Canis lupus familiaris (Dog) (Canis familiaris)
63 825 Escherichia coli (strain UTI89 / UPEC)
64 822 Shigella dysenteriae serotype 1 (strain Sd197)
65 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
66 804 Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
67 803 Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
68 799 Staphylococcus aureus (strain NCTC 8325)
69 793 Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
70 791 Escherichia coli (strain SMS-3-5 / SECEC)
71 787 Aquifex aeolicus (strain VF5)
72 771 Escherichia coli O127:H6 (strain E2348/69 / EPEC)
73 771 Escherichia coli (strain K12 / DH10B)
74 770 Pasteurella multocida (strain Pm70)
75 765 Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)
76 765 Escherichia coli (strain K12 / MC4100 / BW2952)
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)
81 760 Staphylococcus epidermidis (strain ATCC 12228)
82 758 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 Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
87 748 Escherichia coli O157:H7 (strain EC4115 / EHEC)
88 742 Bacillus halodurans
89 739 Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
90 733 Vibrio vulnificus (strain CMCP6)
91 731 Escherichia coli O81 (strain ED1a)
92 725 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
93 722 Salmonella enteritidis PT4 (strain P125109)
94 718 Vibrio vulnificus (strain YJ016)
95 716 Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)
96 715 Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
97 715 Enterobacter sp. (strain 638)
98 715 Yersinia pestis bv. Antiqua (strain Nepal516)
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 newport (strain SL254)
103 713 Salmonella agona (strain SL483)
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 Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)
109 698 Klebsiella pneumoniae (strain 342)
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)
113 686 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 Escherichia coli
117 678 Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)
118 677 Staphylococcus aureus (strain USA300)
119 672 Serratia proteamaculans (strain 568)
120 669 Mycobacterium leprae (strain TN)
121 668 Bacillus cereus
122 667 Yersinia pestis (strain Pestoides F)
123 664 Bradyrhizobium diazoefficiens
124 664 Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
125 657 Sinorhizobium fredii (strain NBRC 101917 / NGR234)
126 653 Debaryomyces hansenii
127 650 Shewanella oneidensis (strain MR-1)
128 650 Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
129 643 Staphylococcus aureus (strain bovine RF122 / ET3-1)
130 642 Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)
131 640 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)
135 622 Methanothermobacter thermautotrophicus
136 618 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
137 615 Xanthomonas campestris pv. campestris
138 614 Staphylococcus haemolyticus (strain JCSC1435)
139 613 Mesorhizobium japonicum (Mesorhizobium loti
140 608 Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
141 603 Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)
142 603 Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
143 602 Staphylococcus saprophyticus subsp. saprophyticus
144 602 Photobacterium profundum (strain SS9)
145 601 Salmonella paratyphi C (strain RKS4594)
146 600 Pseudomonas aeruginosa (strain UCBPP-PA14)
147 600 Yersinia pestis bv. Antiqua (strain Angola)
148 595 Bacillus cereus (strain ATCC 10987 / NRS 248)
149 591 Pectobacterium carotovorum subsp. carotovorum (strain PC1)
150 584 Rickettsia prowazekii (strain Madrid E)
151 582 Neisseria meningitidis serogroup B (strain MC58)
152 579 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)
157 572 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 Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
163 562 Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)
164 562 Bacillus cereus (strain ZK / E33L)
165 559 Clostridium acetobutylicum
166 559 Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
167 557 Xanthomonas axonopodis pv. citri (strain 306)
168 555 Pseudomonas fluorescens (strain Pf0-1)
169 554 Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)
170 553 Oceanobacillus iheyensis
171 552 Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
172 547 Pseudomonas savastanoi pv. phaseolicola (Pseudomonas syringae pv. phaseolicola
173 540 Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)
174 531 Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99)
175 531 Corynebacterium glutamicum
176 530 Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)
177 529 Sodalis glossinidius (strain morsitans)
178 529 Listeria monocytogenes serotype 4b (strain F2365)
179 528 Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)
180 524 Staphylococcus aureus (strain Newman)
181 522 Xylella fastidiosa (strain 9a5c)
182 521 Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
183 518 Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
184 517 Chromobacterium violaceum
185 516 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
186 516 Deinococcus radiodurans
187 515 Xylella fastidiosa (strain Temecula1 / ATCC 700964)
188 512 Pseudomonas aeruginosa (strain PA7)
189 511 Streptomyces avermitilis
190 511 Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
191 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
192 510 Geobacillus kaustophilus (strain HTA426)
193 508 Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)
194 507 Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
195 502 Pseudomonas entomophila (strain L48)
196 501 Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
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)
200 496 Bacillus clausii (strain KSM-K16)
201 496 Burkholderia pseudomallei (strain K96243)
202 496 Rickettsia conorii (strain ATCC VR-613 / Malish 7)
203 494 Proteus mirabilis (strain HI4320)
204 493 Xanthomonas campestris pv. campestris (strain 8004)
205 493 Pyrococcus horikoshii
206 492 Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / FZB42)
207 491 Vibrio campbellii (strain ATCC BAA-1116 / BB120)
208 491 Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
209 488 Methanosarcina mazei
210 487 Shewanella sp. (strain MR-7)
211 486 Brucella abortus (strain 2308)
212 486 Mannheimia succiniciproducens (strain MBEL55E)
213 485 Thermosynechococcus elongatus (strain BP-1)
214 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
215 484 Shewanella sp. (strain MR-4)
216 484 Pseudomonas aeruginosa (strain LESB58)
217 483 Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)
218 482 Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
219 482 Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
220 480 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
221 480 Synechococcus elongatus (strain PCC 7942 / FACHB-805) (Anacystis nidulans R2)
222 480 Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
223 478 Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
224 478 Nicotiana tabacum (Common tobacco)
225 477 Pyrococcus abyssi (strain GE5 / Orsay)
226 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
227 474 Burkholderia lata
228 472 Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
229 469 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
230 468 Clostridium perfringens (strain 13 / Type A)
231 468 Pseudomonas putida (strain GB-1)
232 467 Campylobacter jejuni subsp. jejuni serotype O:2
233 467 Aeromonas hydrophila subsp. hydrophila
234 467 Enterococcus faecalis (strain ATCC 700802 / V583)
235 467 Shewanella frigidimarina (strain NCIMB 400)
236 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
237 466 Shewanella sp. (strain ANA-3)
238 465 Trichormus variabilis (strain ATCC 29413 / PCC 7937) (Anabaena variabilis)
239 463 Burkholderia mallei (strain ATCC 23344)
240 459 Cupriavidus pinatubonensis (strain JMP 134 / LMG 1197) (Cupriavidus necator
241 459 Ovis aries (Sheep)
242 458 Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
243 457 Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
244 455 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
245 455 Staphylococcus aureus (strain JH1)
246 455 Shewanella baltica (strain OS185)
247 453 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
248 453 Pseudomonas putida (strain W619)
249 452 Aeromonas salmonicida (strain A449)
250 450 Caldanaerobacter subterraneus subsp. tengcongensis
2.3 Taxonomic distribution of the sequences
Kingdom sequences (% of the database)
Archaea 19621 ( 3%)
Bacteria 334554 ( 59%)
Eukaryota 191572 ( 34%)
Viruses 17008 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20369 ( 11%) ( 4%)
Other Mammalia 46908 ( 24%) ( 8%)
Other Vertebrata 18556 ( 10%) ( 3%)
Viridiplantae 40435 ( 21%) ( 7%)
Fungi 34686 ( 18%) ( 6%)
Insecta 9365 ( 5%) ( 2%)
Nematoda 5038 ( 3%) ( 1%)
Other 16215 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9711 1001-1100 4032
51- 100 42881 1101-1200 2823
101- 150 59346 1201-1300 2158
151- 200 59120 1301-1400 2028
201- 250 57986 1401-1500 1639
251- 300 51783 1501-1600 804
301- 350 52144 1601-1700 621
351- 400 45226 1701-1800 567
401- 450 37238 1801-1900 486
451- 500 30036 1901-2000 383
501- 550 21780 2001-2100 255
551- 600 15502 2101-2200 353
601- 650 12928 2201-2300 327
651- 700 9277 2301-2400 221
701- 750 7703 2401-2500 172
751- 800 5583 >2500 1352
801- 850 4818
851- 900 5232
901- 950 4064
951-1000 2952
The average sequence length in UniProtKB/Swiss-Prot is 360 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: 2874
4.1 Table of the frequency of journal citations
Journals cited 1x: 917
2x: 404
3x: 174
4x: 134
5x: 117
6x: 84
7x: 77
8x: 65
9x: 39
10x: 29
11- 20x: 236
21- 50x: 235
51-100x: 125
>100x: 238
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 25296 Journal of Biological Chemistry
2 11773 Proceedings of the National Academy of Sciences of the U.S.A.
3 6772 Journal of Bacteriology
4 5748 Biochemical and Biophysical Research Communications
5 5474 Biochemistry
6 5081 Nucleic Acids Research
7 4886 FEBS Letters
8 4832 Gene
9 4748 The EMBO Journal
10 4673 Nature
11 4416 Molecular and Cellular Biology
12 4361 Journal of Molecular Biology
13 3753 Biochimica et Biophysica Acta
14 3641 Cell
15 3433 European Journal of Biochemistry
16 3313 Journal of Virology
17 3101 Science
18 2937 Biochemical Journal
19 2642 Plant Physiology
20 2621 Molecular Microbiology
21 2537 Genomics
22 2259 The American Journal of Human Genetics
23 2235 Journal of Cell Biology
24 2109 PLoS ONE
25 2064 The Plant Cell
26 1914 The Plant Journal
27 1881 Plant Molecular Biology
28 1880 Human Molecular Genetics
29 1865 Genes and Development
30 1824 Virology
31 1790 Nature Genetics
32 1701 Molecular Biology of the Cell
33 1695 Development
34 1596 Molecular Cell
35 1584 Human Mutation
36 1545 Oncogene
37 1525 Journal of Immunology
38 1403 Molecular and General Genetics
39 1384 Structure
40 1366 Journal of Biochemistry
41 1334 Genetics
42 1291 Journal of Cell Science
43 1186 Blood
44 1161 Infection and Immunity
45 1151 Journal of General Virology
46 1097 Microbiology
47 1080 Archives of Biochemistry and Biophysics
48 1079 Current Biology
49 1068 Developmental Biology
50 945 Journal of Neuroscience
51 939 Applied and Environmental Microbiology
52 916 Acta Crystallographica, Section D
53 894 Cancer Research
54 854 FEMS Microbiology Letters
55 840 Yeast
56 801 Toxicon
57 794 Protein Science
58 775 Neuron
59 765 Journal of Clinical Investigation
60 724 PLoS Genetics
61 719 Plant and Cell Physiology
62 712 American Journal of Physiology
63 705 Human Genetics
64 681 The Journal of Experimental Medicine
65 650 Mechanisms of Development
66 646 Nature Structural Biology
67 645 Proteins
68 641 Journal of Medical Genetics
69 596 Nature Communications
70 593 Nature Cell Biology
71 576 Current Genetics
72 570 Nature Structural and Molecular Biology
73 563 Bioscience, Biotechnology, and Biochemistry
74 552 The FEBS Journal
75 549 Journal of Neurochemistry
76 540 Molecular Endocrinology
77 536 Developmental Cell
78 529 The Journal of Clinical Endocrinology and Metabolism
79 514 Endocrinology
80 502 Scientific Reports
81 501 Antimicrobial Agents and Chemotherapy
82 488 Mammalian Genome
83 468 Experimental Cell Research
84 454 Molecular and Biochemical Parasitology
85 438 Peptides
86 438 Eukaryotic Cell
87 435 Planta
88 430 RNA
89 430 Immunogenetics
90 429 PLoS Pathogens
91 412 Journal of the American Chemical Society
92 407 Journal of Experimental Botany
93 405 Journal of Molecular Evolution
94 401 Molecular Biology and Evolution
95 390 Molecular Pharmacology
96 389 DNA and Cell Biology
97 383 EMBO Reports
98 382 American Journal of Medical Genetics. Part A
99 382 The FASEB Journal
100 376 Acta Crystallographica, Section F
101 375 DNA Sequence
102 375 Neurology
103 373 Journal of Investigative Dermatology
104 372 Molecular Plant-Microbe Interactions
105 367 European Journal of Human Genetics
106 355 Comparative Biochemistry and Physiology
107 354 Immunity
108 353 Biology of Reproduction
109 340 Brain Research. Molecular Brain Research
110 339 Biochimie
111 331 Virus Research
112 330 Genes to Cells
113 324 The New England Journal of Medicine
114 322 Clinical Genetics
115 320 Developmental Dynamics
116 305 Annals of Neurology
117 300 Genome Research
118 298 Biological Chemistry Hoppe-Seyler
119 291 Journal of Lipid Research
120 289 European Journal of Immunology
121 288 BMC Genomics
122 287 Nature Immunology
123 282 Cytogenetics and Cell Genetics
124 281 Investigative Ophthalmology and Visual Science
125 273 Applied Microbiology and Biotechnology
126 272 Journal of General Microbiology
127 267 Journal of Human Genetics
128 267 Cell Reports
129 266 Journal of Medicinal Chemistry
130 264 PLoS Biology
131 252 Glycobiology
132 250 Archives of Microbiology
133 240 Traffic
134 239 Molecular Immunology
135 238 Journal of Cellular Biochemistry
136 233 Molecular Genetics and Metabolism
137 232 DNA Research
138 225 Cell Cycle
139 222 Protein Expression and Purification
140 221 Diabetes
141 219 Phytochemistry
142 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
143 217 Circulation Research
144 217 Archives of Virology
145 215 Nature Medicine
146 213 Fungal Genetics and Biology
147 208 Molecular and Cellular Endocrinology
148 201
149 200 Nature Chemical Biology
150 199 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) 1244302 2.21
Journal 1068224 460508 1.90 1
Submitted to EMBL/GenBank/DDBJ 165011 149391 0.29 2
Submitted to other databases 7508 6919 0.01 3
Book citation 1834 1811 <0.01 4
Plant Gene Register 612 599 <0.01 5
Unpublished observations 460 456 <0.01 6
Thesis 437 434 <0.01 7
Patent 210 204 <0.01 8
Worm Breeder's Gazette 6 6 <0.01 9
Total number of distinct authors cited in UniProtKB/Swiss-Prot: 424821
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2602188 4.62
ACTIVITY REGULATION 15695 15690 0.03 17
ALLERGEN 906 906 <0.01 26
ALTERNATIVE PRODUCTS 25423 25423 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 9096 9089 0.02 20
BIOTECHNOLOGY 1257 1240 <0.01 25
CATALYTIC ACTIVITY 303256 242532 0.54 4
CAUTION 13402 13125 0.02 18
COFACTOR 127417 115829 0.23 7
DEVELOPMENTAL STAGE 12691 12682 0.02 19
DISEASE 7426 4985 0.01 21
DISRUPTION PHENOTYPE 16105 16101 0.03 16
DOMAIN 51177 43830 0.09 9
FUNCTION 472478 451041 0.84 2
INDUCTION 22345 22314 0.04 15
INTERACTION 22481 22481 0.04 14
MASS SPECTROMETRY 6970 5365 0.01 23
MISCELLANEOUS 43933 38643 0.08 12
PATHWAY 140428 127112 0.25 6
PHARMACEUTICAL 136 130 <0.01 29
POLYMORPHISM 1279 1224 <0.01 24
PTM 58815 42950 0.10 8
RNA EDITING 628 628 <0.01 28
SEQUENCE CAUTION 44483 44411 0.08 11
SIMILARITY 511586 507405 0.91 1
SUBCELLULAR LOCATION 352792 345069 0.63 3
SUBUNIT 284674 281266 0.51 5
TISSUE SPECIFICITY 47397 47337 0.08 10
TOXIC DOSE 753 621 <0.01 27
WEB RESOURCE 7159 5982 0.01 22
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4629208 8.23
ACT_SITE 166384 100744 0.30 10
BINDING 413818 109917 0.74 2
CA_BIND 4211 1747 0.01 36
CARBOHYD 118407 30386 0.21 15
CHAIN 570910 555513 1.01 1
COILED 22126 15318 0.04 27
COMPBIAS 59211 31860 0.11 21
CONFLICT 136856 47768 0.24 13
CROSSLNK 23916 8594 0.04 26
DISULFID 127890 34235 0.23 14
DNA_BIND 11929 10670 0.02 32
DOMAIN 205049 126188 0.36 8
HELIX 274878 24982 0.49 6
INIT_MET 17384 17336 0.03 28
INTRAMEM 2799 1283 <0.01 37
LIPID 13266 8562 0.02 30
METAL 403361 97471 0.72 3
MOD_RES 255220 72666 0.45 7
MOTIF 44626 29149 0.08 23
MUTAGEN 77197 16638 0.14 18
NON_CONS 2523 820 <0.01 38
NON_STD 358 283 <0.01 39
NON_TER 12545 9615 0.02 31
NP_BIND 159575 86470 0.28 11
PEPTIDE 11910 8166 0.02 33
PROPEP 14545 12402 0.03 29
REGION 203976 95724 0.36 9
REPEAT 106670 14883 0.19 16
SIGNAL 42755 42754 0.08 24
SITE 60330 32602 0.11 20
STRAND 284625 23547 0.51 5
TOPO_DOM 144117 29375 0.26 12
TRANSIT 9222 9106 0.02 34
TRANSMEM 374217 78244 0.66 4
TURN 66264 20317 0.12 19
UNSURE 5573 838 0.01 35
VAR_SEQ 52275 22189 0.09 22
VARIANT 98178 17164 0.17 17
ZN_FING 30112 12867 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) 18928213 33.63
ABCD 1896 1896 <0.01 124 Protocols and materials databases
Allergome 1985 1283 <0.01 123 Protein family/group databases
Antibodypedia 32082 31968 0.06 57 Protocols and materials databases
ArachnoServer 1163 1154 <0.01 133 Organism-specific databases
Araport 16003 15907 0.03 84 Organism-specific databases
Bgee 56889 56889 0.10 42 Gene expression databases
BindingDB 5261 5261 0.01 101 Chemistry
BioCyc 270351 244737 0.48 22 Enzyme and pathway databases
BioGRID 54865 53166 0.10 46 Protein-protein interaction databases
BioGRID-ORCS 38898 38400 0.07 55 Other
BioMuta 20313 20298 0.04 72 Polymorphism and mutation databases
BRENDA 12975 12193 0.02 87 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 135 PTM databases
CAZy 9529 8588 0.02 91 Protein family/group databases
CCDS 48836 34355 0.09 49 Sequence databases
CDD 184724 167613 0.33 28 Family and domain databases
CGD 2000 1983 <0.01 122 Organism-specific databases
ChEMBL 7818 7655 0.01 95 Chemistry
ChiTaRS 29624 29587 0.05 59 Other
CLAE 356 353 <0.01 150 Protein family/group databases
CollecTF 135 135 <0.01 157 Gene expression databases
ComplexPortal 10221 5660 0.02 90 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 158 2D gel databases
ConoServer 957 873 <0.01 137 Organism-specific databases
CORUM 5805 5805 0.01 100 Protein-protein interaction databases
CPTAC 2221 1423 <0.01 120 Proteomic databases
CTD 75272 74371 0.13 40 Organism-specific databases
DEPOD 239 239 <0.01 155 PTM databases
dictyBase 4214 4100 0.01 110 Organism-specific databases
DIP 17435 17396 0.03 80 Protein-protein interaction databases
DisGeNET 15646 15415 0.03 85 Organism-specific databases
DisProt 1379 1367 <0.01 130 Family and domain databases
DMDM 16197 16195 0.03 83 Polymorphism and mutation databases
DNASU 19056 18990 0.03 74 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 156 2D gel databases
DrugBank 28101 4590 0.05 63 Chemistry
DrugCentral 2532 2532 <0.01 117 Chemistry
EchoBASE 4158 4158 0.01 111 Organism-specific databases
eggNOG 667204 332867 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 125 Protein-protein interaction databases
EMBL 987951 550647 1.76 3 Sequence databases
Ensembl 98086 51353 0.17 36 Genome annotation databases
EnsemblBacteria 356229 337021 0.63 16 Genome annotation databases
EnsemblFungi 29787 28221 0.05 58 Genome annotation databases
EnsemblMetazoa 17898 10410 0.03 78 Genome annotation databases
EnsemblPlants 28264 21164 0.05 62 Genome annotation databases
EnsemblProtists 5022 4843 0.01 103 Genome annotation databases
EPD 21130 21130 0.04 68 Proteomic databases
ESTHER 2564 2563 <0.01 116 Protein family/group databases
euHCVdb 55 44 <0.01 160 Organism-specific databases
EuPathDB 39157 38963 0.07 53 Organism-specific databases
EvolutionaryTrace 16644 16644 0.03 82 Other
ExpressionAtlas 48079 48079 0.09 50 Gene expression databases
FlyBase 4907 4781 0.01 105 Organism-specific databases
Gene3D 411415 319697 0.73 14 Family and domain databases
GeneCards 20331 20159 0.04 70 Organism-specific databases
GeneDB 589 533 <0.01 143 Genome annotation databases
GeneID 288063 279084 0.51 20 Genome annotation databases
GeneReviews 1479 1475 <0.01 126 Organism-specific databases
GeneTree 59856 59812 0.11 41 Phylogenomic databases
Genevisible 55242 55242 0.10 45 Gene expression databases
GeneWiki 10350 10267 0.02 89 Other
GenomeRNAi 22160 22160 0.04 66 Other
GlyConnect 2243 2107 <0.01 118 PTM databases
GO 3062717 537676 5.44 1 Ontologies
Gramene 28264 21164 0.05 61 Genome annotation databases
GuidetoPHARMACOLOGY 2012 2012 <0.01 121 Chemistry
HAMAP 330290 327370 0.59 17 Family and domain databases
HGNC 20315 20176 0.04 71 Organism-specific databases
HOGENOM 423356 423356 0.75 12 Phylogenomic databases
HPA 18987 18852 0.03 75 Organism-specific databases
IDEAL 985 985 <0.01 136 Family and domain databases
IMGT_GENE-DB 267 267 <0.01 154 Protein family/group databases
InParanoid 140095 140095 0.25 29 Phylogenomic databases
IntAct 55322 55322 0.10 44 Protein-protein interaction databases
InterPro 2309351 543883 4.10 2 Family and domain databases
iPTMnet 52671 52671 0.09 47 PTM databases
jPOST 26792 26792 0.05 64 Proteomic databases
KEGG 505480 476464 0.90 8 Genome annotation databases
KO 406248 406147 0.72 15 Phylogenomic databases
LegioList 765 763 <0.01 140 Organism-specific databases
Leproma 672 669 <0.01 141 Organism-specific databases
MaizeGDB 520 516 <0.01 146 Organism-specific databases
MalaCards 4737 4733 0.01 106 Organism-specific databases
MassIVE 17475 17475 0.03 79 Proteomic databases
MaxQB 29595 29595 0.05 60 Proteomic databases
MEROPS 11485 11483 0.02 88 Protein family/group databases
MetOSite 3107 3107 0.01 114 PTM databases
MGI 16953 16913 0.03 81 Organism-specific databases
MIM 21642 15284 0.04 67 Organism-specific databases
MINT 22791 22791 0.04 65 Protein-protein interaction databases
MoonDB 348 348 <0.01 151 Protein family/group databases
MoonProt 281 281 <0.01 152 Protein family/group databases
neXtProt 20332 20332 0.04 69 Organism-specific databases
NIAGADS 68 68 <0.01 159 Organism-specific databases
OGP 373 373 <0.01 149 2D gel databases
OMA 413869 413869 0.74 13 Phylogenomic databases
OpenTargets 18433 18280 0.03 76 Organism-specific databases
Orphanet 7658 4083 0.01 96 Organism-specific databases
OrthoDB 245253 245253 0.44 23 Phylogenomic databases
PANTHER 282905 271015 0.50 21 Family and domain databases
PATRIC 92332 92332 0.16 39 Genome annotation databases
PaxDb 125383 125383 0.22 33 Proteomic databases
PDB 192519 28974 0.34 26 3D structure databases
PDBsum 192519 28974 0.34 27 3D structure databases
PeptideAtlas 33378 33378 0.06 56 Proteomic databases
PeroxiBase 782 760 <0.01 139 Protein family/group databases
Pfam 782327 523239 1.39 4 Family and domain databases
PharmGKB 18319 18301 0.03 77 Organism-specific databases
Pharos 20110 20110 0.04 73 Other
PHI-base 1439 1194 <0.01 127 Other
PhosphoSitePlus 39072 39072 0.07 54 PTM databases
PhylomeDB 96935 96935 0.17 37 Phylogenomic databases
PIR 124334 114074 0.22 34 Sequence databases
PIRSF 109134 108105 0.19 35 Family and domain databases
PlantReactome 1159 713 <0.01 134 Enzyme and pathway databases
PomBase 5132 5128 0.01 102 Organism-specific databases
PRIDE 234640 234640 0.42 24 Proteomic databases
PRINTS 130744 115960 0.23 31 Family and domain databases
PRO 96893 96893 0.17 38 Other
ProMEX 467 467 <0.01 148 Proteomic databases
PROSITE 479276 304741 0.85 10 Family and domain databases
Proteomes 499108 465757 0.89 9 Other
ProteomicsDB 56831 35704 0.10 43 Proteomic databases
PseudoCAP 1390 1381 <0.01 129 Organism-specific databases
Reactome 130317 36866 0.23 32 Enzyme and pathway databases
REBASE 619 378 <0.01 142 Protein family/group databases
RefSeq 615359 469214 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 131 2D gel databases
RGD 8031 8028 0.01 94 Organism-specific databases
RNAct 43015 43015 0.08 52 Other
SABIO-RK 4380 4380 0.01 107 Enzyme and pathway databases
SFLD 8127 6036 0.01 93 Family and domain databases
SGD 6740 6735 0.01 98 Organism-specific databases
SignaLink 3102 3102 0.01 115 Enzyme and pathway databases
SIGNOR 4302 4302 0.01 108 Enzyme and pathway databases
SMART 193598 142703 0.34 25 Family and domain databases
SMR 449410 449410 0.80 11 3D structure databases
STRING 329116 329116 0.58 18 Protein-protein interaction databases
SUPFAM 510159 386419 0.91 7 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 132 2D gel databases
SwissLipids 1428 1342 <0.01 128 Chemistry
SwissPalm 8615 8615 0.02 92 PTM databases
TAIR 14782 14726 0.03 86 Organism-specific databases
TCDB 7464 7409 0.01 97 Protein family/group databases
TIGRFAMs 292753 272721 0.52 19 Family and domain databases
TopDownProteomics 3237 2960 0.01 112 Proteomic databases
TreeFam 45675 45670 0.08 51 Phylogenomic databases
TubercuList 2222 2186 <0.01 119 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 147 2D gel databases
UCSC 50216 45832 0.09 48 Genome annotation databases
UniCarbKB 584 584 <0.01 144 PTM databases
UniLectin 276 276 <0.01 153 Protein family/group databases
UniPathway 137831 124659 0.24 30 Enzyme and pathway databases
VectorBase 582 503 <0.01 145 Genome annotation databases
VGNC 4275 4262 0.01 109 Organism-specific databases
WBParaSite 5 5 <0.01 161 Genome annotation databases
World-2DPAGE 931 920 <0.01 138 2D gel databases
WormBase 6301 4728 0.01 99 Organism-specific databases
Xenbase 5009 5000 0.01 104 Organism-specific databases
ZFIN 3132 3127 0.01 113 Organism-specific databases
Total number of cross-referenced databases: 161
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) 6.63
Arg (R) 5.53 Glu (E) 6.72 Lys (K) 5.81 Thr (T) 5.35
Asn (N) 4.06 Gly (G) 7.08 Met (M) 2.41 Trp (W) 1.09
Asp (D) 5.46 His (H) 2.27 Phe (F) 3.86 Tyr (Y) 2.92
Cys (C) 1.38 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 3933 are encoded on a plasmid.
12189 entries are encoded on a plastid,
of which 21 are encoded on apicoplasts,
11624 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: 79900