UniProtKB/Swiss-Prot protein knowledgebase release 2019_07 statistics
1. INTRODUCTION
Release 2019_07 of 31-Jul-19 of UniProtKB/Swiss-Prot contains 560537 sequence entries,
comprising 201466755 amino acids abstracted from 267799 references.
78 sequences have been added since release 2019_06, the sequence data of
18 existing entries has been updated and the annotations of
112753 entries have been revised.
Number of fragments: 9172
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 40097
Protein existence (PE): entries %
1: Evidence at protein level 101247 18.1%
2: Evidence at transcript level 57201 10.2%
3: Inferred from homology 386802 69%
4: Predicted 13464 2.4%
5: Uncertain 1823 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: 13790
The first twenty species represent 121001 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5687
2x: 1974
3x: 1072
4x: 700
5x: 518
6x: 410
7x: 303
8x: 253
9x: 229
10x: 142
11- 20x: 765
21- 50x: 462
51-100x: 224
>100x: 1051
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20431 Homo sapiens (Human)
2 17019 Mus musculus (Mouse)
3 15879 Arabidopsis thaliana (Mouse-ear cress)
4 8071 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 4519 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4147 Dictyostelium discoideum (Slime mold)
11 4068 Caenorhabditis elegans
12 4051 Oryza sativa subsp. japonica (Rice)
13 3573 Drosophila melanogaster (Fruit fly)
14 3445 Xenopus laevis (African clawed frog)
15 3113 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2291 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2181 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 1707 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 1332 Pseudomonas aeruginosa
30 1244 Mycobacterium bovis (strain ATCC BAA-935 / AF2122/97)
31 1174 Macaca fascicularis (Crab-eating macaque) (Cynomolgus monkey)
32 1066 Synechocystis sp. (strain PCC 6803 / Kazusa)
33 1035 Archaeoglobus fulgidus
34 1024 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
38 940 Staphylococcus aureus (strain Mu50 / ATCC 700699)
39 930 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
40 929 Staphylococcus aureus (strain N315)
41 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
42 919 Kluyveromyces lactis
43 909 Acanthamoeba polyphaga mimivirus (APMV)
44 902 Staphylococcus aureus (strain COL)
45 896 Staphylococcus aureus (strain MW2)
46 894 Oryctolagus cuniculus (Rabbit)
47 894 Escherichia coli O6:K15:H31 (strain 536 / UPEC)
48 889 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)
59 829 Shigella boydii serotype 4 (strain Sb227)
60 827 Canis lupus familiaris (Dog) (Canis familiaris)
61 826 Zea mays (Maize)
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)
67 793 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)
70 789 Staphylococcus aureus (strain NCTC 8325)
71 786 Aquifex aeolicus (strain VF5)
72 776 Pasteurella multocida (strain Pm70)
73 771 Escherichia coli O127:H6 (strain E2348/69 / EPEC)
74 771 Escherichia coli (strain K12 / DH10B)
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 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)
88 742 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 Yersinia pestis bv. Antiqua (strain Nepal516)
97 715 Enterobacter sp. (strain 638)
98 715 Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
99 714 Escherichia coli O1:K1 / APEC
100 714 Salmonella paratyphi A (strain AKU_12601)
101 713 Salmonella newport (strain SL254)
102 713 Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)
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 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)
117 675 Staphylococcus aureus (strain USA300)
118 674 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)
125 658 Sinorhizobium fredii (strain NBRC 101917 / NGR234)
126 653 Debaryomyces hansenii
127 650 Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
128 650 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)
131 640 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)
137 614 Staphylococcus haemolyticus (strain JCSC1435)
138 614 Xanthomonas campestris pv. campestris
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 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)
146 598 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)
150 586 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 Mycobacterium 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 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
173 540 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 Sodalis glossinidius (strain morsitans)
177 529 Corynebacterium glutamicum
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 Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)
190 510 Geobacillus kaustophilus (strain HTA426)
191 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
192 508 Streptomyces avermitilis
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 Rickettsia conorii (strain ATCC VR-613 / Malish 7)
200 497 Haemophilus influenzae (strain 86-028NP)
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)
207 491 Vibrio campbellii (strain ATCC BAA-1116 / BB120)
208 488 Methanosarcina mazei
209 488 Pyrococcus horikoshii
210 487 Shewanella sp. (strain MR-7)
211 486 Mannheimia succiniciproducens (strain MBEL55E)
212 486 Brucella abortus (strain 2308)
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)
218 481 Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
219 481 Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
220 480 Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
221 479 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)
224 476 Nicotiana tabacum (Common tobacco)
225 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
226 474 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
227 474 Burkholderia lata
228 472 Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
229 469 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
230 468 Clostridium perfringens (strain 13 / Type A)
231 468 Pseudomonas putida (strain GB-1)
232 467 Shewanella frigidimarina (strain NCIMB 400)
233 467 Campylobacter jejuni subsp. jejuni serotype O:2
234 466 Shewanella sp. (strain ANA-3)
235 466 Aeromonas hydrophila subsp. hydrophila
236 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
237 465 Anabaena variabilis (strain ATCC 29413 / PCC 7937)
238 465 Enterococcus faecalis (strain ATCC 700802 / V583)
239 463 Burkholderia mallei (strain ATCC 23344)
240 459 Cupriavidus necator (strain JMP 134 / LMG 1197) (Ralstonia eutropha
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 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
245 455 Staphylococcus aureus (strain JH1)
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 19561 ( 3%)
Bacteria 334117 ( 60%)
Eukaryota 189998 ( 34%)
Viruses 16861 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20432 ( 11%) ( 4%)
Other Mammalia 46753 ( 25%) ( 8%)
Other Vertebrata 18395 ( 10%) ( 3%)
Viridiplantae 40050 ( 21%) ( 7%)
Fungi 34106 ( 18%) ( 6%)
Insecta 9319 ( 5%) ( 2%)
Nematoda 4977 ( 3%) ( 1%)
Other 15966 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9668 1001-1100 4005
51- 100 42705 1101-1200 2808
101- 150 59182 1201-1300 2148
151- 200 58999 1301-1400 2013
201- 250 57860 1401-1500 1627
251- 300 51565 1501-1600 800
301- 350 51961 1601-1700 621
351- 400 45108 1701-1800 561
401- 450 37074 1801-1900 478
451- 500 29907 1901-2000 378
501- 550 21614 2001-2100 250
551- 600 15400 2101-2200 344
601- 650 12853 2201-2300 318
651- 700 9238 2301-2400 214
701- 750 7667 2401-2500 163
751- 800 5546 >2500 1314
801- 850 4786
851- 900 5210
901- 950 4052
951-1000 2928
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: 2814
4.1 Table of the frequency of journal citations
Journals cited 1x: 893
2x: 407
3x: 162
4x: 129
5x: 111
6x: 101
7x: 73
8x: 57
9x: 34
10x: 36
11- 20x: 222
21- 50x: 234
51-100x: 121
>100x: 234
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24866 Journal of Biological Chemistry
2 11565 Proceedings of the National Academy of Sciences of the U.S.A.
3 6652 Journal of Bacteriology
4 5677 Biochemical and Biophysical Research Communications
5 5387 Biochemistry
6 5020 Nucleic Acids Research
7 4853 FEBS Letters
8 4817 Gene
9 4711 The EMBO Journal
10 4600 Nature
11 4364 Molecular and Cellular Biology
12 4297 Journal of Molecular Biology
13 3678 Biochimica et Biophysica Acta
14 3600 Cell
15 3406 European Journal of Biochemistry
16 3278 Journal of Virology
17 3050 Science
18 2880 Biochemical Journal
19 2589 Plant Physiology
20 2553 Molecular Microbiology
21 2536 Genomics
22 2211 Journal of Cell Biology
23 2183 The American Journal of Human Genetics
24 2023 The Plant Cell
25 1976 PLoS ONE
26 1871 Plant Molecular Biology
27 1867 The Plant Journal
28 1842 Genes and Development
29 1837 Human Molecular Genetics
30 1813 Virology
31 1764 Nature Genetics
32 1681 Molecular Biology of the Cell
33 1679 Development
34 1578 Human Mutation
35 1560 Molecular Cell
36 1543 Oncogene
37 1496 Journal of Immunology
38 1395 Molecular and General Genetics
39 1361 Structure
40 1347 Journal of Biochemistry
41 1318 Genetics
42 1270 Journal of Cell Science
43 1167 Blood
44 1149 Journal of General Virology
45 1134 Infection and Immunity
46 1073 Microbiology
47 1060 Current Biology
48 1058 Archives of Biochemistry and Biophysics
49 1055 Developmental Biology
50 918 Journal of Neuroscience
51 908 Applied and Environmental Microbiology
52 895 Acta Crystallographica, Section D
53 887 Cancer Research
54 844 FEMS Microbiology Letters
55 838 Yeast
56 781 Protein Science
57 780 Toxicon
58 765 Neuron
59 745 Journal of Clinical Investigation
60 697 Human Genetics
61 694 American Journal of Physiology
62 692 Plant and Cell Physiology
63 661 PLoS Genetics
64 658 The Journal of Experimental Medicine
65 649 Mechanisms of Development
66 646 Nature Structural Biology
67 631 Proteins
68 620 Journal of Medical Genetics
69 581 Nature Cell Biology
70 574 Current Genetics
71 554 Bioscience, Biotechnology, and Biochemistry
72 546 Nature Structural and Molecular Biology
73 539 Journal of Neurochemistry
74 539 Molecular Endocrinology
75 524 The FEBS Journal
76 521 The Journal of Clinical Endocrinology and Metabolism
77 519 Developmental Cell
78 506 Endocrinology
79 491 Nature Communications
80 489 Mammalian Genome
81 477 Antimicrobial Agents and Chemotherapy
82 475 Immunogenetics
83 461 Experimental Cell Research
84 450 Molecular and Biochemical Parasitology
85 433 Planta
86 432 Eukaryotic Cell
87 419 RNA
88 417 Peptides
89 409 Scientific Reports
90 407 Journal of Molecular Evolution
91 398 Molecular Biology and Evolution
92 396 PLoS Pathogens
93 392 Journal of Experimental Botany
94 389 Journal of the American Chemical Society
95 388 DNA and Cell Biology
96 382 Molecular Pharmacology
97 375 DNA Sequence
98 370 Neurology
99 370 The FASEB Journal
100 369 EMBO Reports
101 366 Journal of Investigative Dermatology
102 361 American Journal of Medical Genetics. Part A
103 358 Acta Crystallographica, Section F
104 355 Molecular Plant-Microbe Interactions
105 352 Comparative Biochemistry and Physiology
106 349 Biology of Reproduction
107 345 European Journal of Human Genetics
108 342 Immunity
109 340 Brain Research. Molecular Brain Research
110 328 Tissue Antigens
111 326 Virus Research
112 325 Genes to Cells
113 321 The New England Journal of Medicine
114 321 Biochimie
115 314 Developmental Dynamics
116 306 Clinical Genetics
117 299 Genome Research
118 297 Biological Chemistry Hoppe-Seyler
119 296 Annals of Neurology
120 284 European Journal of Immunology
121 282 Cytogenetics and Cell Genetics
122 279 BMC Genomics
123 277 Nature Immunology
124 271 Investigative Ophthalmology and Visual Science
125 271 Journal of General Microbiology
126 263 Journal of Lipid Research
127 261 Applied Microbiology and Biotechnology
128 259 Journal of Medicinal Chemistry
129 259 Journal of Human Genetics
130 256 PLoS Biology
131 245 Archives of Microbiology
132 239 Glycobiology
133 233 Journal of Cellular Biochemistry
134 232 Traffic
135 232 Molecular Immunology
136 231 DNA Research
137 230 Cell Reports
138 225 Molecular Genetics and Metabolism
139 221 Cell Cycle
140 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
141 217 Circulation Research
142 214 Diabetes
143 213 Archives of Virology
144 210 Nature Medicine
145 208 Molecular and Cellular Endocrinology
146 207 Phytochemistry
147 205 Protein Expression and Purification
148 205 Fungal Genetics and Biology
149 196 Molecular Genetics and Genomics
150 190 Molecular and Cellular Neuroscience
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) 1230038 2.19
Journal 1053709 457730 1.88 1
Submitted to EMBL/GenBank/DDBJ 165433 149764 0.30 2
Submitted to other databases 7412 6845 0.01 3
Book citation 1810 1787 <0.01 4
Plant Gene Register 612 599 <0.01 5
Thesis 434 431 <0.01 6
Unpublished observations 413 409 <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: 415210
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2558216 4.56
ACTIVITY REGULATION 15179 15178 0.03 16
ALLERGEN 853 853 <0.01 26
ALTERNATIVE PRODUCTS 25311 25311 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8586 8586 0.02 20
BIOTECHNOLOGY 1031 1016 <0.01 25
CATALYTIC ACTIVITY 291054 239675 0.52 4
CAUTION 13154 12889 0.02 18
COFACTOR 126236 114888 0.23 7
DEVELOPMENTAL STAGE 12334 12333 0.02 19
DISEASE 7165 4815 0.01 21
DISRUPTION PHENOTYPE 14927 14924 0.03 17
DOMAIN 49857 42755 0.09 9
FUNCTION 468952 447904 0.84 2
INDUCTION 21531 21519 0.04 14
INTERACTION 19336 19336 0.03 15
MASS SPECTROMETRY 7032 5299 0.01 22
MISCELLANEOUS 38899 35771 0.07 12
PATHWAY 138964 125958 0.25 6
PHARMACEUTICAL 117 113 <0.01 29
POLYMORPHISM 1331 1274 <0.01 24
PTM 57715 42359 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44160 44160 0.08 11
SIMILARITY 509363 505197 0.91 1
SUBCELLULAR LOCATION 350585 343068 0.63 3
SUBUNIT 279810 278900 0.50 5
TISSUE SPECIFICITY 46518 46517 0.08 10
TOXIC DOSE 675 616 <0.01 27
WEB RESOURCE 6914 5748 0.01 23
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4548756 8.11
ACT_SITE 164539 99896 0.29 10
BINDING 408460 108213 0.73 2
CA_BIND 4206 1743 0.01 36
CARBOHYD 116699 30015 0.21 15
CHAIN 568548 553403 1.01 1
COILED 22072 15273 0.04 27
COMPBIAS 59133 31809 0.11 21
CONFLICT 135719 47491 0.24 13
CROSSLNK 23686 8506 0.04 26
DISULFID 126435 33986 0.23 14
DNA_BIND 11848 10600 0.02 32
DOMAIN 197791 121280 0.35 9
HELIX 264533 24248 0.47 6
INIT_MET 17198 17198 0.03 28
INTRAMEM 2791 1275 <0.01 37
LIPID 13109 8463 0.02 30
METAL 392106 95843 0.70 3
MOD_RES 249567 72112 0.45 7
MOTIF 43675 28474 0.08 23
MUTAGEN 73035 15878 0.13 18
NON_CONS 2258 789 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12437 9544 0.02 31
NP_BIND 158223 85956 0.28 11
PEPTIDE 11673 8042 0.02 33
PROPEP 14347 12239 0.03 29
REGION 201173 94658 0.36 8
REPEAT 105727 14799 0.19 16
SIGNAL 42240 42239 0.08 24
SITE 59689 32435 0.11 20
STRAND 274688 22854 0.49 5
TOPO_DOM 141118 28879 0.25 12
TRANSIT 9152 9036 0.02 34
TRANSMEM 372068 77663 0.66 4
TURN 63643 19691 0.11 19
UNSURE 4469 805 0.01 35
VAR_SEQ 52083 22083 0.09 22
VARIANT 97654 17143 0.17 17
ZN_FING 30607 13437 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) 18466894 32.95
ABCD 1376 1376 <0.01 122 Protocols and materials databases
Allergome 1899 1238 <0.01 117 Protein family/group databases
ArachnoServer 1163 1154 <0.01 126 Organism-specific databases
Araport 15900 15804 0.03 79 Organism-specific databases
Bgee 56649 56649 0.10 42 Gene expression databases
BindingDB 5157 5157 0.01 96 Chemistry
BioCyc 269996 244420 0.48 22 Enzyme and pathway databases
BioGrid 52425 51876 0.09 45 Protein-protein interaction databases
BioMuta 20387 20373 0.04 65 Polymorphism and mutation databases
BRENDA 12936 12162 0.02 82 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 127 PTM databases
CAZy 9505 8568 0.02 85 Protein family/group databases
CCDS 48312 34266 0.09 49 Sequence databases
CDD 186506 169460 0.33 26 Family and domain databases
CGD 1998 1981 <0.01 116 Organism-specific databases
ChEMBL 7280 7159 0.01 91 Chemistry
ChiTaRS 20491 20479 0.04 64 Other
CollecTF 133 133 <0.01 149 Gene expression databases
ComplexPortal 8972 4691 0.02 86 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 150 2D gel databases
ConoServer 952 869 <0.01 128 Organism-specific databases
CORUM 5805 5805 0.01 95 Protein-protein interaction databases
CPTAC 2221 1423 <0.01 113 Proteomic databases
CTD 75191 74292 0.13 40 Organism-specific databases
DEPOD 239 239 <0.01 146 PTM databases
dictyBase 4212 4098 0.01 104 Organism-specific databases
DIP 17394 17362 0.03 75 Protein-protein interaction databases
DisGeNET 15731 15500 0.03 80 Organism-specific databases
DisProt 700 700 <0.01 132 Family and domain databases
DMDM 16274 16272 0.03 78 Polymorphism and mutation databases
DNASU 19010 18944 0.03 70 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 148 2D gel databases
DrugBank 18747 3637 0.03 71 Chemistry
EchoBASE 4159 4159 0.01 106 Organism-specific databases
EcoGene 4293 4293 0.01 102 Organism-specific databases
eggNOG 665883 332214 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 118 Protein-protein interaction databases
EMBL 984958 548626 1.76 3 Sequence databases
Ensembl 91453 50528 0.16 39 Genome annotation databases
EnsemblBacteria 355757 336589 0.63 16 Genome annotation databases
EnsemblFungi 29516 27961 0.05 55 Genome annotation databases
EnsemblMetazoa 17460 10208 0.03 74 Genome annotation databases
EnsemblPlants 27943 20923 0.05 57 Genome annotation databases
EnsemblProtists 5089 4903 0.01 98 Genome annotation databases
EPD 22055 22055 0.04 62 Proteomic databases
ESTHER 2537 2536 <0.01 111 Protein family/group databases
euHCVdb 55 44 <0.01 152 Organism-specific databases
EuPathDB 19677 19665 0.04 69 Organism-specific databases
EvolutionaryTrace 16640 16640 0.03 77 Other
ExpressionAtlas 49453 49453 0.09 48 Gene expression databases
FlyBase 4878 4752 0.01 99 Organism-specific databases
Gene3D 391107 305419 0.70 15 Family and domain databases
GeneCards 20385 20214 0.04 66 Organism-specific databases
GeneDB 578 522 <0.01 135 Genome annotation databases
GeneID 291224 280589 0.52 20 Genome annotation databases
GeneReviews 1479 1475 <0.01 119 Organism-specific databases
GeneTree 59311 59271 0.11 41 Phylogenomic databases
Genevisible 55241 55241 0.10 43 Gene expression databases
GeneWiki 10355 10272 0.02 84 Other
GenomeRNAi 22131 22131 0.04 61 Other
GlyConnect 2250 2162 <0.01 112 PTM databases
GO 2970815 535119 5.30 1 Ontologies
Gramene 27943 20923 0.05 56 Genome annotation databases
GuidetoPHARMACOLOGY 1998 1998 <0.01 115 Chemistry
HAMAP 330023 327120 0.59 17 Family and domain databases
HGNC 20372 20233 0.04 67 Organism-specific databases
HOGENOM 392093 392093 0.70 14 Phylogenomic databases
HPA 27385 16820 0.05 58 Organism-specific databases
IMGT_GENE-DB 266 266 <0.01 145 Protein family/group databases
InParanoid 139779 139779 0.25 29 Phylogenomic databases
IntAct 53654 53654 0.10 44 Protein-protein interaction databases
InterPro 2289155 541896 4.08 2 Family and domain databases
iPTMnet 51311 51311 0.09 46 PTM databases
jPOST 26849 26849 0.05 59 Proteomic databases
KEGG 504477 475578 0.90 7 Genome annotation databases
KO 406894 406448 0.73 13 Phylogenomic databases
LegioList 765 763 <0.01 131 Organism-specific databases
Leproma 672 669 <0.01 133 Organism-specific databases
MaizeGDB 520 516 <0.01 137 Organism-specific databases
MalaCards 4499 4496 0.01 101 Organism-specific databases
MaxQB 29641 29641 0.05 54 Proteomic databases
MEROPS 11427 11426 0.02 83 Protein family/group databases
MGI 16929 16889 0.03 76 Organism-specific databases
MIM 21301 15179 0.04 63 Organism-specific databases
MINT 22632 22632 0.04 60 Protein-protein interaction databases
MoonDB 348 348 <0.01 143 Protein family/group databases
MoonProt 280 280 <0.01 144 Protein family/group databases
mycoCLAP 355 352 <0.01 142 Protein family/group databases
neXtProt 20352 20352 0.04 68 Organism-specific databases
NIAGADS 72 72 <0.01 151 Organism-specific databases
OGP 373 373 <0.01 141 2D gel databases
OMA 409717 409717 0.73 12 Phylogenomic databases
OpenTargets 18427 18269 0.03 72 Organism-specific databases
Orphanet 7539 3992 0.01 90 Organism-specific databases
OrthoDB 256957 256957 0.46 23 Phylogenomic databases
PANTHER 281050 269475 0.50 21 Family and domain databases
PATRIC 92063 92063 0.16 38 Genome annotation databases
PaxDb 124827 124827 0.22 32 Proteomic databases
PDB 180810 27867 0.32 27 3D structure databases
PDBsum 180810 27867 0.32 28 3D structure databases
PeptideAtlas 32534 32534 0.06 53 Proteomic databases
PeroxiBase 781 759 <0.01 130 Protein family/group databases
Pfam 780239 521770 1.39 4 Family and domain databases
PharmGKB 18355 18312 0.03 73 Organism-specific databases
PhosphoSitePlus 39022 39022 0.07 52 PTM databases
PhylomeDB 96419 96419 0.17 36 Phylogenomic databases
PIR 124308 113845 0.22 33 Sequence databases
PIRSF 108960 107931 0.19 35 Family and domain databases
PMAP-CutDB 1401 1401 <0.01 120 Other
PomBase 5132 5128 0.01 97 Organism-specific databases
PRIDE 234480 234480 0.42 24 Proteomic databases
PRINTS 131712 117042 0.23 31 Family and domain databases
PRO 95975 95975 0.17 37 Other
ProMEX 462 462 <0.01 139 Proteomic databases
PROSITE 471615 300044 0.84 10 Family and domain databases
Proteomes 484086 459714 0.86 9 Other
ProteomicsDB 40948 19909 0.07 51 Proteomic databases
PseudoCAP 1340 1331 <0.01 123 Organism-specific databases
Reactome 118721 36302 0.21 34 Enzyme and pathway databases
REBASE 406 406 <0.01 140 Protein family/group databases
RefSeq 612046 466455 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 124 2D gel databases
RGD 7994 7993 0.01 89 Organism-specific databases
SABIO-RK 4263 4263 0.01 103 Enzyme and pathway databases
SFLD 8096 6008 0.01 88 Family and domain databases
SGD 6740 6735 0.01 93 Organism-specific databases
SignaLink 3069 3069 0.01 110 Enzyme and pathway databases
SIGNOR 4199 4199 0.01 105 Enzyme and pathway databases
SMART 192903 142273 0.34 25 Family and domain databases
SMR 445437 445437 0.79 11 3D structure databases
STRING 328460 328460 0.59 18 Protein-protein interaction databases
SUPFAM 499387 378684 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 125 2D gel databases
SwissLipids 1386 1299 <0.01 121 Chemistry
SwissPalm 8602 8602 0.02 87 PTM databases
TAIR 14686 14630 0.03 81 Organism-specific databases
TCDB 7118 7069 0.01 92 Protein family/group databases
TIGRFAMs 292546 272546 0.52 19 Family and domain databases
TopDownProteomics 3240 2963 0.01 108 Proteomic databases
TreeFam 45577 45567 0.08 50 Phylogenomic databases
TubercuList 2199 2163 <0.01 114 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 138 2D gel databases
UCSC 50050 45713 0.09 47 Genome annotation databases
UniCarbKB 584 584 <0.01 134 PTM databases
UniLectin 239 239 <0.01 147 Protein family/group databases
UniPathway 136861 123926 0.24 30 Enzyme and pathway databases
VectorBase 573 497 <0.01 136 Genome annotation databases
VGNC 3951 3951 0.01 107 Organism-specific databases
WBParaSite 32 32 <0.01 153 Genome annotation databases
World-2DPAGE 931 920 <0.01 129 2D gel databases
WormBase 6123 4667 0.01 94 Organism-specific databases
Xenbase 4664 4609 0.01 100 Organism-specific databases
ZFIN 3092 3087 0.01 109 Organism-specific databases
Total number of cross-referenced databases: 153
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 3914 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: 79494