UniProtKB/Swiss-Prot protein knowledgebase release 2019_03 statistics
1. INTRODUCTION
Release 2019_03 of 10-Apr-19 of UniProtKB/Swiss-Prot contains 559634 sequence entries,
comprising 201129965 amino acids abstracted from 265241 references.
411 sequences have been added since release 2019_02, the sequence data of
63 existing entries has been updated and the annotations of
145277 entries have been revised.
Number of fragments: 9168
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40033
Protein existence (PE): entries %
1: Evidence at protein level 100377 17.9%
2: Evidence at transcript level 57168 10.2%
3: Inferred from homology 386786 69.1%
4: Predicted 13478 2.4%
5: Uncertain 1825 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: 13741
The first twenty species represent 120805 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5673
2x: 1970
3x: 1067
4x: 698
5x: 513
6x: 412
7x: 299
8x: 248
9x: 228
10x: 142
11- 20x: 759
21- 50x: 461
51-100x: 220
>100x: 1051
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20415 Homo sapiens (Human)
2 17013 Mus musculus (Mouse)
3 15834 Arabidopsis thaliana (Mouse-ear cress)
4 8061 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6006 Bos taurus (Bovine)
7 5140 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4481 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4146 Dictyostelium discoideum (Slime mold)
11 4043 Caenorhabditis elegans
12 4035 Oryza sativa subsp. japonica (Rice)
13 3558 Drosophila melanogaster (Fruit fly)
14 3445 Xenopus laevis (African clawed frog)
15 3100 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2291 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2173 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2039 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 1707 Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
25 1694 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1683 Shigella flexneri
27 1428 Sus scrofa (Pig)
28 1347 Salmonella typhi
29 1328 Pseudomonas aeruginosa
30 1244 Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
31 1174 Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
32 1064 Synechocystis sp. (strain PCC 6803 / Kazusa)
33 1034 Archaeoglobus fulgidus
34 1022 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)
37 940 Emericella nidulans
38 931 Staphylococcus aureus (strain Mu50 / ATCC 700699)
39 930 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
40 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
41 927 Staphylococcus aureus (strain N315)
42 919 Kluyveromyces lactis
43 909 Acanthamoeba polyphaga mimivirus (APMV)
44 900 Staphylococcus aureus (strain COL)
45 896 Staphylococcus aureus (strain MW2)
46 894 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)
50 883 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
56 841 Escherichia coli O9:H4 (strain HS)
57 839 Oryza sativa subsp. indica (Rice)
58 834 Escherichia coli O139:H28 (strain E24377A / ETEC)
59 829 Shigella boydii serotype 4 (strain Sb227)
60 825 Canis lupus familiaris (Dog) (Canis familiaris)
61 825 Escherichia coli (strain UTI89 / UPEC)
62 822 Shigella dysenteriae serotype 1 (strain Sd197)
63 821 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
64 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
65 814 Zea mays (Maize)
66 803 Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
67 793 Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
68 792 Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
69 791 Escherichia coli (strain SMS-3-5 / SECEC)
70 784 Aquifex aeolicus (strain VF5)
71 776 Pasteurella multocida (strain Pm70)
72 771 Escherichia coli (strain K12 / DH10B)
73 771 Escherichia coli O127:H6 (strain E2348/69 / EPEC)
74 766 Staphylococcus aureus (strain NCTC 8325)
75 765 Escherichia coli 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 (strain SE11)
83 756 Escherichia coli O45:K1 (strain S88 / ExPEC)
84 753 Escherichia coli O7:K1 (strain IAI39 / ExPEC)
85 751 Bacillus anthracis
86 748 Escherichia coli O157:H7 (strain EC4115 / EHEC)
87 746 Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
88 741 Bacillus halodurans
89 737 Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
90 733 Vibrio vulnificus (strain CMCP6)
91 731 Escherichia coli O81 (strain ED1a)
92 722 Salmonella enteritidis PT4 (strain P125109)
93 718 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 Yersinia pestis bv. Antiqua (strain Nepal516)
98 715 Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
99 714 Salmonella paratyphi A (strain AKU_12601)
100 714 Escherichia coli O1:K1 / APEC
101 713 Salmonella agona (strain SL483)
102 713 Salmonella newport (strain SL254)
103 713 Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)
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)
113 687 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)
117 674 Escherichia coli
118 673 Staphylococcus aureus (strain USA300)
119 672 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
127 650 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
136 615 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
137 614 Staphylococcus haemolyticus (strain JCSC1435)
138 611 Mesorhizobium japonicum (Mesorhizobium loti
139 610 Xanthomonas campestris pv. campestris
140 603 Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)
141 603 Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
142 602 Staphylococcus saprophyticus subsp. saprophyticus
143 602 Photobacterium profundum (strain SS9)
144 601 Salmonella paratyphi C (strain RKS4594)
145 600 Yersinia pestis bv. Antiqua (strain Angola)
146 595 Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
147 594 Bacillus cereus (strain ATCC 10987 / NRS 248)
148 594 Pseudomonas aeruginosa (strain UCBPP-PA14)
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 Staphylococcus aureus (strain Newman)
186 513 Deinococcus radiodurans
187 513 Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
188 512 Pseudomonas aeruginosa (strain PA7)
189 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
190 510 Geobacillus kaustophilus (strain HTA426)
191 508 Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)
192 508 Streptomyces avermitilis
193 507 Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
194 502 Pseudomonas entomophila (strain L48)
195 501 Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
196 501 Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
197 499 Brucella abortus biovar 1 (strain 9-941)
198 498 Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
199 497 Rickettsia conorii (strain ATCC VR-613 / Malish 7)
200 497 Haemophilus influenzae (strain 86-028NP)
201 496 Burkholderia pseudomallei (strain K96243)
202 496 Bacillus clausii (strain KSM-K16)
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 Pyrococcus horikoshii
210 487 Shewanella sp. (strain MR-7)
211 486 Mannheimia succiniciproducens (strain MBEL55E)
212 485 Thermosynechococcus elongatus (strain BP-1)
213 485 Brucella abortus (strain 2308)
214 484 Pseudomonas aeruginosa (strain LESB58)
215 484 Shewanella sp. (strain MR-4)
216 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
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)
220 479 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)
223 477 Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
224 476 Nicotiana tabacum (Common tobacco)
225 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
226 474 Burkholderia lata
227 472 Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
228 468 Clostridium perfringens (strain 13 / Type A)
229 468 Pseudomonas putida (strain GB-1)
230 467 Shewanella frigidimarina (strain NCIMB 400)
231 467 Campylobacter jejuni subsp. jejuni serotype O:2
232 466 Shewanella sp. (strain ANA-3)
233 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
234 466 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
235 465 Anabaena variabilis (strain ATCC 29413 / PCC 7937)
236 465 Enterococcus faecalis (strain ATCC 700802 / V583)
237 464 Aeromonas hydrophila subsp. hydrophila
238 463 Burkholderia mallei (strain ATCC 23344)
239 459 Cupriavidus necator (strain JMP 134 / LMG 1197) (Ralstonia eutropha
240 459 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
241 458 Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
242 457 Ovis aries (Sheep)
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)
246 453 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
247 453 Pseudomonas putida (strain W619)
248 452 Aeromonas salmonicida (strain A449)
249 452 Shewanella baltica (strain OS185)
250 450 Caldanaerobacter subterraneus subsp. tengcongensis
2.3 Taxonomic distribution of the sequences
Kingdom sequences (% of the database)
Archaea 19553 ( 3%)
Bacteria 333879 ( 60%)
Eukaryota 189358 ( 34%)
Viruses 16844 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20416 ( 11%) ( 4%)
Other Mammalia 46721 ( 25%) ( 8%)
Other Vertebrata 18371 ( 10%) ( 3%)
Viridiplantae 39840 ( 21%) ( 7%)
Fungi 34064 ( 18%) ( 6%)
Insecta 9236 ( 5%) ( 2%)
Nematoda 4949 ( 3%) ( 1%)
Other 15761 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9590 1001-1100 3999
51- 100 42641 1101-1200 2802
101- 150 59080 1201-1300 2145
151- 200 58916 1301-1400 2004
201- 250 57774 1401-1500 1625
251- 300 51502 1501-1600 794
301- 350 51896 1601-1700 619
351- 400 45036 1701-1800 560
401- 450 37012 1801-1900 475
451- 500 29857 1901-2000 378
501- 550 21574 2001-2100 250
551- 600 15377 2101-2200 341
601- 650 12839 2201-2300 315
651- 700 9226 2301-2400 214
701- 750 7654 2401-2500 163
751- 800 5540 >2500 1306
801- 850 4777
851- 900 5208
901- 950 4051
951-1000 2926
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: 2781
4.1 Table of the frequency of journal citations
Journals cited 1x: 879
2x: 396
3x: 164
4x: 136
5x: 108
6x: 99
7x: 72
8x: 54
9x: 34
10x: 39
11- 20x: 217
21- 50x: 231
51-100x: 121
>100x: 231
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24633 Journal of Biological Chemistry
2 11446 Proceedings of the National Academy of Sciences of the U.S.A.
3 6625 Journal of Bacteriology
4 5647 Biochemical and Biophysical Research Communications
5 5350 Biochemistry
6 5005 Nucleic Acids Research
7 4830 FEBS Letters
8 4808 Gene
9 4695 The EMBO Journal
10 4543 Nature
11 4346 Molecular and Cellular Biology
12 4271 Journal of Molecular Biology
13 3640 Biochimica et Biophysica Acta
14 3580 Cell
15 3400 European Journal of Biochemistry
16 3262 Journal of Virology
17 3019 Science
18 2864 Biochemical Journal
19 2562 Plant Physiology
20 2537 Molecular Microbiology
21 2535 Genomics
22 2203 Journal of Cell Biology
23 2155 The American Journal of Human Genetics
24 1999 The Plant Cell
25 1921 PLoS ONE
26 1863 Plant Molecular Biology
27 1840 The Plant Journal
28 1837 Genes and Development
29 1814 Human Molecular Genetics
30 1803 Virology
31 1757 Nature Genetics
32 1673 Development
33 1667 Molecular Biology of the Cell
34 1576 Human Mutation
35 1547 Molecular Cell
36 1541 Oncogene
37 1469 Journal of Immunology
38 1395 Molecular and General Genetics
39 1348 Structure
40 1340 Journal of Biochemistry
41 1314 Genetics
42 1258 Journal of Cell Science
43 1159 Blood
44 1146 Journal of General Virology
45 1118 Infection and Immunity
46 1060 Microbiology
47 1051 Current Biology
48 1049 Developmental Biology
49 1047 Archives of Biochemistry and Biophysics
50 906 Journal of Neuroscience
51 904 Applied and Environmental Microbiology
52 884 Acta Crystallographica, Section D
53 884 Cancer Research
54 838 Yeast
55 837 FEMS Microbiology Letters
56 775 Protein Science
57 772 Toxicon
58 751 Neuron
59 732 Journal of Clinical Investigation
60 692 Human Genetics
61 677 American Journal of Physiology
62 676 Plant and Cell Physiology
63 649 Mechanisms of Development
64 647 The Journal of Experimental Medicine
65 646 Nature Structural Biology
66 643 PLoS Genetics
67 621 Proteins
68 608 Journal of Medical Genetics
69 576 Nature Cell Biology
70 574 Current Genetics
71 551 Bioscience, Biotechnology, and Biochemistry
72 539 Nature Structural and Molecular Biology
73 536 Journal of Neurochemistry
74 533 Molecular Endocrinology
75 520 The Journal of Clinical Endocrinology and Metabolism
76 518 Developmental Cell
77 511 The FEBS Journal
78 503 Endocrinology
79 489 Mammalian Genome
80 473 Immunogenetics
81 467 Antimicrobial Agents and Chemotherapy
82 459 Experimental Cell Research
83 448 Molecular and Biochemical Parasitology
84 444 Nature Communications
85 431 Eukaryotic Cell
86 429 Planta
87 417 RNA
88 412 Peptides
89 407 Journal of Molecular Evolution
90 398 Molecular Biology and Evolution
91 388 Journal of Experimental Botany
92 388 DNA and Cell Biology
93 384 Journal of the American Chemical Society
94 378 Molecular Pharmacology
95 374 DNA Sequence
96 373 PLoS Pathogens
97 370 Scientific Reports
98 369 Neurology
99 366 EMBO Reports
100 362 Journal of Investigative Dermatology
101 358 The FASEB Journal
102 350 Comparative Biochemistry and Physiology
103 350 Acta Crystallographica, Section F
104 348 Biology of Reproduction
105 344 American Journal of Medical Genetics. Part A
106 342 Molecular Plant-Microbe Interactions
107 339 European Journal of Human Genetics
108 339 Brain Research. Molecular Brain Research
109 336 Immunity
110 326 Tissue Antigens
111 324 Virus Research
112 320 The New England Journal of Medicine
113 319 Genes to Cells
114 319 Biochimie
115 314 Developmental Dynamics
116 299 Clinical Genetics
117 298 Genome Research
118 296 Biological Chemistry Hoppe-Seyler
119 291 Annals of Neurology
120 284 European Journal of Immunology
121 282 Cytogenetics and Cell Genetics
122 272 Nature Immunology
123 271 BMC Genomics
124 271 Journal of General Microbiology
125 268 Investigative Ophthalmology and Visual Science
126 261 Applied Microbiology and Biotechnology
127 255 Journal of Human Genetics
128 254 Journal of Medicinal Chemistry
129 246 PLoS Biology
130 242 Archives of Microbiology
131 237 Journal of Lipid Research
132 235 Glycobiology
133 231 DNA Research
134 231 Journal of Cellular Biochemistry
135 230 Traffic
136 224 Molecular Genetics and Metabolism
137 220 Cell Cycle
138 219 Molecular Immunology
139 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
140 216 Circulation Research
141 213 Archives of Virology
142 212 Cell Reports
143 212 Diabetes
144 208 Molecular and Cellular Endocrinology
145 206 Nature Medicine
146 205 Phytochemistry
147 204 Protein Expression and Purification
148 204 Fungal Genetics and Biology
149 196 Molecular Genetics and Genomics
150 187 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) 1223354 2.19
Journal 1046418 455995 1.87 1
Submitted to EMBL/GenBank/DDBJ 166105 150455 0.30 2
Submitted to other databases 7391 6823 0.01 3
Book citation 1772 1749 <0.01 4
Plant Gene Register 612 599 <0.01 5
Thesis 434 431 <0.01 6
Unpublished observations 407 403 <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: 410399
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2542077 4.54
ACTIVITY REGULATION 14924 14924 0.03 16
ALLERGEN 774 774 <0.01 26
ALTERNATIVE PRODUCTS 25273 25273 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8348 8348 0.01 20
BIOTECHNOLOGY 1005 990 <0.01 25
CATALYTIC ACTIVITY 285167 238633 0.51 4
CAUTION 13023 12761 0.02 18
COFACTOR 124248 113744 0.22 7
DEVELOPMENTAL STAGE 12222 12221 0.02 19
DISEASE 7060 4741 0.01 21
DISRUPTION PHENOTYPE 14548 14545 0.03 17
DOMAIN 49201 42263 0.09 9
FUNCTION 467636 446818 0.84 2
INDUCTION 21094 21082 0.04 14
INTERACTION 19234 19234 0.03 15
MASS SPECTROMETRY 6972 5261 0.01 22
MISCELLANEOUS 38672 35586 0.07 12
PATHWAY 138514 125660 0.25 6
PHARMACEUTICAL 117 113 <0.01 29
POLYMORPHISM 1323 1267 <0.01 24
PTM 57212 42070 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44082 44082 0.08 11
SIMILARITY 508552 504404 0.91 1
SUBCELLULAR LOCATION 349710 342280 0.62 3
SUBUNIT 278915 278067 0.50 5
TISSUE SPECIFICITY 46080 46079 0.08 10
TOXIC DOSE 671 613 <0.01 27
WEB RESOURCE 6873 5711 0.01 23
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4512213 8.06
ACT_SITE 164291 99730 0.29 10
BINDING 406856 107749 0.73 2
CA_BIND 4177 1730 0.01 36
CARBOHYD 116314 29890 0.21 15
CHAIN 567612 552545 1.01 1
COILED 22039 15232 0.04 27
COMPBIAS 59073 31776 0.11 21
CONFLICT 135379 47390 0.24 13
CROSSLNK 23651 8488 0.04 26
DISULFID 125790 33822 0.22 14
DNA_BIND 11678 10556 0.02 32
DOMAIN 197127 120870 0.35 9
HELIX 257934 23793 0.46 6
INIT_MET 17173 17173 0.03 28
INTRAMEM 2706 1223 <0.01 37
LIPID 13067 8439 0.02 30
METAL 382309 94663 0.68 3
MOD_RES 249151 71952 0.45 7
MOTIF 43320 28215 0.08 23
MUTAGEN 71238 15534 0.13 18
NON_CONS 2258 788 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12410 9526 0.02 31
NP_BIND 157851 85795 0.28 11
PEPTIDE 11617 7994 0.02 33
PROPEP 14275 12171 0.03 29
REGION 199883 94187 0.36 8
REPEAT 105602 14770 0.19 16
SIGNAL 41894 41893 0.07 24
SITE 59215 32235 0.11 20
STRAND 268686 22399 0.48 5
TOPO_DOM 140500 28782 0.25 12
TRANSIT 9111 8995 0.02 34
TRANSMEM 371283 77505 0.66 4
TURN 62193 19298 0.11 19
UNSURE 4461 803 0.01 35
VAR_SEQ 52030 22040 0.09 22
VARIANT 97151 17104 0.17 17
ZN_FING 30551 13418 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) 19010780 33.97
Allergome 1805 1179 <0.01 121 Protein family/group databases
ArachnoServer 1145 1136 <0.01 130 Organism-specific databases
Araport 15855 15759 0.03 83 Organism-specific databases
Bgee 56548 56548 0.10 45 Gene expression databases
BindingDB 5001 5001 0.01 102 Chemistry
BioCyc 269794 244259 0.48 23 Enzyme and pathway databases
BioGrid 51782 51278 0.09 48 Protein-protein interaction databases
BioMuta 20371 20359 0.04 70 Polymorphism and mutation databases
BRENDA 12919 12145 0.02 86 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 129 PTM databases
CAZy 9499 8563 0.02 89 Protein family/group databases
CCDS 48190 34163 0.09 51 Sequence databases
CDD 185307 169310 0.33 27 Family and domain databases
CGD 1998 1981 <0.01 118 Organism-specific databases
ChEMBL 6869 6869 0.01 96 Chemistry
ChiTaRS 20481 20470 0.04 69 Other
CollecTF 133 133 <0.01 152 Gene expression databases
ComplexPortal 8717 4621 0.02 90 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 153 2D gel databases
ConoServer 952 869 <0.01 131 Organism-specific databases
CORUM 5802 5802 0.01 99 Protein-protein interaction databases
CTD 75058 74156 0.13 43 Organism-specific databases
DEPOD 239 239 <0.01 149 PTM databases
dictyBase 4220 4105 0.01 108 Organism-specific databases
DIP 17387 17355 0.03 78 Protein-protein interaction databases
DisGeNET 14834 14602 0.03 84 Organism-specific databases
DisProt 708 703 <0.01 135 3D structure databases
DMDM 16274 16272 0.03 82 Polymorphism and mutation databases
DNASU 18999 18933 0.03 74 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 151 2D gel databases
DrugBank 18747 3637 0.03 75 Chemistry
EchoBASE 4159 4159 0.01 109 Organism-specific databases
EcoGene 4293 4293 0.01 107 Organism-specific databases
eggNOG 665317 331940 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 120 Protein-protein interaction databases
EMBL 985520 547789 1.76 3 Sequence databases
Ensembl 91577 50673 0.16 41 Genome annotation databases
EnsemblBacteria 355532 336401 0.64 17 Genome annotation databases
EnsemblFungi 29481 27926 0.05 59 Genome annotation databases
EnsemblMetazoa 17380 10162 0.03 79 Genome annotation databases
EnsemblPlants 28020 20940 0.05 62 Genome annotation databases
EnsemblProtists 4997 4812 0.01 103 Genome annotation databases
EPD 21830 21830 0.04 67 Proteomic databases
ESTHER 2518 2518 <0.01 116 Protein family/group databases
euHCVdb 55 44 <0.01 155 Organism-specific databases
EuPathDB 38827 38634 0.07 55 Organism-specific databases
EvolutionaryTrace 16632 16632 0.03 81 Other
ExpressionAtlas 41010 41010 0.07 53 Gene expression databases
FlyBase 4863 4737 0.01 104 Organism-specific databases
Gene3D 368325 293931 0.66 16 Family and domain databases
GeneCards 20369 20198 0.04 71 Organism-specific databases
GeneDB 575 519 <0.01 139 Genome annotation databases
GeneID 290244 280259 0.52 22 Genome annotation databases
GeneReviews 1479 1475 <0.01 122 Organism-specific databases
GeneTree 59087 59045 0.11 44 Phylogenomic databases
Genevisible 55239 55239 0.10 46 Gene expression databases
GeneWiki 10355 10272 0.02 88 Other
GenomeRNAi 22116 22116 0.04 66 Other
GlyConnect 1435 1367 <0.01 123 PTM databases
GO 2946731 533574 5.27 1 Ontologies
Gramene 28020 20940 0.05 61 Genome annotation databases
GuidetoPHARMACOLOGY 1957 1957 <0.01 119 Chemistry
H-InvDB 5626 4800 0.01 100 Organism-specific databases
HAMAP 329890 327004 0.59 18 Family and domain databases
HGNC 20355 20216 0.04 73 Organism-specific databases
HOGENOM 391885 391885 0.70 15 Phylogenomic databases
HOVERGEN 76141 76141 0.14 42 Phylogenomic databases
HPA 27387 16821 0.05 63 Organism-specific databases
IMGT_GENE-DB 253 253 <0.01 148 Protein family/group databases
InParanoid 139651 139651 0.25 30 Phylogenomic databases
IntAct 53396 53396 0.10 47 Protein-protein interaction databases
InterPro 2252569 541240 4.03 2 Family and domain databases
iPTMnet 51309 51309 0.09 49 PTM databases
jPOST 26831 26831 0.05 64 Proteomic databases
KEGG 502314 475047 0.90 7 Genome annotation databases
KO 405342 404902 0.72 14 Phylogenomic databases
LegioList 765 763 <0.01 134 Organism-specific databases
Leproma 672 669 <0.01 136 Organism-specific databases
MaizeGDB 510 506 <0.01 140 Organism-specific databases
MalaCards 4499 4496 0.01 106 Organism-specific databases
MaxQB 29634 29634 0.05 58 Proteomic databases
MEROPS 11409 11409 0.02 87 Protein family/group databases
MGI 16923 16883 0.03 80 Organism-specific databases
MIM 21149 15129 0.04 68 Organism-specific databases
MINT 22414 22414 0.04 65 Protein-protein interaction databases
MoonDB 348 348 <0.01 146 Protein family/group databases
MoonProt 280 280 <0.01 147 Protein family/group databases
mycoCLAP 355 352 <0.01 145 Protein family/group databases
neXtProt 20358 20358 0.04 72 Organism-specific databases
OGP 373 373 <0.01 144 2D gel databases
OMA 408955 408955 0.73 13 Phylogenomic databases
OpenTargets 18388 18229 0.03 76 Organism-specific databases
Orphanet 7478 3953 0.01 94 Organism-specific databases
OrthoDB 256669 256669 0.46 24 Phylogenomic databases
PANTHER 295623 281644 0.53 20 Family and domain databases
PATRIC 91950 91950 0.16 40 Genome annotation databases
PaxDb 124745 124745 0.22 33 Proteomic databases
PDB 173839 27359 0.31 29 3D structure databases
PDBsum 173839 27359 0.31 28 3D structure databases
PeptideAtlas 32157 32157 0.06 57 Proteomic databases
PeroxiBase 780 758 <0.01 133 Protein family/group databases
Pfam 764654 519673 1.37 4 Family and domain databases
PharmGKB 18356 18314 0.03 77 Organism-specific databases
PhosphoSitePlus 39020 39020 0.07 54 PTM databases
PhylomeDB 96379 96379 0.17 38 Phylogenomic databases
PIR 124224 113771 0.22 34 Sequence databases
PIRSF 108967 107938 0.19 37 Family and domain databases
PMAP-CutDB 1401 1401 <0.01 124 Other
PomBase 5132 5128 0.01 101 Organism-specific databases
PRIDE 230739 230739 0.41 25 Proteomic databases
PRINTS 132836 117258 0.24 32 Family and domain databases
PRO 95975 95975 0.17 39 Other
ProDom 29155 28972 0.05 60 Family and domain databases
ProMEX 457 457 <0.01 142 Proteomic databases
PROSITE 470252 299488 0.84 10 Family and domain databases
ProteinModelPortal 449322 449322 0.80 11 3D structure databases
Proteomes 482085 457797 0.86 9 Other
ProteomicsDB 36364 19821 0.06 56 Proteomic databases
PseudoCAP 1336 1327 <0.01 126 Organism-specific databases
Reactome 114798 36411 0.21 35 Enzyme and pathway databases
REBASE 407 407 <0.01 143 Protein family/group databases
RefSeq 608531 463264 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 127 2D gel databases
RGD 7985 7984 0.01 92 Organism-specific databases
SABIO-RK 4099 4099 0.01 110 Enzyme and pathway databases
SFLD 8078 5989 0.01 91 Family and domain databases
SGD 6740 6735 0.01 97 Organism-specific databases
SignaLink 3065 3065 0.01 115 Enzyme and pathway databases
SIGNOR 4083 4083 0.01 111 Enzyme and pathway databases
SMART 192599 142044 0.34 26 Family and domain databases
SMR 445310 445310 0.80 12 3D structure databases
STRING 328201 328201 0.59 19 Protein-protein interaction databases
SUPFAM 498790 378239 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 128 2D gel databases
SwissLipids 1367 1279 <0.01 125 Chemistry
SwissPalm 7683 7683 0.01 93 PTM databases
TAIR 14642 14586 0.03 85 Organism-specific databases
TCDB 6977 6924 0.01 95 Protein family/group databases
TIGRFAMs 292468 272476 0.52 21 Family and domain databases
TopDownProteomics 3241 2964 0.01 113 Proteomic databases
TreeFam 45532 45522 0.08 52 Phylogenomic databases
TubercuList 2191 2155 <0.01 117 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 141 2D gel databases
UCSC 49972 45646 0.09 50 Genome annotation databases
UniCarbKB 584 584 <0.01 138 PTM databases
UniGene 109966 96369 0.20 36 Sequence databases
UniLectin 238 238 <0.01 150 Protein family/group databases
UniPathway 136487 123677 0.24 31 Enzyme and pathway databases
VectorBase 597 517 <0.01 137 Genome annotation databases
VGNC 3924 3924 0.01 112 Organism-specific databases
WBParaSite 57 56 <0.01 154 Genome annotation databases
World-2DPAGE 931 920 <0.01 132 2D gel databases
WormBase 6075 4642 0.01 98 Organism-specific databases
Xenbase 4649 4603 0.01 105 Organism-specific databases
ZFIN 3079 3074 0.01 114 Organism-specific databases
Total number of cross-referenced databases: 155
6. AMINO ACID COMPOSITION
6.1 Composition in percent for the complete database
Ala (A) 8.25 Gln (Q) 3.93 Leu (L) 9.65 Ser (S) 6.62
Arg (R) 5.53 Glu (E) 6.73 Lys (K) 5.81 Thr (T) 5.35
Asn (N) 4.05 Gly (G) 7.07 Met (M) 2.41 Trp (W) 1.09
Asp (D) 5.46 His (H) 2.27 Phe (F) 3.86 Tyr (Y) 2.92
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 3897 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: 79347