UniProtKB/Swiss-Prot protein knowledgebase release 2019_09 statistics
1. INTRODUCTION
Release 2019_09 of 16-Oct-19 of UniProtKB/Swiss-Prot contains 561176 sequence entries,
comprising 201758313 amino acids abstracted from 268833 references.
560 sequences have been added since release 2019_08, the sequence data of
19 existing entries has been updated and the annotations of
220237 entries have been revised.
Number of fragments: 9178
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40190
Protein existence (PE): entries %
1: Evidence at protein level 101731 18.1%
2: Evidence at transcript level 57295 10.2%
3: Inferred from homology 386908 68.9%
4: Predicted 13420 2.4%
5: Uncertain 1822 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: 13822
The first twenty species represent 121023 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5698
2x: 1975
3x: 1076
4x: 703
5x: 518
6x: 410
7x: 305
8x: 254
9x: 227
10x: 144
11- 20x: 772
21- 50x: 465
51-100x: 222
>100x: 1053
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20365 Homo sapiens (Human)
2 17025 Mus musculus (Mouse)
3 15896 Arabidopsis thaliana (Mouse-ear cress)
4 8075 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6008 Bos taurus (Bovine)
7 5140 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4518 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4148 Dictyostelium discoideum (Slime mold)
11 4090 Caenorhabditis elegans
12 4059 Oryza sativa subsp. japonica (Rice)
13 3586 Drosophila melanogaster (Fruit fly)
14 3447 Xenopus laevis (African clawed frog)
15 3125 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2291 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2185 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2040 Escherichia coli O157:H7
20 1898 Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
21 1797 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 1694 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1685 Shigella flexneri
27 1431 Sus scrofa (Pig)
28 1347 Salmonella typhi
29 1331 Pseudomonas aeruginosa
30 1244 Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
31 1175 Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
32 1066 Synechocystis sp. (strain PCC 6803 / Kazusa)
33 1035 Archaeoglobus fulgidus
34 1025 Yersinia pestis
35 1010 Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
36 977 Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
37 941 Staphylococcus aureus (strain Mu50 / ATCC 700699)
38 940 Emericella nidulans
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 Escherichia coli O6:K15:H31 (strain 536 / UPEC)
47 894 Oryctolagus cuniculus (Rabbit)
48 889 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
54 863 Yersinia pseudotuberculosis serotype I (strain IP32953)
55 856 Neurospora crassa
56 844 Oryza sativa subsp. indica (Rice)
57 841 Escherichia coli O9:H4 (strain HS)
58 834 Escherichia coli O139:H28 (strain E24377A / ETEC)
59 831 Zea mays (Maize)
60 829 Shigella boydii serotype 4 (strain Sb227)
61 827 Canis lupus familiaris (Dog) (Canis familiaris)
62 825 Escherichia coli (strain UTI89 / UPEC)
63 822 Shigella dysenteriae serotype 1 (strain Sd197)
64 821 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
65 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
66 803 Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
67 801 Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
68 794 Staphylococcus aureus (strain NCTC 8325)
69 793 Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
70 791 Escherichia coli (strain SMS-3-5 / SECEC)
71 786 Aquifex aeolicus (strain VF5)
72 771 Escherichia coli (strain K12 / DH10B)
73 770 Escherichia coli O127:H6 (strain E2348/69 / EPEC)
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)
81 759 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 laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
88 742 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)
93 721 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
94 718 Vibrio vulnificus (strain YJ016)
95 716 Salmonella paratyphi B (strain ATCC BAA-1250 / SPB7)
96 715 Enterobacter sp. (strain 638)
97 715 Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
98 715 Yersinia pestis bv. Antiqua (strain Nepal516)
99 714 Escherichia coli O1:K1 / APEC
100 714 Salmonella paratyphi A (strain AKU_12601)
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 Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)
117 677 Staphylococcus aureus (strain USA300)
118 676 Escherichia coli
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)
135 620 Methanothermobacter thermautotrophicus
136 615 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
137 615 Xanthomonas campestris pv. campestris
138 614 Staphylococcus haemolyticus (strain JCSC1435)
139 611 Mesorhizobium japonicum (Mesorhizobium loti
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)
146 598 Pseudomonas aeruginosa (strain UCBPP-PA14)
147 595 Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
148 594 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)
152 580 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)
164 560 Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
165 559 Clostridium acetobutylicum
166 557 Xanthomonas axonopodis pv. citri (strain 306)
167 555 Pseudomonas fluorescens (strain Pf0-1)
168 554 Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)
169 553 Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
170 553 Oceanobacillus iheyensis
171 550 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)
175 530 Corynebacterium glutamicum
176 529 Listeria monocytogenes serotype 4b (strain F2365)
177 529 Sodalis glossinidius (strain morsitans)
178 528 Bordetella bronchiseptica (strain ATCC BAA-588 / NCTC 13252 / RB50)
179 524 Staphylococcus aureus (strain Newman)
180 522 Xylella fastidiosa (strain 9a5c)
181 520 Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)
182 517 Chromobacterium violaceum
183 516 Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
184 515 Deinococcus radiodurans
185 515 Xylella fastidiosa (strain Temecula1 / ATCC 700964)
186 514 Aspergillus oryzae (strain ATCC 42149 / RIB 40) (Yellow koji mold)
187 513 Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
188 512 Pseudomonas aeruginosa (strain PA7)
189 511 Streptomyces avermitilis
190 511 Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
191 510 Geobacillus kaustophilus (strain HTA426)
192 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
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)
205 492 Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / FZB42)
206 491 Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
207 491 Vibrio campbellii (strain ATCC BAA-1116 / BB120)
208 488 Pyrococcus horikoshii
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 Pseudomonas aeruginosa (strain LESB58)
215 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
216 484 Shewanella sp. (strain MR-4)
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 Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
221 480 Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
222 478 Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
223 477 Pyrococcus abyssi (strain GE5 / Orsay)
224 477 Nicotiana tabacum (Common tobacco)
225 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
226 474 Burkholderia lata
227 474 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
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 Shewanella frigidimarina (strain NCIMB 400)
233 467 Campylobacter jejuni subsp. jejuni serotype O:2
234 466 Aeromonas hydrophila subsp. hydrophila
235 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
236 466 Shewanella sp. (strain ANA-3)
237 465 Enterococcus faecalis (strain ATCC 700802 / V583)
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
241 458 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 Staphylococcus aureus (strain JH1)
245 455 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
246 455 Shewanella baltica (strain OS185)
247 453 Pseudomonas putida (strain W619)
248 453 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
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 19576 ( 3%)
Bacteria 334287 ( 60%)
Eukaryota 190336 ( 34%)
Viruses 16977 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20366 ( 11%) ( 4%)
Other Mammalia 46768 ( 25%) ( 8%)
Other Vertebrata 18418 ( 10%) ( 3%)
Viridiplantae 40137 ( 21%) ( 7%)
Fungi 34176 ( 18%) ( 6%)
Insecta 9340 ( 5%) ( 2%)
Nematoda 4999 ( 3%) ( 1%)
Other 16132 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9670 1001-1100 4015
51- 100 42736 1101-1200 2814
101- 150 59260 1201-1300 2149
151- 200 59051 1301-1400 2016
201- 250 57906 1401-1500 1629
251- 300 51651 1501-1600 800
301- 350 52015 1601-1700 621
351- 400 45091 1701-1800 563
401- 450 37124 1801-1900 480
451- 500 29956 1901-2000 379
501- 550 21664 2001-2100 250
551- 600 15436 2101-2200 345
601- 650 12871 2201-2300 321
651- 700 9246 2301-2400 215
701- 750 7680 2401-2500 167
751- 800 5554 >2500 1321
801- 850 4794
851- 900 5216
901- 950 4055
951-1000 2937
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: 2832
4.1 Table of the frequency of journal citations
Journals cited 1x: 901
2x: 404
3x: 169
4x: 133
5x: 107
6x: 95
7x: 78
8x: 62
9x: 36
10x: 31
11- 20x: 225
21- 50x: 234
51-100x: 122
>100x: 235
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24959 Journal of Biological Chemistry
2 11614 Proceedings of the National Academy of Sciences of the U.S.A.
3 6675 Journal of Bacteriology
4 5691 Biochemical and Biophysical Research Communications
5 5402 Biochemistry
6 5023 Nucleic Acids Research
7 4860 FEBS Letters
8 4823 Gene
9 4717 The EMBO Journal
10 4620 Nature
11 4378 Molecular and Cellular Biology
12 4305 Journal of Molecular Biology
13 3690 Biochimica et Biophysica Acta
14 3605 Cell
15 3411 European Journal of Biochemistry
16 3290 Journal of Virology
17 3057 Science
18 2891 Biochemical Journal
19 2600 Plant Physiology
20 2576 Molecular Microbiology
21 2537 Genomics
22 2214 Journal of Cell Biology
23 2201 The American Journal of Human Genetics
24 2033 The Plant Cell
25 2008 PLoS ONE
26 1880 The Plant Journal
27 1873 Plant Molecular Biology
28 1851 Human Molecular Genetics
29 1846 Genes and Development
30 1813 Virology
31 1773 Nature Genetics
32 1689 Molecular Biology of the Cell
33 1684 Development
34 1581 Human Mutation
35 1568 Molecular Cell
36 1543 Oncogene
37 1496 Journal of Immunology
38 1395 Molecular and General Genetics
39 1368 Structure
40 1350 Journal of Biochemistry
41 1323 Genetics
42 1277 Journal of Cell Science
43 1172 Blood
44 1149 Journal of General Virology
45 1142 Infection and Immunity
46 1077 Microbiology
47 1064 Current Biology
48 1062 Archives of Biochemistry and Biophysics
49 1058 Developmental Biology
50 926 Journal of Neuroscience
51 923 Applied and Environmental Microbiology
52 898 Acta Crystallographica, Section D
53 887 Cancer Research
54 845 FEMS Microbiology Letters
55 839 Yeast
56 788 Toxicon
57 786 Protein Science
58 766 Neuron
59 748 Journal of Clinical Investigation
60 702 Human Genetics
61 701 Plant and Cell Physiology
62 697 American Journal of Physiology
63 680 PLoS Genetics
64 658 The Journal of Experimental Medicine
65 649 Mechanisms of Development
66 646 Nature Structural Biology
67 635 Proteins
68 626 Journal of Medical Genetics
69 584 Nature Cell Biology
70 574 Current Genetics
71 556 Bioscience, Biotechnology, and Biochemistry
72 552 Nature Structural and Molecular Biology
73 540 Journal of Neurochemistry
74 539 Molecular Endocrinology
75 531 The FEBS Journal
76 521 The Journal of Clinical Endocrinology and Metabolism
77 521 Developmental Cell
78 516 Nature Communications
79 506 Endocrinology
80 488 Mammalian Genome
81 479 Antimicrobial Agents and Chemotherapy
82 464 Experimental Cell Research
83 450 Molecular and Biochemical Parasitology
84 440 Immunogenetics
85 433 Planta
86 433 Eukaryotic Cell
87 429 Scientific Reports
88 419 RNA
89 417 Peptides
90 407 Journal of Molecular Evolution
91 402 PLoS Pathogens
92 398 Molecular Biology and Evolution
93 393 Journal of the American Chemical Society
94 393 Journal of Experimental Botany
95 388 DNA and Cell Biology
96 382 Molecular Pharmacology
97 375 DNA Sequence
98 373 EMBO Reports
99 372 The FASEB Journal
100 370 Neurology
101 369 American Journal of Medical Genetics. Part A
102 368 Journal of Investigative Dermatology
103 365 Acta Crystallographica, Section F
104 362 Molecular Plant-Microbe Interactions
105 356 European Journal of Human Genetics
106 351 Comparative Biochemistry and Physiology
107 350 Biology of Reproduction
108 341 Immunity
109 340 Brain Research. Molecular Brain Research
110 328 Virus Research
111 326 Genes to Cells
112 323 Biochimie
113 321 The New England Journal of Medicine
114 318 Developmental Dynamics
115 313 Clinical Genetics
116 300 Annals of Neurology
117 299 Genome Research
118 297 Biological Chemistry Hoppe-Seyler
119 285 European Journal of Immunology
120 282 Cytogenetics and Cell Genetics
121 281 BMC Genomics
122 279 Nature Immunology
123 273 Investigative Ophthalmology and Visual Science
124 271 Journal of General Microbiology
125 266 Applied Microbiology and Biotechnology
126 266 Journal of Lipid Research
127 262 Journal of Human Genetics
128 261 PLoS Biology
129 260 Journal of Medicinal Chemistry
130 247 Archives of Microbiology
131 241 Cell Reports
132 240 Tissue Antigens
133 240 Glycobiology
134 235 Journal of Cellular Biochemistry
135 232 DNA Research
136 232 Traffic
137 232 Molecular Immunology
138 227 Molecular Genetics and Metabolism
139 221 Cell Cycle
140 219 Diabetes
141 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
142 217 Circulation Research
143 213 Archives of Virology
144 212 Phytochemistry
145 210 Nature Medicine
146 209 Protein Expression and Purification
147 208 Molecular and Cellular Endocrinology
148 206 Fungal Genetics and Biology
149 196 Molecular Genetics and Genomics
150 190 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) 1232980 2.20
Journal 1056631 458370 1.88 1
Submitted to EMBL/GenBank/DDBJ 165413 149780 0.29 2
Submitted to other databases 7440 6866 0.01 3
Book citation 1815 1792 <0.01 4
Plant Gene Register 612 599 <0.01 5
Thesis 434 431 <0.01 6
Unpublished observations 420 416 <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: 417483
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2566280 4.57
ACTIVITY REGULATION 15312 15310 0.03 16
ALLERGEN 868 868 <0.01 26
ALTERNATIVE PRODUCTS 25344 25344 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8711 8711 0.02 20
BIOTECHNOLOGY 1054 1038 <0.01 25
CATALYTIC ACTIVITY 293790 240022 0.52 4
CAUTION 13211 12945 0.02 18
COFACTOR 126388 115027 0.23 7
DEVELOPMENTAL STAGE 12431 12430 0.02 19
DISEASE 7254 4878 0.01 21
DISRUPTION PHENOTYPE 15221 15218 0.03 17
DOMAIN 50219 43068 0.09 9
FUNCTION 469913 448816 0.84 2
INDUCTION 21819 21807 0.04 14
INTERACTION 19569 19569 0.03 15
MASS SPECTROMETRY 6862 5274 0.01 23
MISCELLANEOUS 39022 35839 0.07 12
PATHWAY 139345 126299 0.25 6
PHARMACEUTICAL 118 114 <0.01 29
POLYMORPHISM 1269 1213 <0.01 24
PTM 57900 42441 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44222 44222 0.08 11
SIMILARITY 510018 505844 0.91 1
SUBCELLULAR LOCATION 351250 343680 0.63 3
SUBUNIT 280236 279314 0.50 5
TISSUE SPECIFICITY 46712 46711 0.08 10
TOXIC DOSE 675 616 <0.01 27
WEB RESOURCE 6920 5752 0.01 22
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4563709 8.13
ACT_SITE 165386 100119 0.29 10
BINDING 409082 108425 0.73 2
CA_BIND 4206 1743 0.01 36
CARBOHYD 116985 30081 0.21 15
CHAIN 569246 554034 1.01 1
COILED 22084 15284 0.04 27
COMPBIAS 59164 31831 0.11 21
CONFLICT 135861 47523 0.24 13
CROSSLNK 23710 8515 0.04 26
DISULFID 126599 33995 0.23 14
DNA_BIND 11875 10618 0.02 32
DOMAIN 199844 122749 0.36 9
HELIX 266601 24383 0.48 6
INIT_MET 17207 17207 0.03 28
INTRAMEM 2791 1275 <0.01 37
LIPID 13156 8488 0.02 30
METAL 395608 96709 0.70 3
MOD_RES 249685 72167 0.44 7
MOTIF 44081 28813 0.08 23
MUTAGEN 74027 16086 0.13 18
NON_CONS 2260 789 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12441 9550 0.02 31
NP_BIND 158449 86059 0.28 11
PEPTIDE 11682 8050 0.02 33
PROPEP 14362 12253 0.03 29
REGION 201701 94777 0.36 8
REPEAT 105876 14822 0.19 16
SIGNAL 42426 42425 0.08 24
SITE 59564 32370 0.11 20
STRAND 276364 22982 0.49 5
TOPO_DOM 141210 28887 0.25 12
TRANSIT 9169 9053 0.02 34
TRANSMEM 372478 77755 0.66 4
TURN 64208 19828 0.11 19
UNSURE 4470 806 0.01 35
VAR_SEQ 52178 22118 0.09 22
VARIANT 97348 17108 0.17 17
ZN_FING 29968 12753 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) 18544943 33.05
ABCD 1373 1373 <0.01 125 Protocols and materials databases
Allergome 1924 1252 <0.01 120 Protein family/group databases
ArachnoServer 1163 1154 <0.01 129 Organism-specific databases
Araport 15916 15820 0.03 81 Organism-specific databases
Bgee 56705 56704 0.10 41 Gene expression databases
BindingDB 5155 5155 0.01 98 Chemistry
BioCyc 270102 244515 0.48 22 Enzyme and pathway databases
BioGrid 54466 52779 0.10 45 Protein-protein interaction databases
BioMuta 20317 20302 0.04 67 Polymorphism and mutation databases
BRENDA 12954 12171 0.02 84 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 130 PTM databases
CAZy 9506 8569 0.02 87 Protein family/group databases
CCDS 48296 34253 0.09 49 Sequence databases
CDD 184175 167176 0.33 26 Family and domain databases
CGD 1998 1981 <0.01 119 Organism-specific databases
ChEMBL 7279 7158 0.01 93 Chemistry
ChiTaRS 29622 29585 0.05 54 Other
CollecTF 133 133 <0.01 153 Gene expression databases
ComplexPortal 9100 4784 0.02 88 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 154 2D gel databases
ConoServer 952 869 <0.01 131 Organism-specific databases
CORUM 5805 5805 0.01 97 Protein-protein interaction databases
CPTAC 2221 1423 <0.01 115 Proteomic databases
CTD 75255 74356 0.13 40 Organism-specific databases
DEPOD 239 239 <0.01 151 PTM databases
dictyBase 4213 4099 0.01 107 Organism-specific databases
DIP 17396 17364 0.03 77 Protein-protein interaction databases
DisGeNET 15661 15430 0.03 82 Organism-specific databases
DisProt 700 700 <0.01 136 Family and domain databases
DMDM 16211 16209 0.03 80 Polymorphism and mutation databases
DNASU 19015 18949 0.03 72 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 152 2D gel databases
DrugBank 27239 4519 0.05 60 Chemistry
DrugCentral 2531 2531 <0.01 114 Chemistry
EchoBASE 4159 4159 0.01 108 Organism-specific databases
EcoGene 4293 4293 0.01 104 Organism-specific databases
eggNOG 666217 332380 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 121 Protein-protein interaction databases
EMBL 985467 549152 1.76 3 Sequence databases
Ensembl 91789 50556 0.16 39 Genome annotation databases
EnsemblBacteria 355935 336759 0.63 16 Genome annotation databases
EnsemblFungi 29538 27983 0.05 56 Genome annotation databases
EnsemblMetazoa 17645 10333 0.03 75 Genome annotation databases
EnsemblPlants 28020 20971 0.05 57 Genome annotation databases
EnsemblProtists 4919 4740 0.01 101 Genome annotation databases
EPD 22035 22035 0.04 64 Proteomic databases
ESTHER 2539 2538 <0.01 113 Protein family/group databases
euHCVdb 55 44 <0.01 156 Organism-specific databases
EuPathDB 19694 19682 0.04 71 Organism-specific databases
EvolutionaryTrace 16631 16631 0.03 79 Other
ExpressionAtlas 49467 49467 0.09 48 Gene expression databases
FlyBase 4891 4765 0.01 102 Organism-specific databases
Gene3D 391368 305612 0.70 15 Family and domain databases
GeneCards 20345 20172 0.04 66 Organism-specific databases
GeneDB 579 523 <0.01 140 Genome annotation databases
GeneID 289890 279968 0.52 20 Genome annotation databases
GeneReviews 1479 1475 <0.01 122 Organism-specific databases
GeneTree 55884 55834 0.10 42 Phylogenomic databases
Genevisible 55234 55234 0.10 43 Gene expression databases
GeneWiki 10352 10269 0.02 86 Other
GenomeRNAi 22142 22142 0.04 63 Other
GlyConnect 2201 2113 <0.01 117 PTM databases
GO 2974593 535739 5.30 1 Ontologies
Gramene 28020 20971 0.05 58 Genome annotation databases
GuidetoPHARMACOLOGY 1998 1998 <0.01 118 Chemistry
HAMAP 330109 327206 0.59 17 Family and domain databases
HGNC 20310 20171 0.04 68 Organism-specific databases
HOGENOM 392234 392234 0.70 14 Phylogenomic databases
HPA 27373 16808 0.05 59 Organism-specific databases
IMGT_GENE-DB 266 266 <0.01 150 Protein family/group databases
InParanoid 139847 139847 0.25 29 Phylogenomic databases
IntAct 54671 54671 0.10 44 Protein-protein interaction databases
InterPro 2290236 542183 4.08 2 Family and domain databases
iPTMnet 52596 52596 0.09 46 PTM databases
jPOST 26780 26780 0.05 61 Proteomic databases
KEGG 504681 475748 0.90 7 Genome annotation databases
KO 407748 407301 0.73 13 Phylogenomic databases
LegioList 765 763 <0.01 135 Organism-specific databases
Leproma 672 669 <0.01 137 Organism-specific databases
MaizeGDB 520 516 <0.01 141 Organism-specific databases
MalaCards 4604 4600 0.01 103 Organism-specific databases
MassIVE 17458 17458 0.03 76 Proteomic databases
MaxQB 29592 29592 0.05 55 Proteomic databases
MEROPS 11449 11447 0.02 85 Protein family/group databases
MGI 16935 16895 0.03 78 Organism-specific databases
MIM 21335 15140 0.04 65 Organism-specific databases
MINT 22774 22774 0.04 62 Protein-protein interaction databases
MoonDB 348 348 <0.01 147 Protein family/group databases
MoonProt 280 280 <0.01 148 Protein family/group databases
mycoCLAP 355 352 <0.01 146 Protein family/group databases
neXtProt 20278 20278 0.04 69 Organism-specific databases
NIAGADS 72 72 <0.01 155 Organism-specific databases
OGP 373 373 <0.01 145 2D gel databases
OMA 411627 411627 0.73 12 Phylogenomic databases
OpenTargets 18422 18268 0.03 73 Organism-specific databases
Orphanet 7560 4011 0.01 92 Organism-specific databases
OrthoDB 257179 257179 0.46 23 Phylogenomic databases
PANTHER 281470 269884 0.50 21 Family and domain databases
PATRIC 92147 92147 0.16 38 Genome annotation databases
PaxDb 124861 124861 0.22 32 Proteomic databases
PDB 184092 28114 0.33 28 3D structure databases
PDBsum 184092 28114 0.33 27 3D structure databases
PeptideAtlas 32486 32486 0.06 53 Proteomic databases
PeroxiBase 782 760 <0.01 134 Protein family/group databases
Pfam 780232 521964 1.39 4 Family and domain databases
PharmGKB 18318 18300 0.03 74 Organism-specific databases
Pharos 20125 20125 0.04 70 Other
PhosphoSitePlus 39015 39015 0.07 52 PTM databases
PhylomeDB 96429 96429 0.17 36 Phylogenomic databases
PIR 124187 113900 0.22 33 Sequence databases
PIRSF 108967 107938 0.19 35 Family and domain databases
PlantReactome 941 671 <0.01 132 Enzyme and pathway databases
PMAP-CutDB 1400 1400 <0.01 123 Other
PomBase 5132 5128 0.01 99 Organism-specific databases
PRIDE 234523 234523 0.42 24 Proteomic databases
PRINTS 131702 117000 0.23 31 Family and domain databases
PRO 95974 95974 0.17 37 Other
ProMEX 462 462 <0.01 143 Proteomic databases
PROSITE 473676 301403 0.84 10 Family and domain databases
Proteomes 484415 460152 0.86 9 Other
ProteomicsDB 40879 19836 0.07 51 Proteomic databases
PseudoCAP 1339 1330 <0.01 126 Organism-specific databases
Reactome 118472 36209 0.21 34 Enzyme and pathway databases
REBASE 406 406 <0.01 144 Protein family/group databases
RefSeq 613081 467293 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 127 2D gel databases
RGD 7999 7997 0.01 91 Organism-specific databases
SABIO-RK 4262 4262 0.01 106 Enzyme and pathway databases
SFLD 8106 6016 0.01 90 Family and domain databases
SGD 6740 6735 0.01 95 Organism-specific databases
SignaLink 3069 3069 0.01 112 Enzyme and pathway databases
SIGNOR 4277 4277 0.01 105 Enzyme and pathway databases
SMART 192996 142300 0.34 25 Family and domain databases
SMR 445592 445592 0.79 11 3D structure databases
STRING 328639 328639 0.59 18 Protein-protein interaction databases
SUPFAM 499675 378911 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 128 2D gel databases
SwissLipids 1392 1305 <0.01 124 Chemistry
SwissPalm 8597 8597 0.02 89 PTM databases
TAIR 14701 14645 0.03 83 Organism-specific databases
TCDB 7208 7158 0.01 94 Protein family/group databases
TIGRFAMs 292592 272589 0.52 19 Family and domain databases
TopDownProteomics 3239 2962 0.01 110 Proteomic databases
TreeFam 45598 45588 0.08 50 Phylogenomic databases
TubercuList 2203 2167 <0.01 116 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 142 2D gel databases
UCSC 50094 45750 0.09 47 Genome annotation databases
UniCarbKB 584 584 <0.01 138 PTM databases
UniLectin 275 275 <0.01 149 Protein family/group databases
UniPathway 137089 124143 0.24 30 Enzyme and pathway databases
VectorBase 581 502 <0.01 139 Genome annotation databases
VGNC 3968 3968 0.01 109 Organism-specific databases
WBParaSite 32 32 <0.01 157 Genome annotation databases
World-2DPAGE 931 920 <0.01 133 2D gel databases
WormBase 6194 4689 0.01 96 Organism-specific databases
Xenbase 5010 4979 0.01 100 Organism-specific databases
ZFIN 3103 3098 0.01 111 Organism-specific databases
Total number of cross-referenced databases: 157
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) 6.73 Lys (K) 5.81 Thr (T) 5.35
Asn (N) 4.06 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) 2.92
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 3916 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: 79572