UniProtKB/Swiss-Prot protein knowledgebase release 2018_10 statistics
1. INTRODUCTION
Release 2018_10 of 07-Nov-18 of UniProtKB/Swiss-Prot contains 558681 sequence entries,
comprising 200603466 amino acids abstracted from 262816 references.
101 sequences have been added since release 2018_09, the sequence data of
15 existing entries has been updated and the annotations of
259269 entries have been revised.
Number of fragments: 9158
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 39980
Protein existence (PE): entries %
1: Evidence at protein level 99594 17.8%
2: Evidence at transcript level 57178 10.2%
3: Inferred from homology 386617 69.2%
4: Predicted 13456 2.4%
5: Uncertain 1836 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: 13682
The first twenty species represent 120677 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5662
2x: 1954
3x: 1067
4x: 694
5x: 511
6x: 408
7x: 297
8x: 249
9x: 229
10x: 139
11- 20x: 747
21- 50x: 457
51-100x: 218
>100x: 1050
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20408 Homo sapiens (Human)
2 17000 Mus musculus (Mouse)
3 15818 Arabidopsis thaliana (Mouse-ear cress)
4 8053 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6003 Bos taurus (Bovine)
7 5141 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4477 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4139 Dictyostelium discoideum (Slime mold)
11 4036 Caenorhabditis elegans
12 4008 Oryza sativa subsp. japonica (Rice)
13 3541 Drosophila melanogaster (Fruit fly)
14 3444 Xenopus laevis (African clawed frog)
15 3083 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 1427 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 Staphylococcus aureus (strain Mu50 / ATCC 700699)
38 930 Salmonella paratyphi A (strain ATCC 9150 / SARB42)
39 927 Ashbya gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)
40 926 Staphylococcus aureus (strain N315)
41 914 Kluyveromyces lactis
42 914 Emericella nidulans
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)
50 882 Salmonella choleraesuis (strain SC-B67)
51 882 Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
52 879 Shigella sonnei (strain Ss046)
53 878 Candida glabrata
54 863 Yersinia pseudotuberculosis serotype I (strain IP32953)
55 855 Neurospora crassa
56 841 Escherichia coli O9:H4 (strain HS)
57 834 Escherichia coli O139:H28 (strain E24377A / ETEC)
58 829 Shigella boydii serotype 4 (strain Sb227)
59 825 Oryza sativa subsp. indica (Rice)
60 825 Escherichia coli (strain UTI89 / UPEC)
61 822 Shigella dysenteriae serotype 1 (strain Sd197)
62 821 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
63 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
64 819 Canis lupus familiaris (Dog) (Canis familiaris)
65 808 Zea mays (Maize)
66 796 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 Staphylococcus epidermidis (strain ATCC 35984 / RP62A)
80 760 Shigella flexneri serotype 5b (strain 8401)
81 759 Staphylococcus epidermidis (strain ATCC 12228)
82 756 Escherichia coli O45:K1 (strain S88 / ExPEC)
83 756 Escherichia coli (strain SE11)
84 753 Escherichia coli O7:K1 (strain IAI39 / ExPEC)
85 751 Bacillus anthracis
86 748 Escherichia coli O157:H7 (strain EC4115 / EHEC)
87 746 Photorhabdus 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 Vibrio vulnificus (strain YJ016)
94 718 Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
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 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)
117 673 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 Treponema pallidum (strain Nichols)
134 622 Cronobacter sakazakii (strain ATCC BAA-894) (Enterobacter sakazakii)
135 620 Methanothermobacter thermautotrophicus
136 614 Staphylococcus haemolyticus (strain JCSC1435)
137 611 Mesorhizobium japonicum (Mesorhizobium loti
138 610 Xanthomonas campestris pv. campestris
139 608 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
140 603 Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)
141 603 Ralstonia solanacearum (strain GMI1000) (Pseudomonas solanacearum)
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)
146 594 Bacillus cereus (strain ATCC 10987 / NRS 248)
147 594 Pseudomonas aeruginosa (strain UCBPP-PA14)
148 594 Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
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 Deinococcus radiodurans
186 513 Staphylococcus aureus (strain Newman)
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 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)
213 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
214 484 Shewanella sp. (strain MR-4)
215 484 Pseudomonas aeruginosa (strain LESB58)
216 483 Mycoplasma genitalium (strain ATCC 33530 / G-37 / NCTC 10195)
217 483 Brucella abortus (strain 2308)
218 480 Synechococcus elongatus (strain PCC 7942) (Anacystis nidulans R2)
219 479 Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
220 478 Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
221 478 Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
222 477 Pyrococcus abyssi (strain GE5 / Orsay)
223 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
224 475 Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
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 Campylobacter jejuni subsp. jejuni serotype O:2
230 467 Shewanella frigidimarina (strain NCIMB 400)
231 466 Shewanella sp. (strain ANA-3)
232 466 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
233 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
234 466 Pseudomonas putida (strain GB-1)
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 Methylococcus capsulatus (strain ATCC 33009 / NCIMB 11132 / Bath)
241 457 Solanum lycopersicum (Tomato) (Lycopersicon esculentum)
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 Pseudomonas putida (strain W619)
247 452 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
248 452 Shewanella baltica (strain OS185)
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 19544 ( 3%)
Bacteria 333711 ( 60%)
Eukaryota 188590 ( 34%)
Viruses 16836 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20409 ( 11%) ( 4%)
Other Mammalia 46685 ( 25%) ( 8%)
Other Vertebrata 18342 ( 10%) ( 3%)
Viridiplantae 39701 ( 21%) ( 7%)
Fungi 33721 ( 18%) ( 6%)
Insecta 9213 ( 5%) ( 2%)
Nematoda 4938 ( 3%) ( 1%)
Other 15581 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9576 1001-1100 3985
51- 100 42547 1101-1200 2799
101- 150 59000 1201-1300 2143
151- 200 58872 1301-1400 2001
201- 250 57719 1401-1500 1621
251- 300 51441 1501-1600 792
301- 350 51811 1601-1700 616
351- 400 44961 1701-1800 552
401- 450 36946 1801-1900 470
451- 500 29785 1901-2000 375
501- 550 21495 2001-2100 248
551- 600 15338 2101-2200 325
601- 650 12801 2201-2300 313
651- 700 9217 2301-2400 212
701- 750 7649 2401-2500 160
751- 800 5526 >2500 1281
801- 850 4770
851- 900 5206
901- 950 4049
951-1000 2921
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: 2753
4.1 Table of the frequency of journal citations
Journals cited 1x: 866
2x: 391
3x: 163
4x: 136
5x: 110
6x: 100
7x: 66
8x: 56
9x: 37
10x: 33
11- 20x: 219
21- 50x: 227
51-100x: 118
>100x: 231
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24439 Journal of Biological Chemistry
2 11326 Proceedings of the National Academy of Sciences of the U.S.A.
3 6606 Journal of Bacteriology
4 5619 Biochemical and Biophysical Research Communications
5 5312 Biochemistry
6 4984 Nucleic Acids Research
7 4816 FEBS Letters
8 4805 Gene
9 4679 The EMBO Journal
10 4501 Nature
11 4333 Molecular and Cellular Biology
12 4248 Journal of Molecular Biology
13 3616 Biochimica et Biophysica Acta
14 3549 Cell
15 3391 European Journal of Biochemistry
16 3218 Journal of Virology
17 2996 Science
18 2842 Biochemical Journal
19 2546 Plant Physiology
20 2534 Genomics
21 2516 Molecular Microbiology
22 2188 Journal of Cell Biology
23 2133 The American Journal of Human Genetics
24 1981 The Plant Cell
25 1876 PLoS ONE
26 1852 Plant Molecular Biology
27 1833 Genes and Development
28 1823 The Plant Journal
29 1795 Human Molecular Genetics
30 1780 Virology
31 1744 Nature Genetics
32 1664 Development
33 1656 Molecular Biology of the Cell
34 1567 Human Mutation
35 1540 Oncogene
36 1528 Molecular Cell
37 1417 Journal of Immunology
38 1394 Molecular and General Genetics
39 1334 Journal of Biochemistry
40 1329 Structure
41 1310 Genetics
42 1242 Journal of Cell Science
43 1146 Blood
44 1135 Journal of General Virology
45 1106 Infection and Immunity
46 1051 Microbiology
47 1044 Developmental Biology
48 1043 Current Biology
49 1042 Archives of Biochemistry and Biophysics
50 900 Applied and Environmental Microbiology
51 885 Journal of Neuroscience
52 882 Cancer Research
53 873 Acta Crystallographica, Section D
54 838 Yeast
55 836 FEMS Microbiology Letters
56 769 Protein Science
57 767 Toxicon
58 739 Neuron
59 720 Journal of Clinical Investigation
60 688 Human Genetics
61 672 American Journal of Physiology
62 670 Plant and Cell Physiology
63 648 Mechanisms of Development
64 645 Nature Structural Biology
65 629 PLoS Genetics
66 627 The Journal of Experimental Medicine
67 615 Proteins
68 599 Journal of Medical Genetics
69 574 Current Genetics
70 568 Nature Cell Biology
71 550 Bioscience, Biotechnology, and Biochemistry
72 532 Molecular Endocrinology
73 530 Journal of Neurochemistry
74 529 Nature Structural and Molecular Biology
75 517 The Journal of Clinical Endocrinology and Metabolism
76 507 Developmental Cell
77 502 Endocrinology
78 501 The FEBS Journal
79 488 Mammalian Genome
80 472 Immunogenetics
81 464 Antimicrobial Agents and Chemotherapy
82 457 Experimental Cell Research
83 448 Molecular and Biochemical Parasitology
84 431 Eukaryotic Cell
85 423 Planta
86 416 RNA
87 410 Peptides
88 407 Journal of Molecular Evolution
89 397 Molecular Biology and Evolution
90 392 Nature Communications
91 386 DNA and Cell Biology
92 381 Journal of Experimental Botany
93 374 DNA Sequence
94 374 Journal of the American Chemical Society
95 373 Molecular Pharmacology
96 359 EMBO Reports
97 358 Neurology
98 358 Journal of Investigative Dermatology
99 357 PLoS Pathogens
100 351 The FASEB Journal
101 349 Comparative Biochemistry and Physiology
102 347 Biology of Reproduction
103 345 Acta Crystallographica, Section F
104 339 Brain Research. Molecular Brain Research
105 339 Molecular Plant-Microbe Interactions
106 336 American Journal of Medical Genetics. Part A
107 333 European Journal of Human Genetics
108 327 Scientific Reports
109 326 Tissue Antigens
110 323 Immunity
111 317 Biochimie
112 317 Virus Research
113 316 Genes to Cells
114 315 The New England Journal of Medicine
115 312 Developmental Dynamics
116 296 Biological Chemistry Hoppe-Seyler
117 296 Genome Research
118 293 Clinical Genetics
119 286 Annals of Neurology
120 282 Cytogenetics and Cell Genetics
121 271 Journal of General Microbiology
122 270 European Journal of Immunology
123 269 BMC Genomics
124 266 Investigative Ophthalmology and Visual Science
125 266 Nature Immunology
126 260 Applied Microbiology and Biotechnology
127 253 Journal of Human Genetics
128 249 Journal of Medicinal Chemistry
129 244 PLoS Biology
130 240 Archives of Microbiology
131 233 Glycobiology
132 231 DNA Research
133 229 Journal of Cellular Biochemistry
134 224 Traffic
135 220 Cell Cycle
136 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
137 218 Molecular Genetics and Metabolism
138 216 Journal of Lipid Research
139 215 Circulation Research
140 213 Molecular Immunology
141 209 Archives of Virology
142 208 Diabetes
143 207 Molecular and Cellular Endocrinology
144 204 Protein Expression and Purification
145 203 Phytochemistry
146 199 Fungal Genetics and Biology
147 198 Nature Medicine
148 196 Molecular Genetics and Genomics
149 194 Cell Reports
150 183 Insect Biochemistry and Molecular 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) 1217150 2.18
Journal 1039800 454453 1.86 1
Submitted to EMBL/GenBank/DDBJ 166562 150930 0.30 2
Submitted to other databases 7364 6799 0.01 3
Book citation 1757 1734 <0.01 4
Plant Gene Register 611 598 <0.01 5
Thesis 433 430 <0.01 6
Unpublished observations 408 404 <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: 406039
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2513974 4.50
ACTIVITY REGULATION 14722 14722 0.03 16
ALLERGEN 722 722 <0.01 26
ALTERNATIVE PRODUCTS 25239 25239 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8165 8165 0.01 20
BIOTECHNOLOGY 945 931 <0.01 25
CATALYTIC ACTIVITY 268440 236499 0.48 5
CAUTION 12791 12554 0.02 18
COFACTOR 123055 112672 0.22 7
DEVELOPMENTAL STAGE 12082 12081 0.02 19
DISEASE 6976 4682 0.01 21
DISRUPTION PHENOTYPE 14125 14124 0.03 17
DOMAIN 48593 41855 0.09 9
FUNCTION 465198 444787 0.83 2
INDUCTION 20819 20807 0.04 14
INTERACTION 19120 19120 0.03 15
MASS SPECTROMETRY 6918 5213 0.01 22
MISCELLANEOUS 38515 35456 0.07 12
PATHWAY 137976 125168 0.25 6
PHARMACEUTICAL 115 111 <0.01 29
POLYMORPHISM 1309 1253 <0.01 24
PTM 56181 41634 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44009 44009 0.08 11
SIMILARITY 507626 503478 0.91 1
SUBCELLULAR LOCATION 348563 341274 0.62 3
SUBUNIT 278053 277261 0.50 4
TISSUE SPECIFICITY 45672 45671 0.08 10
TOXIC DOSE 666 609 <0.01 27
WEB RESOURCE 6752 5591 0.01 23
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4479559 8.02
ACT_SITE 163560 99292 0.29 10
BINDING 404320 106475 0.72 2
CA_BIND 4176 1729 0.01 36
CARBOHYD 115703 29756 0.21 15
CHAIN 566504 551610 1.01 1
COILED 22012 15221 0.04 27
COMPBIAS 58979 31736 0.11 20
CONFLICT 135109 47314 0.24 13
CROSSLNK 23591 8458 0.04 26
DISULFID 124686 33650 0.22 14
DNA_BIND 11632 10524 0.02 32
DOMAIN 194239 119725 0.35 9
HELIX 253182 23419 0.45 6
INIT_MET 17154 17154 0.03 28
INTRAMEM 2656 1199 <0.01 37
LIPID 13019 8404 0.02 30
METAL 380572 94104 0.68 3
MOD_RES 248510 71803 0.44 7
MOTIF 42934 28040 0.08 23
MUTAGEN 69387 15242 0.12 18
NON_CONS 2257 787 <0.01 38
NON_STD 357 282 <0.01 39
NON_TER 12391 9506 0.02 31
NP_BIND 156735 85175 0.28 11
PEPTIDE 11567 7966 0.02 33
PROPEP 14211 12118 0.03 29
REGION 197546 93578 0.35 8
REPEAT 105422 14737 0.19 16
SIGNAL 41628 41626 0.07 24
SITE 57210 31722 0.10 21
STRAND 263773 22046 0.47 5
TOPO_DOM 140313 28758 0.25 12
TRANSIT 9088 8972 0.02 34
TRANSMEM 370471 77297 0.66 4
TURN 60979 18981 0.11 19
UNSURE 4454 796 0.01 35
VAR_SEQ 51963 22005 0.09 22
VARIANT 96747 17075 0.17 17
ZN_FING 30522 13402 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) 18904424 33.84
Allergome 1758 1148 <0.01 121 Protein family/group databases
ArachnoServer 1145 1136 <0.01 130 Organism-specific databases
Araport 15839 15743 0.03 83 Organism-specific databases
Bgee 56453 56453 0.10 45 Gene expression databases
BindingDB 5000 5000 0.01 104 Chemistry
BioCyc 158125 154060 0.28 29 Enzyme and pathway databases
BioGrid 50997 50497 0.09 50 Protein-protein interaction databases
BioMuta 17236 17227 0.03 79 Polymorphism and mutation databases
BRENDA 12910 12136 0.02 87 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 128 PTM databases
CAZy 9483 8548 0.02 90 Protein family/group databases
CCDS 48139 34128 0.09 52 Sequence databases
CDD 184998 169025 0.33 26 Family and domain databases
CGD 1997 1980 <0.01 118 Organism-specific databases
ChEMBL 6868 6868 0.01 96 Chemistry
ChiTaRS 20475 20464 0.04 69 Other
CleanEx 30013 29382 0.05 59 Gene expression databases
CollecTF 133 133 <0.01 152 Gene expression databases
ComplexPortal 8537 4488 0.02 91 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 153 2D gel databases
ConoServer 951 868 <0.01 131 Organism-specific databases
CORUM 5168 5168 0.01 101 Protein-protein interaction databases
CTD 74929 74051 0.13 43 Organism-specific databases
DEPOD 239 239 <0.01 148 PTM databases
dictyBase 4215 4100 0.01 108 Organism-specific databases
DIP 17350 17318 0.03 77 Protein-protein interaction databases
DisGeNET 14840 14606 0.03 85 Organism-specific databases
DisProt 708 703 <0.01 135 3D structure databases
DMDM 16277 16277 0.03 82 Polymorphism and mutation databases
DNASU 18994 18927 0.03 73 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 150 2D gel databases
DrugBank 18747 3637 0.03 74 Chemistry
EchoBASE 4159 4159 0.01 109 Organism-specific databases
EcoGene 4293 4293 0.01 107 Organism-specific databases
eggNOG 664769 331670 1.19 5 Phylogenomic databases
ELM 1811 1811 <0.01 120 Protein-protein interaction databases
EMBL 984094 546966 1.76 3 Sequence databases
Ensembl 90229 50323 0.16 41 Genome annotation databases
EnsemblBacteria 354635 335506 0.63 17 Genome annotation databases
EnsemblFungi 30822 28977 0.06 58 Genome annotation databases
EnsemblMetazoa 17336 10146 0.03 78 Genome annotation databases
EnsemblPlants 27447 20482 0.05 63 Genome annotation databases
EnsemblProtists 5016 4830 0.01 103 Genome annotation databases
EPD 21826 21826 0.04 66 Proteomic databases
ESTHER 2503 2503 <0.01 116 Protein family/group databases
euHCVdb 55 44 <0.01 154 Organism-specific databases
EuPathDB 31153 30961 0.06 57 Organism-specific databases
EvolutionaryTrace 16625 16625 0.03 81 Other
ExpressionAtlas 51735 51735 0.09 48 Gene expression databases
FlyBase 6169 5873 0.01 98 Organism-specific databases
Gene3D 366738 292693 0.66 16 Family and domain databases
GeneCards 20360 20189 0.04 71 Organism-specific databases
GeneDB 575 519 <0.01 139 Genome annotation databases
GeneID 290242 279963 0.52 23 Genome annotation databases
GeneReviews 1154 1151 <0.01 129 Organism-specific databases
GeneTree 59463 59441 0.11 44 Phylogenomic databases
Genevisible 55238 55238 0.10 46 Gene expression databases
GeneWiki 10356 10273 0.02 89 Other
GenomeRNAi 22044 22044 0.04 65 Other
GlyConnect 1439 1353 <0.01 122 PTM databases
GO 2931260 532502 5.25 1 Ontologies
Gramene 27447 20482 0.05 62 Genome annotation databases
GuidetoPHARMACOLOGY 1957 1957 <0.01 119 Chemistry
H-InvDB 5628 4802 0.01 100 Organism-specific databases
HAMAP 329828 326952 0.59 19 Family and domain databases
HGNC 20347 20207 0.04 72 Organism-specific databases
HOGENOM 391700 391700 0.70 15 Phylogenomic databases
HOVERGEN 76120 76120 0.14 42 Phylogenomic databases
HPA 27402 16829 0.05 64 Organism-specific databases
IMGT_GENE-DB 142 142 <0.01 151 Protein family/group databases
InParanoid 139563 139563 0.25 30 Phylogenomic databases
IntAct 52728 52728 0.09 47 Protein-protein interaction databases
InterPro 2246772 540217 4.02 2 Family and domain databases
iPTMnet 51306 51306 0.09 49 PTM databases
KEGG 502782 475415 0.90 7 Genome annotation databases
KO 405196 404752 0.73 14 Phylogenomic databases
LegioList 765 763 <0.01 134 Organism-specific databases
Leproma 672 669 <0.01 136 Organism-specific databases
MaizeGDB 509 505 <0.01 140 Organism-specific databases
MalaCards 4499 4496 0.01 106 Organism-specific databases
MaxQB 29709 29709 0.05 60 Proteomic databases
MEROPS 11396 11396 0.02 88 Protein family/group databases
MGI 16906 16866 0.03 80 Organism-specific databases
MIM 21020 15072 0.04 68 Organism-specific databases
MINT 21793 21793 0.04 67 Protein-protein interaction databases
MoonDB 348 348 <0.01 146 Protein family/group databases
MoonProt 279 279 <0.01 147 Protein family/group databases
mycoCLAP 355 352 <0.01 145 Protein family/group databases
neXtProt 20371 20371 0.04 70 Organism-specific databases
OGP 373 373 <0.01 144 2D gel databases
OMA 408602 408602 0.73 13 Phylogenomic databases
OpenTargets 18379 18218 0.03 75 Organism-specific databases
Orphanet 7425 3912 0.01 93 Organism-specific databases
OrthoDB 293558 293558 0.53 20 Phylogenomic databases
PANTHER 293205 279576 0.52 21 Family and domain databases
PATRIC 91862 91862 0.16 40 Genome annotation databases
PaxDb 124674 124674 0.22 33 Proteomic databases
PDB 168573 26924 0.30 28 3D structure databases
PDBsum 168573 26924 0.30 27 3D structure databases
PeptideAtlas 32139 32139 0.06 56 Proteomic databases
PeroxiBase 780 758 <0.01 133 Protein family/group databases
Pfam 761600 518559 1.36 4 Family and domain databases
PharmGKB 18359 18317 0.03 76 Organism-specific databases
PhosphoSitePlus 39021 39021 0.07 54 PTM databases
PhylomeDB 96330 96330 0.17 38 Phylogenomic databases
PIR 124187 113737 0.22 34 Sequence databases
PIRSF 108915 107886 0.19 37 Family and domain databases
PMAP-CutDB 1401 1401 <0.01 123 Other
PomBase 5133 5129 0.01 102 Organism-specific databases
PRIDE 230699 230699 0.41 24 Proteomic databases
PRINTS 132710 117158 0.24 32 Family and domain databases
PRO 95984 95984 0.17 39 Other
ProDom 29163 28980 0.05 61 Family and domain databases
ProMEX 457 457 <0.01 142 Proteomic databases
PROSITE 467429 298895 0.84 10 Family and domain databases
ProteinModelPortal 449116 449116 0.80 11 3D structure databases
Proteomes 479445 455315 0.86 9 Other
ProteomicsDB 36382 19831 0.07 55 Proteomic databases
PseudoCAP 1334 1325 <0.01 125 Organism-specific databases
Reactome 123647 36729 0.22 35 Enzyme and pathway databases
REBASE 395 395 <0.01 143 Protein family/group databases
RefSeq 608447 463427 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 126 2D gel databases
RGD 7977 7976 0.01 92 Organism-specific databases
SABIO-RK 3963 3963 0.01 111 Enzyme and pathway databases
SFLD 15543 7107 0.03 84 Family and domain databases
SGD 6739 6734 0.01 97 Organism-specific databases
SignaLink 3066 3066 0.01 114 Enzyme and pathway databases
SIGNOR 4081 4081 0.01 110 Enzyme and pathway databases
SMART 192268 141835 0.34 25 Family and domain databases
SMR 444421 444421 0.80 12 3D structure databases
STRING 332705 332705 0.60 18 Protein-protein interaction databases
SUPFAM 498029 377697 0.89 8 Family and domain databases
SWISS-2DPAGE 1177 1177 <0.01 127 2D gel databases
SwissLipids 1360 1273 <0.01 124 Chemistry
SwissPalm 7298 7298 0.01 94 PTM databases
TAIR 14626 14570 0.03 86 Organism-specific databases
TCDB 6877 6831 0.01 95 Protein family/group databases
TIGRFAMs 292361 272375 0.52 22 Family and domain databases
TopDownProteomics 3241 2964 0.01 113 Proteomic databases
TreeFam 45483 45473 0.08 53 Phylogenomic databases
TubercuList 2191 2155 <0.01 117 Organism-specific databases
UCD-2DPAGE 496 496 <0.01 141 2D gel databases
UCSC 49914 45604 0.09 51 Genome annotation databases
UniCarbKB 584 584 <0.01 138 PTM databases
UniGene 109788 96226 0.20 36 Sequence databases
UniLectin 238 238 <0.01 149 Protein family/group databases
UniPathway 136333 123547 0.24 31 Enzyme and pathway databases
VectorBase 597 517 <0.01 137 Genome annotation databases
VGNC 3893 3893 0.01 112 Organism-specific databases
WBParaSite 34 34 <0.01 155 Genome annotation databases
World-2DPAGE 930 919 <0.01 132 2D gel databases
WormBase 6025 4595 0.01 99 Organism-specific databases
Xenbase 4558 4552 0.01 105 Organism-specific databases
ZFIN 3063 3058 0.01 115 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) 2.91
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 3883 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: 79233