UniProtKB/Swiss-Prot protein knowledgebase release 2019_01 statistics
1. INTRODUCTION
Release 2019_01 of 16-Jan-19 of UniProtKB/Swiss-Prot contains 559077 sequence entries,
comprising 200828568 amino acids abstracted from 264040 references.
199 sequences have been added since release 2018_11, the sequence data of
22 existing entries has been updated and the annotations of
362788 entries have been revised.
Number of fragments: 9159
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40019
Protein existence (PE): entries %
1: Evidence at protein level 99969 17.9%
2: Evidence at transcript level 57170 10.2%
3: Inferred from homology 386615 69.2%
4: Predicted 13489 2.4%
5: Uncertain 1834 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: 13709
The first twenty species represent 120750 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5663
2x: 1963
3x: 1071
4x: 694
5x: 515
6x: 410
7x: 298
8x: 249
9x: 228
10x: 142
11- 20x: 749
21- 50x: 457
51-100x: 220
>100x: 1050
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20413 Homo sapiens (Human)
2 17006 Mus musculus (Mouse)
3 15828 Arabidopsis thaliana (Mouse-ear cress)
4 8054 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6004 Bos taurus (Bovine)
7 5141 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4475 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4146 Dictyostelium discoideum (Slime mold)
11 4038 Caenorhabditis elegans
12 4034 Oryza sativa subsp. japonica (Rice)
13 3551 Drosophila melanogaster (Fruit fly)
14 3444 Xenopus laevis (African clawed frog)
15 3090 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2291 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2173 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2037 Escherichia coli O157:H7
20 1898 Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
21 1796 Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
22 1787 Methanocaldococcus jannaschii
23 1707 Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
24 1706 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
25 1694 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1683 Shigella flexneri
27 1428 Sus scrofa (Pig)
28 1347 Salmonella typhi
29 1326 Pseudomonas aeruginosa
30 1244 Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
31 1173 Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
32 1064 Synechocystis sp. (strain PCC 6803 / Kazusa)
33 1034 Archaeoglobus fulgidus
34 1022 Yersinia pestis
35 1009 Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast)
36 975 Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
37 930 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
38 930 Staphylococcus aureus (strain Mu50 / ATCC 700699)
39 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
40 926 Staphylococcus aureus (strain N315)
41 925 Emericella nidulans
42 919 Kluyveromyces lactis
43 909 Acanthamoeba polyphaga mimivirus (APMV)
44 899 Staphylococcus aureus (strain COL)
45 895 Staphylococcus aureus (strain MW2)
46 893 Oryctolagus cuniculus (Rabbit)
47 892 Escherichia coli O6:K15:H31 (strain 536 / UPEC)
48 889 Staphylococcus aureus (strain MSSA476)
49 888 Staphylococcus aureus (strain MRSA252)
50 883 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 Escherichia coli (strain UTI89 / UPEC)
61 822 Canis lupus familiaris (Dog) (Canis familiaris)
62 822 Shigella dysenteriae serotype 1 (strain Sd197)
63 821 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
64 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
65 810 Zea mays (Maize)
66 803 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 (strain K12 / MC4100 / BW2952)
76 765 Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)
77 762 Escherichia coli (strain 55989 / EAEC)
78 761 Escherichia coli O8 (strain IAI1)
79 760 Shigella flexneri serotype 5b (strain 8401)
80 760 Staphylococcus epidermidis (strain ATCC 35984 / RP62A)
81 759 Staphylococcus epidermidis (strain ATCC 12228)
82 756 Escherichia coli O45:K1 (strain S88 / ExPEC)
83 756 Escherichia coli (strain SE11)
84 753 Escherichia coli O7:K1 (strain IAI39 / ExPEC)
85 751 Bacillus anthracis
86 748 Escherichia coli O157:H7 (strain EC4115 / EHEC)
87 746 Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)
88 741 Bacillus halodurans
89 737 Yersinia enterocolitica serotype O:8 / biotype 1B (strain NCTC 13174 / 8081)
90 733 Vibrio vulnificus (strain CMCP6)
91 731 Escherichia coli O81 (strain ED1a)
92 722 Salmonella enteritidis PT4 (strain P125109)
93 718 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 Yersinia pestis bv. Antiqua (strain Nepal516)
97 715 Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
98 715 Enterobacter sp. (strain 638)
99 714 Escherichia coli O1:K1 / APEC
100 714 Salmonella paratyphi A (strain AKU_12601)
101 713 Salmonella agona (strain SL483)
102 713 Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)
103 713 Salmonella newport (strain SL254)
104 712 Salmonella schwarzengrund (strain CVM19633)
105 711 Yersinia pestis bv. Antiqua (strain Antiqua)
106 710 Salmonella heidelberg (strain SL476)
107 702 Salmonella dublin (strain CT_02021853)
108 698 Klebsiella pneumoniae (strain 342)
109 698 Shigella boydii serotype 18 (strain CDC 3083-94 / BS512)
110 695 Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 0568-73)
111 693 Pan troglodytes (Chimpanzee)
112 692 Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)
113 687 Mycoplasma pneumoniae (strain ATCC 29342 / M129)
114 684 Salmonella gallinarum (strain 287/91 / NCTC 13346)
115 680 Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)
116 678 Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696)
117 674 Escherichia coli
118 673 Staphylococcus aureus (strain USA300)
119 670 Serratia proteamaculans (strain 568)
120 669 Mycobacterium leprae (strain TN)
121 667 Yersinia pestis (strain Pestoides F)
122 665 Bacillus cereus
123 664 Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
124 664 Bradyrhizobium diazoefficiens
125 658 Sinorhizobium fredii (strain NBRC 101917 / NGR234)
126 653 Debaryomyces hansenii
127 646 Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
128 645 Shewanella oneidensis (strain MR-1)
129 643 Staphylococcus aureus (strain bovine RF122 / ET3-1)
130 642 Salmonella arizonae (strain ATCC BAA-731 / CDC346-86 / RSK2980)
131 638 Yersinia pseudotuberculosis serotype O:3 (strain YPIII)
132 634 Yersinia pseudotuberculosis serotype IB (strain PB1/+)
133 622 Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)
134 622 Treponema pallidum (strain Nichols)
135 620 Methanothermobacter thermautotrophicus
136 615 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
137 614 Staphylococcus haemolyticus (strain JCSC1435)
138 611 Mesorhizobium japonicum (Mesorhizobium loti
139 610 Xanthomonas campestris pv. campestris
140 603 Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)
141 603 Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
142 602 Photobacterium profundum (strain SS9)
143 602 Staphylococcus saprophyticus subsp. saprophyticus
144 601 Salmonella paratyphi C (strain RKS4594)
145 600 Yersinia pestis bv. Antiqua (strain Angola)
146 594 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 Buchnera aphidicola subsp. Schizaphis graminum (strain Sg)
163 562 Bacillus cereus (strain ZK / E33L)
164 559 Clostridium acetobutylicum
165 557 Xanthomonas axonopodis pv. citri (strain 306)
166 555 Pseudomonas fluorescens (strain Pf0-1)
167 555 Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155)
168 554 Neisseria meningitidis serogroup A / serotype 4A (strain Z2491)
169 553 Oceanobacillus iheyensis
170 551 Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
171 550 Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
172 547 Pseudomonas savastanoi pv. phaseolicola (Pseudomonas syringae pv. phaseolicola
173 537 Lactococcus lactis subsp. lactis (strain IL1403) (Streptococcus lactis)
174 531 Erwinia tasmaniensis (strain DSM 17950 / CIP 109463 / Et1/99)
175 529 Corynebacterium glutamicum
176 529 Listeria monocytogenes serotype 4b (strain F2365)
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
187 512 Pseudomonas aeruginosa (strain PA7)
188 511 Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
189 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
190 510 Geobacillus kaustophilus (strain HTA426)
191 508 Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)
192 508 Streptomyces avermitilis
193 507 Buchnera aphidicola subsp. Baizongia pistaciae (strain Bp)
194 502 Pseudomonas entomophila (strain L48)
195 501 Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
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)
200 497 Rickettsia conorii (strain ATCC VR-613 / Malish 7)
201 496 Bacillus clausii (strain KSM-K16)
202 496 Burkholderia pseudomallei (strain K96243)
203 494 Proteus mirabilis (strain HI4320)
204 493 Xanthomonas campestris pv. campestris (strain 8004)
205 492 Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / FZB42)
206 491 Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)
207 490 Vibrio campbellii (strain ATCC BAA-1116 / BB120)
208 488 Methanosarcina mazei
209 487 Shewanella sp. (strain MR-7)
210 487 Pyrococcus horikoshii
211 486 Mannheimia succiniciproducens (strain MBEL55E)
212 485 Thermosynechococcus elongatus (strain BP-1)
213 484 Pseudomonas aeruginosa (strain LESB58)
214 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
215 484 Shewanella sp. (strain MR-4)
216 483 Brucella abortus (strain 2308)
217 483 Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)
218 480 Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
219 479 Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
220 479 Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
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)
224 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
225 475 Nicotiana tabacum (Common tobacco)
226 474 Burkholderia lata
227 472 Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
228 468 Clostridium perfringens (strain 13 / Type A)
229 467 Shewanella frigidimarina (strain NCIMB 400)
230 467 Campylobacter jejuni subsp. jejuni serotype O:2
231 466 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
232 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
233 466 Pseudomonas putida (strain GB-1)
234 466 Shewanella sp. (strain ANA-3)
235 465 Anabaena variabilis (strain ATCC 29413 / PCC 7937)
236 464 Aeromonas hydrophila subsp. hydrophila
237 463 Enterococcus faecalis (strain ATCC 700802 / V583)
238 462 Burkholderia mallei (strain ATCC 23344)
239 459 Cupriavidus necator (strain JMP 134 / LMG 1197) (Ralstonia eutropha
240 458 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
241 458 Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
242 457 Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
243 457 Ovis aries (Sheep)
244 455 Staphylococcus aureus (strain JH1)
245 454 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
246 453 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
247 453 Pseudomonas putida (strain W619)
248 452 Shewanella baltica (strain OS185)
249 452 Aeromonas salmonicida (strain A449)
250 450 Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)
2.3 Taxonomic distribution of the sequences
Kingdom sequences (% of the database)
Archaea 19549 ( 3%)
Bacteria 333792 ( 60%)
Eukaryota 188892 ( 34%)
Viruses 16844 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20414 ( 11%) ( 4%)
Other Mammalia 46697 ( 25%) ( 8%)
Other Vertebrata 18356 ( 10%) ( 3%)
Viridiplantae 39787 ( 21%) ( 7%)
Fungi 33866 ( 18%) ( 6%)
Insecta 9229 ( 5%) ( 2%)
Nematoda 4944 ( 3%) ( 1%)
Other 15599 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9586 1001-1100 3992
51- 100 42554 1101-1200 2801
101- 150 59023 1201-1300 2144
151- 200 58896 1301-1400 2003
201- 250 57741 1401-1500 1622
251- 300 51475 1501-1600 791
301- 350 51851 1601-1700 616
351- 400 44994 1701-1800 558
401- 450 36975 1801-1900 474
451- 500 29809 1901-2000 378
501- 550 21523 2001-2100 248
551- 600 15354 2101-2200 340
601- 650 12829 2201-2300 315
651- 700 9224 2301-2400 212
701- 750 7651 2401-2500 161
751- 800 5534 >2500 1284
801- 850 4776
851- 900 5209
901- 950 4049
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: 2764
4.1 Table of the frequency of journal citations
Journals cited 1x: 869
2x: 395
3x: 166
4x: 133
5x: 109
6x: 94
7x: 73
8x: 54
9x: 39
10x: 35
11- 20x: 219
21- 50x: 226
51-100x: 121
>100x: 231
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24531 Journal of Biological Chemistry
2 11390 Proceedings of the National Academy of Sciences of the U.S.A.
3 6617 Journal of Bacteriology
4 5628 Biochemical and Biophysical Research Communications
5 5324 Biochemistry
6 4991 Nucleic Acids Research
7 4826 FEBS Letters
8 4806 Gene
9 4689 The EMBO Journal
10 4520 Nature
11 4338 Molecular and Cellular Biology
12 4261 Journal of Molecular Biology
13 3627 Biochimica et Biophysica Acta
14 3565 Cell
15 3395 European Journal of Biochemistry
16 3245 Journal of Virology
17 3004 Science
18 2856 Biochemical Journal
19 2559 Plant Physiology
20 2534 Genomics
21 2529 Molecular Microbiology
22 2191 Journal of Cell Biology
23 2147 The American Journal of Human Genetics
24 1991 The Plant Cell
25 1895 PLoS ONE
26 1859 Plant Molecular Biology
27 1834 Genes and Development
28 1833 The Plant Journal
29 1803 Human Molecular Genetics
30 1799 Virology
31 1750 Nature Genetics
32 1667 Development
33 1661 Molecular Biology of the Cell
34 1571 Human Mutation
35 1541 Molecular Cell
36 1540 Oncogene
37 1449 Journal of Immunology
38 1394 Molecular and General Genetics
39 1339 Journal of Biochemistry
40 1335 Structure
41 1312 Genetics
42 1248 Journal of Cell Science
43 1155 Blood
44 1144 Journal of General Virology
45 1111 Infection and Immunity
46 1055 Microbiology
47 1048 Developmental Biology
48 1047 Current Biology
49 1044 Archives of Biochemistry and Biophysics
50 902 Applied and Environmental Microbiology
51 896 Journal of Neuroscience
52 882 Cancer Research
53 881 Acta Crystallographica, Section D
54 838 Yeast
55 836 FEMS Microbiology Letters
56 771 Protein Science
57 770 Toxicon
58 743 Neuron
59 724 Journal of Clinical Investigation
60 691 Human Genetics
61 675 Plant and Cell Physiology
62 673 American Journal of Physiology
63 648 Mechanisms of Development
64 645 Nature Structural Biology
65 640 PLoS Genetics
66 637 The Journal of Experimental Medicine
67 620 Proteins
68 601 Journal of Medical Genetics
69 574 Current Genetics
70 571 Nature Cell Biology
71 551 Bioscience, Biotechnology, and Biochemistry
72 533 Nature Structural and Molecular Biology
73 532 Molecular Endocrinology
74 532 Journal of Neurochemistry
75 519 The Journal of Clinical Endocrinology and Metabolism
76 511 Developmental Cell
77 507 The FEBS Journal
78 503 Endocrinology
79 489 Mammalian Genome
80 472 Immunogenetics
81 466 Antimicrobial Agents and Chemotherapy
82 457 Experimental Cell Research
83 448 Molecular and Biochemical Parasitology
84 431 Eukaryotic Cell
85 425 Planta
86 418 Nature Communications
87 417 RNA
88 412 Peptides
89 407 Journal of Molecular Evolution
90 397 Molecular Biology and Evolution
91 388 DNA and Cell Biology
92 384 Journal of Experimental Botany
93 377 Journal of the American Chemical Society
94 375 Molecular Pharmacology
95 374 DNA Sequence
96 367 PLoS Pathogens
97 362 EMBO Reports
98 360 Neurology
99 359 Journal of Investigative Dermatology
100 355 The FASEB Journal
101 350 Comparative Biochemistry and Physiology
102 347 Biology of Reproduction
103 347 Acta Crystallographica, Section F
104 346 Scientific Reports
105 342 Molecular Plant-Microbe Interactions
106 339 Brain Research. Molecular Brain Research
107 339 American Journal of Medical Genetics. Part A
108 336 European Journal of Human Genetics
109 331 Immunity
110 326 Tissue Antigens
111 322 Virus Research
112 318 Biochimie
113 318 The New England Journal of Medicine
114 317 Genes to Cells
115 313 Developmental Dynamics
116 296 Biological Chemistry Hoppe-Seyler
117 296 Clinical Genetics
118 296 Genome Research
119 288 Annals of Neurology
120 282 Cytogenetics and Cell Genetics
121 277 European Journal of Immunology
122 271 Journal of General Microbiology
123 271 Nature Immunology
124 269 BMC Genomics
125 266 Investigative Ophthalmology and Visual Science
126 260 Applied Microbiology and Biotechnology
127 254 Journal of Human Genetics
128 250 Journal of Medicinal Chemistry
129 245 PLoS Biology
130 241 Archives of Microbiology
131 235 Glycobiology
132 231 DNA Research
133 230 Journal of Lipid Research
134 229 Journal of Cellular Biochemistry
135 224 Traffic
136 220 Molecular Genetics and Metabolism
137 220 Cell Cycle
138 219 Molecular Immunology
139 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
140 215 Circulation Research
141 213 Archives of Virology
142 208 Diabetes
143 207 Molecular and Cellular Endocrinology
144 204 Protein Expression and Purification
145 204 Phytochemistry
146 203 Fungal Genetics and Biology
147 202 Cell Reports
148 199 Nature Medicine
149 196 Molecular Genetics and Genomics
150 186 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) 1220237 2.18
Journal 1042774 454852 1.87 1
Submitted to EMBL/GenBank/DDBJ 166641 150996 0.30 2
Submitted to other databases 7382 6817 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: 408124
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2532318 4.53
ACTIVITY REGULATION 14807 14807 0.03 16
ALLERGEN 764 764 <0.01 26
ALTERNATIVE PRODUCTS 25265 25265 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8251 8251 0.01 20
BIOTECHNOLOGY 974 960 <0.01 25
CATALYTIC ACTIVITY 282182 237510 0.50 4
CAUTION 12858 12612 0.02 18
COFACTOR 123171 112770 0.22 7
DEVELOPMENTAL STAGE 12154 12153 0.02 19
DISEASE 7031 4716 0.01 21
DISRUPTION PHENOTYPE 14316 14314 0.03 17
DOMAIN 48832 42035 0.09 9
FUNCTION 466212 445565 0.83 2
INDUCTION 20976 20964 0.04 14
INTERACTION 19170 19170 0.03 15
MASS SPECTROMETRY 6938 5229 0.01 22
MISCELLANEOUS 38582 35515 0.07 12
PATHWAY 138188 125357 0.25 6
PHARMACEUTICAL 117 113 <0.01 29
POLYMORPHISM 1324 1268 <0.01 24
PTM 56591 41747 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44055 44055 0.08 11
SIMILARITY 507948 503800 0.91 1
SUBCELLULAR LOCATION 349160 341774 0.62 3
SUBUNIT 278602 277779 0.50 5
TISSUE SPECIFICITY 45806 45805 0.08 10
TOXIC DOSE 668 610 <0.01 27
WEB RESOURCE 6749 5589 0.01 23
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4492023 8.03
ACT_SITE 163831 99371 0.29 10
BINDING 405195 107285 0.72 2
CA_BIND 4177 1730 0.01 36
CARBOHYD 115929 29801 0.21 15
CHAIN 567012 552004 1.01 1
COILED 22034 15227 0.04 27
COMPBIAS 59057 31773 0.11 20
CONFLICT 135285 47370 0.24 13
CROSSLNK 23621 8468 0.04 26
DISULFID 125136 33714 0.22 14
DNA_BIND 11671 10549 0.02 32
DOMAIN 194557 119928 0.35 9
HELIX 255508 23605 0.46 6
INIT_MET 17164 17164 0.03 28
INTRAMEM 2668 1196 <0.01 37
LIPID 13037 8422 0.02 30
METAL 381033 94213 0.68 3
MOD_RES 248764 71878 0.44 7
MOTIF 43131 28126 0.08 23
MUTAGEN 70268 15377 0.13 18
NON_CONS 2258 788 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12403 9517 0.02 31
NP_BIND 157134 85388 0.28 11
PEPTIDE 11579 7969 0.02 33
PROPEP 14220 12130 0.03 29
REGION 198127 93754 0.35 8
REPEAT 105511 14752 0.19 16
SIGNAL 41698 41697 0.07 24
SITE 57940 31788 0.10 21
STRAND 266064 22221 0.48 5
TOPO_DOM 140348 28757 0.25 12
TRANSIT 9098 8982 0.02 34
TRANSMEM 370742 77378 0.66 4
TURN 61535 19133 0.11 19
UNSURE 4455 797 0.01 35
VAR_SEQ 52010 22029 0.09 22
VARIANT 96908 17092 0.17 17
ZN_FING 30558 13417 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) 18992526 33.97
Allergome 1789 1169 <0.01 122 Protein family/group databases
ArachnoServer 1145 1136 <0.01 131 Organism-specific databases
Araport 15849 15753 0.03 84 Organism-specific databases
Bgee 56497 56497 0.10 45 Gene expression databases
BindingDB 5001 5001 0.01 105 Chemistry
BioCyc 237386 232881 0.42 24 Enzyme and pathway databases
BioGrid 51078 50576 0.09 50 Protein-protein interaction databases
BioMuta 20371 20359 0.04 71 Polymorphism and mutation databases
BRENDA 12912 12138 0.02 87 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 130 PTM databases
CAZy 9492 8557 0.02 90 Protein family/group databases
CCDS 48188 34164 0.09 52 Sequence databases
CDD 185221 169237 0.33 27 Family and domain databases
CGD 1997 1980 <0.01 119 Organism-specific databases
ChEMBL 6869 6869 0.01 97 Chemistry
ChiTaRS 20479 20468 0.04 70 Other
CleanEx 30009 29378 0.05 58 Gene expression databases
CollecTF 133 133 <0.01 153 Gene expression databases
ComplexPortal 8554 4502 0.02 91 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 154 2D gel databases
ConoServer 951 868 <0.01 132 Organism-specific databases
CORUM 5802 5802 0.01 101 Protein-protein interaction databases
CTD 75010 74108 0.13 43 Organism-specific databases
DEPOD 239 239 <0.01 150 PTM databases
dictyBase 4221 4106 0.01 109 Organism-specific databases
DIP 17361 17329 0.03 80 Protein-protein interaction databases
DisGeNET 14838 14604 0.03 85 Organism-specific databases
DisProt 708 703 <0.01 136 3D structure databases
DMDM 16275 16274 0.03 83 Polymorphism and mutation databases
DNASU 18999 18932 0.03 75 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 152 2D gel databases
DrugBank 18747 3637 0.03 76 Chemistry
EchoBASE 4159 4159 0.01 110 Organism-specific databases
EcoGene 4293 4293 0.01 108 Organism-specific databases
eggNOG 665065 331818 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 121 Protein-protein interaction databases
EMBL 984948 547340 1.76 3 Sequence databases
Ensembl 90926 50625 0.16 41 Genome annotation databases
EnsemblBacteria 355463 336333 0.64 17 Genome annotation databases
EnsemblFungi 29339 27837 0.05 60 Genome annotation databases
EnsemblMetazoa 17369 10159 0.03 79 Genome annotation databases
EnsemblPlants 27564 20586 0.05 63 Genome annotation databases
EnsemblProtists 5017 4831 0.01 104 Genome annotation databases
EPD 21825 21825 0.04 68 Proteomic databases
ESTHER 2518 2518 <0.01 117 Protein family/group databases
euHCVdb 55 44 <0.01 155 Organism-specific databases
EuPathDB 31173 30982 0.06 57 Organism-specific databases
EvolutionaryTrace 16628 16628 0.03 82 Other
ExpressionAtlas 51782 51782 0.09 48 Gene expression databases
FlyBase 6179 5883 0.01 99 Organism-specific databases
Gene3D 368040 293716 0.66 16 Family and domain databases
GeneCards 20367 20196 0.04 72 Organism-specific databases
GeneDB 575 519 <0.01 140 Genome annotation databases
GeneID 290097 280132 0.52 22 Genome annotation databases
GeneReviews 1479 1475 <0.01 123 Organism-specific databases
GeneTree 59122 59047 0.11 44 Phylogenomic databases
Genevisible 55240 55240 0.10 46 Gene expression databases
GeneWiki 10355 10272 0.02 89 Other
GenomeRNAi 22107 22107 0.04 66 Other
GlyConnect 1435 1367 <0.01 124 PTM databases
GO 2939518 532857 5.26 1 Ontologies
Gramene 27564 20586 0.05 62 Genome annotation databases
GuidetoPHARMACOLOGY 1957 1957 <0.01 120 Chemistry
H-InvDB 5626 4800 0.01 102 Organism-specific databases
HAMAP 329844 326968 0.59 19 Family and domain databases
HGNC 20352 20213 0.04 74 Organism-specific databases
HOGENOM 391804 391804 0.70 15 Phylogenomic databases
HOVERGEN 76128 76128 0.14 42 Phylogenomic databases
HPA 27390 16823 0.05 64 Organism-specific databases
IMGT_GENE-DB 253 253 <0.01 149 Protein family/group databases
InParanoid 139601 139601 0.25 30 Phylogenomic databases
IntAct 52814 52814 0.09 47 Protein-protein interaction databases
InterPro 2248370 540803 4.02 2 Family and domain databases
iPTMnet 51310 51310 0.09 49 PTM databases
jPOST 26838 26838 0.05 65 Proteomic databases
KEGG 502324 474870 0.90 7 Genome annotation databases
KO 405210 404765 0.72 14 Phylogenomic databases
LegioList 765 763 <0.01 135 Organism-specific databases
Leproma 672 669 <0.01 137 Organism-specific databases
MaizeGDB 510 506 <0.01 141 Organism-specific databases
MalaCards 4499 4496 0.01 107 Organism-specific databases
MaxQB 29713 29713 0.05 59 Proteomic databases
MEROPS 11401 11401 0.02 88 Protein family/group databases
MGI 16916 16876 0.03 81 Organism-specific databases
MIM 21094 15095 0.04 69 Organism-specific databases
MINT 21868 21868 0.04 67 Protein-protein interaction databases
MoonDB 348 348 <0.01 147 Protein family/group databases
MoonProt 279 279 <0.01 148 Protein family/group databases
mycoCLAP 355 352 <0.01 146 Protein family/group databases
neXtProt 20361 20361 0.04 73 Organism-specific databases
OGP 373 373 <0.01 145 2D gel databases
OMA 408786 408786 0.73 13 Phylogenomic databases
OpenTargets 18387 18228 0.03 77 Organism-specific databases
Orphanet 7456 3933 0.01 94 Organism-specific databases
OrthoDB 256521 256521 0.46 23 Phylogenomic databases
PANTHER 295544 281577 0.53 20 Family and domain databases
PATRIC 91909 91909 0.16 40 Genome annotation databases
PaxDb 124707 124707 0.22 33 Proteomic databases
PDB 170989 27117 0.31 28 3D structure databases
PDBsum 170989 27117 0.31 29 3D structure databases
PeptideAtlas 32145 32145 0.06 56 Proteomic databases
PeroxiBase 780 758 <0.01 134 Protein family/group databases
Pfam 760851 518484 1.36 4 Family and domain databases
PharmGKB 18357 18315 0.03 78 Organism-specific databases
PhosphoSitePlus 39019 39019 0.07 54 PTM databases
PhylomeDB 96355 96355 0.17 38 Phylogenomic databases
PIR 124207 113756 0.22 34 Sequence databases
PIRSF 108931 107902 0.19 37 Family and domain databases
PMAP-CutDB 1401 1401 <0.01 125 Other
PomBase 5133 5129 0.01 103 Organism-specific databases
PRIDE 230711 230711 0.41 25 Proteomic databases
PRINTS 132712 117169 0.24 32 Family and domain databases
PRO 95976 95976 0.17 39 Other
ProDom 29154 28971 0.05 61 Family and domain databases
ProMEX 457 457 <0.01 143 Proteomic databases
PROSITE 467832 299082 0.84 10 Family and domain databases
ProteinModelPortal 449218 449218 0.80 11 3D structure databases
Proteomes 480005 455928 0.86 9 Other
ProteomicsDB 36368 19824 0.07 55 Proteomic databases
PseudoCAP 1334 1325 <0.01 127 Organism-specific databases
Reactome 123274 36353 0.22 35 Enzyme and pathway databases
REBASE 409 409 <0.01 144 Protein family/group databases
RefSeq 608842 463703 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 128 2D gel databases
RGD 7978 7977 0.01 93 Organism-specific databases
SABIO-RK 4098 4098 0.01 111 Enzyme and pathway databases
SFLD 8065 5979 0.01 92 Family and domain databases
SGD 6740 6735 0.01 98 Organism-specific databases
SignaLink 3065 3065 0.01 116 Enzyme and pathway databases
SIGNOR 4083 4083 0.01 112 Enzyme and pathway databases
SMART 192454 141955 0.34 26 Family and domain databases
SMR 444726 444726 0.80 12 3D structure databases
STRING 332842 332842 0.60 18 Protein-protein interaction databases
SUPFAM 498424 377960 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 129 2D gel databases
SwissLipids 1361 1274 <0.01 126 Chemistry
SwissPalm 7372 7372 0.01 95 PTM databases
TAIR 14636 14580 0.03 86 Organism-specific databases
TCDB 6950 6899 0.01 96 Protein family/group databases
TIGRFAMs 292404 272415 0.52 21 Family and domain databases
TopDownProteomics 3241 2964 0.01 114 Proteomic databases
TreeFam 45501 45491 0.08 53 Phylogenomic databases
TubercuList 2191 2155 <0.01 118 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 142 2D gel databases
UCSC 49950 45629 0.09 51 Genome annotation databases
UniCarbKB 584 584 <0.01 139 PTM databases
UniGene 109919 96322 0.20 36 Sequence databases
UniLectin 238 238 <0.01 151 Protein family/group databases
UniPathway 136363 123572 0.24 31 Enzyme and pathway databases
VectorBase 597 517 <0.01 138 Genome annotation databases
VGNC 3919 3919 0.01 113 Organism-specific databases
WBParaSite 34 34 <0.01 156 Genome annotation databases
World-2DPAGE 930 919 <0.01 133 2D gel databases
WormBase 6027 4597 0.01 100 Organism-specific databases
Xenbase 4565 4556 0.01 106 Organism-specific databases
ZFIN 3070 3065 0.01 115 Organism-specific databases
Total number of cross-referenced databases: 156
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 3887 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: 79317