UniProtKB/Swiss-Prot protein knowledgebase release 2018_06 statistics
1. INTRODUCTION
Release 2018_06 of 20-Jun-18 of UniProtKB/Swiss-Prot contains 557713 sequence entries,
comprising 200130199 amino acids abstracted from 260117 references.
225 sequences have been added since release 2018_05, the sequence data of
25 existing entries has been updated and the annotations of
103253 entries have been revised.
Number of fragments: 9151
Number of additional sequences produced by alternative splicing, initiation or promoter usage, or ribosomal frameshifting: 39896
Protein existence (PE): entries %
1: Evidence at protein level 98669 17.7%
2: Evidence at transcript level 57241 10.3%
3: Inferred from homology 386324 69.3%
4: Predicted 13613 2.4%
5: Uncertain 1866 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: 13634
The first twenty species represent 120347 sequences: 21.6 % of the total
number of entries.
2.1 Table of the frequency of occurrence of species
Species represented 1x: 5652
2x: 1943
3x: 1058
4x: 690
5x: 509
6x: 408
7x: 296
8x: 247
9x: 229
10x: 134
11- 20x: 750
21- 50x: 451
51-100x: 218
>100x: 1049
2.2 Table of the most represented species
------ --------- --------------------------------------------
Number Frequency Species
------ --------- --------------------------------------------
1 20360 Homo sapiens (Human)
2 16976 Mus musculus (Mouse)
3 15759 Arabidopsis thaliana (Mouse-ear cress)
4 8027 Rattus norvegicus (Rat)
5 6721 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6 6002 Bos taurus (Bovine)
7 5141 Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
8 4443 Escherichia coli (strain K12)
9 4188 Bacillus subtilis (strain 168)
10 4136 Dictyostelium discoideum (Slime mold)
11 4022 Caenorhabditis elegans
12 3956 Oryza sativa subsp. japonica (Rice)
13 3518 Drosophila melanogaster (Fruit fly)
14 3428 Xenopus laevis (African clawed frog)
15 3057 Danio rerio (Zebrafish) (Brachydanio rerio)
16 2290 Gallus gallus (Chicken)
17 2218 Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
18 2171 Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
19 2036 Escherichia coli O157:H7
20 1898 Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
21 1795 Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
22 1787 Methanocaldococcus jannaschii
23 1707 Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
24 1705 Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
25 1694 Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC)
26 1683 Shigella flexneri
27 1423 Sus scrofa (Pig)
28 1347 Salmonella typhi
29 1324 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 1031 Archaeoglobus fulgidus
34 1022 Yersinia pestis
35 1006 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 Emericella nidulans
42 914 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)
50 882 Salmonella choleraesuis (strain SC-B67)
51 881 Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
52 879 Shigella sonnei (strain Ss046)
53 871 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 Escherichia coli (strain UTI89 / UPEC)
60 822 Shigella dysenteriae serotype 1 (strain Sd197)
61 819 Canis lupus familiaris (Dog) (Canis familiaris)
62 819 Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)
63 818 Oryza sativa subsp. indica (Rice)
64 804 Zea mays (Maize)
65 796 Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
66 793 Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633)
67 793 Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100)
68 791 Escherichia coli (strain SMS-3-5 / SECEC)
69 784 Aquifex aeolicus (strain VF5)
70 776 Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
71 776 Pasteurella multocida (strain Pm70)
72 771 Escherichia coli (strain K12 / DH10B)
73 771 Escherichia coli O127:H6 (strain E2348/69 / EPEC)
74 765 Escherichia coli (strain K12 / MC4100 / BW2952)
75 765 Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC)
76 762 Escherichia coli (strain 55989 / EAEC)
77 761 Escherichia coli O8 (strain IAI1)
78 760 Shigella flexneri serotype 5b (strain 8401)
79 760 Staphylococcus epidermidis (strain ATCC 35984 / RP62A)
80 759 Staphylococcus epidermidis (strain ATCC 12228)
81 758 Staphylococcus aureus (strain NCTC 8325)
82 756 Escherichia coli (strain SE11)
83 756 Escherichia coli O45:K1 (strain S88 / ExPEC)
84 753 Escherichia coli O7:K1 (strain IAI39 / ExPEC)
85 749 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 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 Salmonella agona (strain SL483)
103 713 Yersinia pseudotuberculosis serotype O:1b (strain IP 31758)
104 712 Salmonella schwarzengrund (strain CVM19633)
105 711 Yersinia pestis bv. Antiqua (strain Antiqua)
106 710 Salmonella heidelberg (strain SL476)
107 702 Salmonella dublin (strain CT_02021853)
108 698 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)
117 673 Staphylococcus aureus (strain USA300)
118 673 Escherichia coli
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 Bradyrhizobium diazoefficiens
124 658 Sinorhizobium fredii (strain NBRC 101917 / NGR234)
125 653 Debaryomyces hansenii
126 650 Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
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
136 613 Staphylococcus haemolyticus (strain JCSC1435)
137 611 Mesorhizobium japonicum (Mesorhizobium loti
138 610 Xanthomonas campestris pv. campestris
139 607 Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
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 Bacillus cereus (strain ATCC 10987 / NRS 248)
147 594 Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori)
148 593 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)
152 579 Brucella suis biovar 1 (strain 1330)
153 578 Caenorhabditis briggsae
154 574 Brucella melitensis biotype 1 (strain 16M / ATCC 23456 / NCTC 10094)
155 573 Vibrio fischeri (strain ATCC 700601 / ES114)
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
170 550 Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
171 550 Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
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 Sodalis glossinidius (strain morsitans)
177 528 Corynebacterium glutamicum
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
186 512 Pseudomonas aeruginosa (strain PA7)
187 511 Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 / C2A)
188 511 Staphylococcus aureus (strain Newman)
189 510 Haemophilus ducreyi (strain 35000HP / ATCC 700724)
190 510 Geobacillus kaustophilus (strain HTA426)
191 508 Streptomyces avermitilis
192 508 Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253)
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)
196 499 Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
197 499 Brucella abortus biovar 1 (strain 9-941)
198 497 Rickettsia conorii (strain ATCC VR-613 / Malish 7)
199 497 Haemophilus influenzae (strain 86-028NP)
200 496 Bacillus clausii (strain KSM-K16)
201 496 Burkholderia pseudomallei (strain K96243)
202 494 Proteus mirabilis (strain HI4320)
203 493 Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)
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)
210 486 Mannheimia succiniciproducens (strain MBEL55E)
211 485 Pyrococcus horikoshii
212 485 Thermosynechococcus elongatus (strain BP-1)
213 484 Shewanella sp. (strain MR-4)
214 484 Pseudomonas aeruginosa (strain LESB58)
215 484 Staphylococcus aureus (strain Mu3 / ATCC 700698)
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 Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
221 478 Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)
222 477 Pyrococcus abyssi (strain GE5 / Orsay)
223 475 Cupriavidus necator (strain ATCC 17699 / H16 / DSM 428 / Stanier 337)
224 475 Nicotiana tabacum (Common tobacco)
225 474 Burkholderia lata
226 474 Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
227 472 Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)
228 468 Clostridium perfringens (strain 13 / Type A)
229 466 Shewanella frigidimarina (strain NCIMB 400)
230 466 Shewanella sp. (strain ANA-3)
231 466 Pseudomonas putida (strain GB-1)
232 466 Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)
233 466 Xanthomonas campestris pv. vesicatoria (strain 85-10)
234 465 Anabaena variabilis (strain ATCC 29413 / PCC 7937)
235 464 Aeromonas hydrophila subsp. hydrophila
236 463 Campylobacter jejuni subsp. jejuni serotype O:2
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 Ovis aries (Sheep)
242 457 Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi)
243 455 Staphylococcus aureus (strain JH1)
244 454 Xanthomonas oryzae pv. oryzae (strain MAFF 311018)
245 453 Pseudomonas putida (strain W619)
246 452 Shewanella baltica (strain OS185)
247 452 Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
248 452 Aeromonas salmonicida (strain A449)
249 450 Dechloromonas aromatica (strain RCB)
250 450 Caldanaerobacter subterraneus subsp. tengcongensis
2.3 Taxonomic distribution of the sequences
Kingdom sequences (% of the database)
Archaea 19521 ( 4%)
Bacteria 333552 ( 60%)
Eukaryota 187848 ( 34%)
Viruses 16792 ( 3%)
Within Eukaryota:
Category sequences (% of Eukaryota) (% of the complete database)
Human 20361 ( 11%) ( 4%)
Other Mammalia 46629 ( 25%) ( 8%)
Other Vertebrata 18259 ( 10%) ( 3%)
Viridiplantae 39539 ( 21%) ( 7%)
Fungi 33465 ( 18%) ( 6%)
Insecta 9180 ( 5%) ( 2%)
Nematoda 4922 ( 3%) ( 1%)
Other 15493 ( 8%) ( 3%)
3. SEQUENCE SIZE
Repartition of the sequences by size (excluding fragments)
From To Number From To Number
1- 50 9495 1001-1100 3977
51- 100 42459 1101-1200 2788
101- 150 58937 1201-1300 2135
151- 200 58821 1301-1400 1986
201- 250 57660 1401-1500 1609
251- 300 51357 1501-1600 786
301- 350 51750 1601-1700 613
351- 400 44908 1701-1800 549
401- 450 36882 1801-1900 468
451- 500 29738 1901-2000 376
501- 550 21425 2001-2100 245
551- 600 15299 2101-2200 323
601- 650 12765 2201-2300 311
651- 700 9209 2301-2400 208
701- 750 7639 2401-2500 157
751- 800 5507 >2500 1264
801- 850 4760
851- 900 5202
901- 950 4044
951-1000 2910
The average sequence length in UniProtKB/Swiss-Prot is 358 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: 2730
4.1 Table of the frequency of journal citations
Journals cited 1x: 860
2x: 387
3x: 167
4x: 134
5x: 110
6x: 97
7x: 63
8x: 52
9x: 42
10x: 36
11- 20x: 213
21- 50x: 222
51-100x: 119
>100x: 228
4.2 List of the most cited journals in UniProtKB/Swiss-Prot
Nb Citations Journal name
-- --------- -------------------------------------------------------------
1 24268 Journal of Biological Chemistry
2 11208 Proceedings of the National Academy of Sciences of the U.S.A.
3 6559 Journal of Bacteriology
4 5573 Biochemical and Biophysical Research Communications
5 5253 Biochemistry
6 4966 Nucleic Acids Research
7 4801 Gene
8 4797 FEBS Letters
9 4656 The EMBO Journal
10 4448 Nature
11 4315 Molecular and Cellular Biology
12 4223 Journal of Molecular Biology
13 3596 Biochimica et Biophysica Acta
14 3530 Cell
15 3386 European Journal of Biochemistry
16 3138 Journal of Virology
17 2966 Science
18 2828 Biochemical Journal
19 2533 Genomics
20 2504 Plant Physiology
21 2476 Molecular Microbiology
22 2164 Journal of Cell Biology
23 2098 The American Journal of Human Genetics
24 1946 The Plant Cell
25 1843 Plant Molecular Biology
26 1815 Genes and Development
27 1810 PLoS ONE
28 1788 The Plant Journal
29 1781 Human Molecular Genetics
30 1745 Virology
31 1730 Nature Genetics
32 1648 Development
33 1641 Molecular Biology of the Cell
34 1561 Human Mutation
35 1534 Oncogene
36 1506 Molecular Cell
37 1407 Journal of Immunology
38 1393 Molecular and General Genetics
39 1332 Journal of Biochemistry
40 1309 Structure
41 1305 Genetics
42 1226 Journal of Cell Science
43 1138 Blood
44 1117 Journal of General Virology
45 1100 Infection and Immunity
46 1045 Microbiology
47 1038 Archives of Biochemistry and Biophysics
48 1038 Current Biology
49 1028 Developmental Biology
50 885 Applied and Environmental Microbiology
51 879 Cancer Research
52 878 Journal of Neuroscience
53 864 Acta Crystallographica, Section D
54 837 Yeast
55 830 FEMS Microbiology Letters
56 766 Protein Science
57 762 Toxicon
58 734 Neuron
59 712 Journal of Clinical Investigation
60 682 Human Genetics
61 666 American Journal of Physiology
62 661 Plant and Cell Physiology
63 644 Nature Structural Biology
64 643 Mechanisms of Development
65 621 The Journal of Experimental Medicine
66 612 Proteins
67 600 PLoS Genetics
68 587 Journal of Medical Genetics
69 570 Current Genetics
70 564 Nature Cell Biology
71 543 Bioscience, Biotechnology, and Biochemistry
72 532 Molecular Endocrinology
73 527 Journal of Neurochemistry
74 518 Nature Structural and Molecular Biology
75 514 The Journal of Clinical Endocrinology and Metabolism
76 498 Developmental Cell
77 497 Endocrinology
78 490 The FEBS Journal
79 488 Mammalian Genome
80 472 Immunogenetics
81 452 Experimental Cell Research
82 448 Molecular and Biochemical Parasitology
83 434 Antimicrobial Agents and Chemotherapy
84 424 Eukaryotic Cell
85 419 Planta
86 413 RNA
87 409 Peptides
88 408 Journal of Molecular Evolution
89 396 Molecular Biology and Evolution
90 386 DNA and Cell Biology
91 374 DNA Sequence
92 370 Molecular Pharmacology
93 366 Nature Communications
94 365 Journal of the American Chemical Society
95 364 Journal of Experimental Botany
96 357 Journal of Investigative Dermatology
97 356 Neurology
98 353 EMBO Reports
99 347 Comparative Biochemistry and Physiology
100 347 The FASEB Journal
101 342 Biology of Reproduction
102 341 Acta Crystallographica, Section F
103 340 Brain Research. Molecular Brain Research
104 326 Tissue Antigens
105 325 European Journal of Human Genetics
106 323 American Journal of Medical Genetics. Part A
107 322 PLoS Pathogens
108 321 Molecular Plant-Microbe Interactions
109 320 Immunity
110 314 Biochimie
111 313 Genes to Cells
112 311 The New England Journal of Medicine
113 308 Developmental Dynamics
114 303 Virus Research
115 296 Biological Chemistry Hoppe-Seyler
116 296 Genome Research
117 287 Clinical Genetics
118 282 Cytogenetics and Cell Genetics
119 278 Annals of Neurology
120 271 Journal of General Microbiology
121 266 BMC Genomics
122 266 European Journal of Immunology
123 265 Scientific Reports
124 263 Investigative Ophthalmology and Visual Science
125 263 Nature Immunology
126 255 Applied Microbiology and Biotechnology
127 250 Journal of Human Genetics
128 246 Journal of Medicinal Chemistry
129 239 Archives of Microbiology
130 237 PLoS Biology
131 231 Glycobiology
132 229 DNA Research
133 228 Journal of Cellular Biochemistry
134 223 Traffic
135 218 Molecular Genetics and Metabolism
136 218 Hoppe-Seyler's Zeitschrift fur Physiologische Chemie
137 216 Cell Cycle
138 213 Circulation Research
139 213 Journal of Lipid Research
140 208 Molecular Immunology
141 208 Archives of Virology
142 208 Diabetes
143 206 Molecular and Cellular Endocrinology
144 204 Protein Expression and Purification
145 202 Phytochemistry
146 194 Nature Medicine
147 193 Fungal Genetics and Biology
148 191 Molecular Genetics and Genomics
149 183 Molecular and Cellular Neuroscience
150 182 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) 1209101 2.17
Journal 1031991 453420 1.85 1
Submitted to EMBL/GenBank/DDBJ 166331 150732 0.30 2
Submitted to other databases 7381 6818 0.01 3
Book citation 1736 1713 <0.01 4
Plant Gene Register 611 598 <0.01 5
Thesis 436 433 <0.01 6
Unpublished observations 408 404 <0.01 7
Patent 201 196 <0.01 8
Worm Breeder's Gazette 6 6 <0.01 9
Total number of distinct authors cited in UniProtKB/Swiss-Prot: 401589
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Comments (CC) 2501980 4.49
ALLERGEN 719 719 <0.01 26
ALTERNATIVE PRODUCTS 25176 25176 0.05 13
BIOPHYSICOCHEMICAL PROPERTIES 8013 8013 0.01 20
BIOTECHNOLOGY 912 901 <0.01 25
CATALYTIC ACTIVITY 266122 235548 0.48 5
CAUTION 12726 12480 0.02 18
COFACTOR 122745 112388 0.22 7
DEVELOPMENTAL STAGE 11896 11895 0.02 19
DISEASE 6837 4578 0.01 22
DISRUPTION PHENOTYPE 13619 13619 0.02 17
DOMAIN 47924 41328 0.09 9
ENZYME REGULATION 14587 14585 0.03 16
FUNCTION 463638 443444 0.83 2
INDUCTION 20382 20370 0.04 14
INTERACTION 19187 19187 0.03 15
MASS SPECTROMETRY 6779 5099 0.01 23
MISCELLANEOUS 38182 35200 0.07 12
PATHWAY 137723 124925 0.25 6
PHARMACEUTICAL 114 111 <0.01 29
POLYMORPHISM 1289 1233 <0.01 24
PTM 55375 41108 0.10 8
RNA EDITING 627 627 <0.01 28
SEQUENCE CAUTION 44123 44123 0.08 11
SIMILARITY 506181 502036 0.91 1
SUBCELLULAR LOCATION 347477 340300 0.62 3
SUBUNIT 276848 276336 0.50 4
TISSUE SPECIFICITY 45179 45178 0.08 10
TOXIC DOSE 668 611 <0.01 27
WEB RESOURCE 6932 5775 0.01 21
Total number of comment topics: 29
Total Number of Average
Line type / subtype number entries per entry Rank
------------------------------------ -------- --------- --------- ----
Features (FT) 4450935 7.98
ACT_SITE 163116 98959 0.29 10
BINDING 402997 106068 0.72 2
CA_BIND 4168 1727 0.01 36
CARBOHYD 115549 29635 0.21 15
CHAIN 565568 550735 1.01 1
COILED 21978 15190 0.04 27
COMPBIAS 58888 31685 0.11 20
CONFLICT 134850 47203 0.24 13
CROSSLNK 23474 8414 0.04 26
DISULFID 123551 33387 0.22 14
DNA_BIND 11600 10492 0.02 32
DOMAIN 192904 118869 0.35 9
HELIX 248459 23027 0.45 6
INIT_MET 17131 17131 0.03 28
INTRAMEM 2641 1197 <0.01 37
LIPID 12959 8367 0.02 30
METAL 377199 93669 0.68 3
MOD_RES 247594 71448 0.44 7
MOTIF 42395 27798 0.08 23
MUTAGEN 67238 14864 0.12 18
NON_CONS 2257 787 <0.01 38
NON_STD 358 283 <0.01 39
NON_TER 12374 9492 0.02 31
NP_BIND 156491 85054 0.28 11
PEPTIDE 11456 7871 0.02 33
PROPEP 14128 12040 0.03 29
REGION 195884 92949 0.35 8
REPEAT 105048 14694 0.19 16
SIGNAL 41469 41467 0.07 24
SITE 56853 31530 0.10 21
STRAND 259186 21680 0.46 5
TOPO_DOM 139744 28698 0.25 12
TRANSIT 9048 8932 0.02 34
TRANSMEM 369689 77133 0.66 4
TURN 59826 18669 0.11 19
UNSURE 4429 788 0.01 35
VAR_SEQ 51862 21948 0.09 22
VARIANT 96196 17040 0.17 17
ZN_FING 30378 13323 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) 18709557 33.55
Allergome 1751 1146 <0.01 121 Protein family/group databases
ArachnoServer 1149 1140 <0.01 129 Organism-specific databases
Araport 15780 15684 0.03 83 Organism-specific databases
Bgee 56304 56302 0.10 45 Gene expression databases
BindingDB 5013 5013 0.01 103 Chemistry
BioCyc 158042 153981 0.28 29 Enzyme and pathway databases
BioGrid 50660 50165 0.09 50 Protein-protein interaction databases
BioMuta 17245 17240 0.03 78 Polymorphism and mutation databases
BRENDA 12873 12101 0.02 87 Enzyme and pathway databases
CarbonylDB 1157 1157 <0.01 127 PTM databases
CAZy 9454 8528 0.02 90 Protein family/group databases
CCDS 47710 33947 0.09 52 Sequence databases
CDD 181089 166066 0.32 26 Family and domain databases
CGD 1987 1970 <0.01 119 Organism-specific databases
ChEMBL 6527 6527 0.01 96 Chemistry
ChiTaRS 20458 20448 0.04 68 Other
CleanEx 30019 29387 0.05 59 Gene expression databases
CollecTF 133 133 <0.01 151 Gene expression databases
ComplexPortal 6849 4286 0.01 93 Protein-protein interaction databases
COMPLUYEAST-2DPAGE 97 97 <0.01 152 2D gel databases
ConoServer 949 866 <0.01 130 Organism-specific databases
CORUM 5168 5168 0.01 101 Protein-protein interaction databases
CTD 74777 73893 0.13 43 Organism-specific databases
DEPOD 239 239 <0.01 148 PTM databases
dictyBase 4212 4097 0.01 108 Organism-specific databases
DIP 17346 17314 0.03 77 Protein-protein interaction databases
DisGeNET 14852 14615 0.03 84 Organism-specific databases
DisProt 708 703 <0.01 134 3D structure databases
DMDM 16360 16296 0.03 81 Polymorphism and mutation databases
DNASU 18971 18900 0.03 73 Protocols and materials databases
DOSAC-COBS-2DPAGE 145 145 <0.01 149 2D gel databases
DrugBank 18751 3639 0.03 74 Chemistry
EchoBASE 4159 4159 0.01 109 Organism-specific databases
EcoGene 4293 4293 0.01 107 Organism-specific databases
eggNOG 664003 331301 1.19 5 Phylogenomic databases
ELM 1809 1809 <0.01 120 Protein-protein interaction databases
EMBL 984795 546066 1.77 3 Sequence databases
Ensembl 89971 50160 0.16 41 Genome annotation databases
EnsemblBacteria 354498 335383 0.64 17 Genome annotation databases
EnsemblFungi 30744 28900 0.06 58 Genome annotation databases
EnsemblMetazoa 15936 10365 0.03 82 Genome annotation databases
EnsemblPlants 28805 21275 0.05 63 Genome annotation databases
EnsemblProtists 4975 4796 0.01 104 Genome annotation databases
EPD 20233 20233 0.04 71 Proteomic databases
ESTHER 2493 2493 <0.01 116 Protein family/group databases
euHCVdb 55 44 <0.01 153 Organism-specific databases
EuPathDB 37902 37707 0.07 55 Organism-specific databases
EvolutionaryTrace 16620 16620 0.03 80 Other
ExpressionAtlas 51578 51578 0.09 47 Gene expression databases
FlyBase 6146 5849 0.01 97 Organism-specific databases
Gene3D 364625 291845 0.65 16 Family and domain databases
GeneCards 20311 20146 0.04 69 Organism-specific databases
GeneDB 572 516 <0.01 138 Genome annotation databases
GeneID 290256 279920 0.52 22 Genome annotation databases
GeneReviews 1155 1152 <0.01 128 Organism-specific databases
GeneTree 59200 59176 0.11 44 Phylogenomic databases
Genevisible 55226 55226 0.10 46 Gene expression databases
GeneWiki 10366 10282 0.02 89 Other
GenomeRNAi 22017 22014 0.04 65 Other
GlyConnect 568 495 <0.01 139 PTM databases
GO 2825442 531170 5.07 1 Ontologies
Gramene 28805 21275 0.05 62 Genome annotation databases
GuidetoPHARMACOLOGY 2028 2028 <0.01 118 Chemistry
H-InvDB 5589 4769 0.01 100 Organism-specific databases
HAMAP 329799 326928 0.59 19 Family and domain databases
HGNC 20299 20158 0.04 70 Organism-specific databases
HOGENOM 391084 391084 0.70 15 Phylogenomic databases
HOVERGEN 75943 75943 0.14 42 Phylogenomic databases
HPA 27411 16833 0.05 64 Organism-specific databases
IMGT_GENE-DB 142 142 <0.01 150 Protein family/group databases
InParanoid 136872 136872 0.25 30 Phylogenomic databases
IntAct 51294 51294 0.09 48 Protein-protein interaction databases
InterPro 2223831 538691 3.99 2 Family and domain databases
iPTMnet 51233 51233 0.09 49 PTM databases
KEGG 503370 475102 0.90 7 Genome annotation databases
KO 403646 403205 0.72 14 Phylogenomic databases
LegioList 765 763 <0.01 133 Organism-specific databases
Leproma 672 669 <0.01 135 Organism-specific databases
MaizeGDB 509 505 <0.01 140 Organism-specific databases
MalaCards 4438 4435 0.01 106 Organism-specific databases
MaxQB 29689 29689 0.05 60 Proteomic databases
MEROPS 11388 11388 0.02 88 Protein family/group databases
MGI 16880 16840 0.03 79 Organism-specific databases
MIM 20817 15005 0.04 67 Organism-specific databases
MINT 21788 21788 0.04 66 Protein-protein interaction databases
MoonDB 349 349 <0.01 146 Protein family/group databases
MoonProt 279 279 <0.01 147 Protein family/group databases
mycoCLAP 359 354 <0.01 145 Protein family/group databases
neXtProt 20186 20183 0.04 72 Organism-specific databases
OGP 374 374 <0.01 144 2D gel databases
OMA 416366 416366 0.75 13 Phylogenomic databases
OpenTargets 18305 18149 0.03 76 Organism-specific databases
Orphanet 6144 3286 0.01 98 Organism-specific databases
OrthoDB 293165 293165 0.53 20 Phylogenomic databases
PANTHER 270341 258049 0.48 23 Family and domain databases
PATRIC 91781 91781 0.16 40 Genome annotation databases
PaxDb 124356 124356 0.22 33 Proteomic databases
PDB 161944 26436 0.29 28 3D structure databases
PDBsum 161944 26436 0.29 27 3D structure databases
PeptideAtlas 32094 32094 0.06 57 Proteomic databases
PeroxiBase 773 755 <0.01 132 Protein family/group databases
Pfam 756015 514288 1.36 4 Family and domain databases
PharmGKB 18363 18321 0.03 75 Organism-specific databases
PhosphoSitePlus 39008 39008 0.07 54 PTM databases
PhylomeDB 95565 95565 0.17 38 Phylogenomic databases
PIR 124093 113651 0.22 34 Sequence databases
PIRSF 108698 107669 0.19 37 Family and domain databases
PMAP-CutDB 1462 1462 <0.01 122 Other
PomBase 5133 5129 0.01 102 Organism-specific databases
PRIDE 224932 224932 0.40 24 Proteomic databases
PRINTS 132752 117274 0.24 32 Family and domain databases
PRO 95561 95561 0.17 39 Other
ProDom 29134 28951 0.05 61 Family and domain databases
ProMEX 454 454 <0.01 142 Proteomic databases
PROSITE 465961 298037 0.84 10 Family and domain databases
ProteinModelPortal 448010 448010 0.80 11 3D structure databases
Proteomes 478427 454370 0.86 9 Other
ProteomicsDB 36419 19847 0.07 56 Proteomic databases
PseudoCAP 1332 1323 <0.01 124 Organism-specific databases
Reactome 123216 36734 0.22 35 Enzyme and pathway databases
REBASE 397 397 <0.01 143 Protein family/group databases
RefSeq 607330 462667 1.09 6 Sequence databases
REPRODUCTION-2DPAGE 1259 1038 <0.01 125 2D gel databases
RGD 7951 7950 0.01 91 Organism-specific databases
SABIO-RK 3925 3925 0.01 111 Enzyme and pathway databases
SFLD 14127 6502 0.03 86 Family and domain databases
SGD 6739 6734 0.01 94 Organism-specific databases
SignaLink 3026 3026 0.01 115 Enzyme and pathway databases
SIGNOR 4067 4067 0.01 110 Enzyme and pathway databases
SMART 191808 141597 0.34 25 Family and domain databases
SMR 443752 443752 0.80 12 3D structure databases
STRING 332307 332307 0.60 18 Protein-protein interaction databases
SUPFAM 495713 376409 0.89 8 Family and domain databases
SWISS-2DPAGE 1178 1178 <0.01 126 2D gel databases
SwissLipids 1345 1258 <0.01 123 Chemistry
SwissPalm 7256 7256 0.01 92 PTM databases
TAIR 14575 14519 0.03 85 Organism-specific databases
TCDB 6731 6690 0.01 95 Protein family/group databases
TIGRFAMs 292621 272599 0.52 21 Family and domain databases
TopDownProteomics 3247 2967 0.01 113 Proteomic databases
TreeFam 45275 45267 0.08 53 Phylogenomic databases
TubercuList 2189 2153 <0.01 117 Organism-specific databases
UCD-2DPAGE 497 497 <0.01 141 2D gel databases
UCSC 49830 45531 0.09 51 Genome annotation databases
UniCarbKB 584 584 <0.01 136 PTM databases
UniGene 109623 96247 0.20 36 Sequence databases
UniPathway 136240 123455 0.24 31 Enzyme and pathway databases
VectorBase 577 497 <0.01 137 Genome annotation databases
VGNC 3731 3731 0.01 112 Organism-specific databases
WBParaSite 34 34 <0.01 154 Genome annotation databases
World-2DPAGE 929 918 <0.01 131 2D gel databases
WormBase 5996 4579 0.01 99 Organism-specific databases
Xenbase 4546 4540 0.01 105 Organism-specific databases
ZFIN 3037 3032 0.01 114 Organism-specific databases
Total number of cross-referenced databases: 154
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) 4.06 Gly (G) 7.07 Met (M) 2.41 Trp (W) 1.09
Asp (D) 5.46 His (H) 2.27 Phe (F) 3.86 Tyr (Y) 2.91
Cys (C) 1.38 Ile (I) 5.92 Pro (P) 4.72 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 3871 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: 79172