Protein Domain Annotations (Pfam)
proteindomain_annotation.RdA curated annotation table of protein domains based on Pfam identifiers. This dataset provides structured mappings from Pfam domain IDs to domain names, supporting the annotation and interpretation of domain-level biological features in knowledge graphs used by the tKOI framework.
Format
A data frame with 14193 rows and 2 columns:
- identifier
A character string representing the Pfam domain identifier (e.g., "PF19543").
- name
The name or description of the domain, often including structural or functional attributes (e.g., "Glycoside hydrolase 123, N-terminal domain").
Source
Pfam Database https://pfam.xfam.org/
Details
Protein domains represent conserved functional or structural units within proteins. This dataset enables enrichment and network-based inference at the domain level.
The identifier column can be joined to graph nodes representing domains in tKOI output, while the name column adds interpretability for visualization and reporting.
Domains include a variety of structural motifs, enzyme catalytic regions, and uncharacterized conserved segments (e.g., DUFs).
Examples
data(proteindomain_annotation)
subset(proteindomain_annotation, grepl("hydrolase", name, ignore.case = TRUE))
#> identifier
#> 1 PF19543
#> 46 PF00657
#> 144 PF00933
#> 170 PF08307
#> 224 PF02964
#> 231 PF02275
#> 356 PF13318
#> 362 PF01670
#> 411 PF03512
#> 470 PF03636
#> 610 PF14508
#> 648 PF01915
#> 667 PF14323
#> 788 PF02638
#> 793 PF02550
#> 827 PF09370
#> 897 PF19420
#> 930 PF16923
#> 978 PF06342
#> 980 PF00443
#> 1101 PF16317
#> 1226 PF18271
#> 1278 PF00670
#> 1303 PF01227
#> 1311 PF13647
#> 1322 PF12471
#> 1343 PF02156
#> 1352 PF10605
#> 1417 PF16255
#> 1519 PF14196
#> 1583 PF13869
#> 1584 PF03747
#> 1667 PF07745
#> 1689 PF04273
#> 1700 PF18089
#> 1928 PF00723
#> 1931 PF05908
#> 1993 PF00722
#> 2006 PF17433
#> 2047 PF02011
#> 2114 PF16875
#> 2131 PF12215
#> 2190 PF02057
#> 2247 PF14587
#> 2340 PF03662
#> 2378 PF01183
#> 2491 PF00332
#> 2532 PF04996
#> 2552 PF06439
#> 2582 PF09752
#> 2618 PF20091
#> 2619 PF14509
#> 2647 PF00704
#> 2673 PF13423
#> 2868 PF03663
#> 3098 PF17167
#> 3153 PF02633
#> 3171 PF05838
#> 3185 PF01074
#> 3480 PF12697
#> 3509 PF12535
#> 3515 PF11308
#> 3652 PF08282
#> 3658 PF18565
#> 3832 PF18034
#> 3922 PF02015
#> 4000 PF08472
#> 4046 PF10566
#> 4078 PF10340
#> 4143 PF15979
#> 4146 PF07858
#> 4157 PF16862
#> 4172 PF18564
#> 4178 PF03537
#> 4193 PF02882
#> 4302 PF11790
#> 4314 PF01156
#> 4320 PF07461
#> 4326 PF00925
#> 4327 PF05165
#> 4429 PF07488
#> 4459 PF03403
#> 4524 PF02148
#> 4547 PF01503
#> 4610 PF01981
#> 4658 PF12891
#> 4660 PF07826
#> 4781 PF07859
#> 4865 PF14885
#> 4917 PF02837
#> 4963 PF17189
#> 4994 PF08306
#> 5028 PF14871
#> 5126 PF19718
#> 5328 PF02838
#> 5366 PF00150
#> 5390 PF01738
#> 5490 PF08244
#> 5628 PF17451
#> 5705 PF14883
#> 5801 PF03648
#> 6030 PF13419
#> 6102 PF13199
#> 6130 PF06259
#> 6132 PF09081
#> 6141 PF00728
#> 6154 PF03959
#> 6164 PF02836
#> 6204 PF06399
#> 6233 PF12695
#> 6237 PF00702
#> 6754 PF16123
#> 6755 PF17387
#> 6763 PF03664
#> 6802 PF04685
#> 6880 PF01301
#> 6967 PF01270
#> 6981 PF12715
#> 7028 PF00232
#> 7165 PF01374
#> 7255 PF03659
#> 7278 PF18031
#> 7435 PF12888
#> 7500 PF14736
#> 7576 PF04909
#> 7620 PF00457
#> 7686 PF17678
#> 7694 PF03632
#> 7697 PF13336
#> 7756 PF01088
#> 7948 PF02649
#> 8047 PF07521
#> 8106 PF02055
#> 8178 PF04616
#> 8189 PF17890
#> 8397 PF07477
#> 8484 PF01195
#> 8561 PF02324
#> 8636 PF08840
#> 8652 PF17652
#> 8694 PF12710
#> 8978 PF01979
#> 9013 PF09127
#> 9050 PF17677
#> 9124 PF03065
#> 9176 PF07486
#> 9192 PF05116
#> 9217 PF10230
#> 9506 PF03633
#> 9716 PF14872
#> 9724 PF03200
#> 9729 PF18230
#> 9732 PF03644
#> 9766 PF00295
#> 9805 PF18088
#> 9980 PF11975
#> 9991 PF03639
#> 10035 PF16874
#> 10057 PF16674
#> 10089 PF02289
#> 10090 PF03718
#> 10203 PF13472
#> 10273 PF07969
#> 10336 PF01557
#> 10408 PF01229
#> 10445 PF00703
#> 10481 PF05221
#> 10559 PF05013
#> 10619 PF00251
#> 10626 PF07176
#> 10659 PF20408
#> 10842 PF07335
#> 10878 PF10081
#> 11021 PF16822
#> 11038 PF09663
#> 11073 PF00795
#> 11088 PF00331
#> 11215 PF00561
#> 11263 PF09994
#> 11385 PF13872
#> 11420 PF03819
#> 11586 PF01341
#> 11683 PF00840
#> 11693 PF01532
#> 11700 PF01373
#> 11838 PF18438
#> 11913 PF00759
#> 11916 PF02056
#> 11935 PF13286
#> 12016 PF18290
#> 12044 PF14498
#> 12103 PF04447
#> 12158 PF13344
#> 12201 PF07748
#> 12302 PF04083
#> 12343 PF20309
#> 12352 PF04307
#> 12441 PF06441
#> 12459 PF17829
#> 12516 PF06821
#> 12597 PF07698
#> 12653 PF00763
#> 12724 PF01502
#> 12727 PF13200
#> 12854 PF04775
#> 13003 PF05990
#> 13019 PF07470
#> 13065 PF06028
#> 13075 PF14606
#> 13085 PF05382
#> 13161 PF07971
#> 13247 PF21365
#> 13258 PF07632
#> 13270 PF21246
#> 13290 PF08924
#> 13388 PF13320
#> 13426 PF16141
#> 13471 PF13802
#> 13519 PF21252
#> 13526 PF20811
#> 13529 PF21570
#> 13651 PF21087
#> 13658 PF05028
#> 13875 PF01055
#> 13941 PF21104
#> 14018 PF16347
#> name
#> 1 Glycoside hydrolase 123, N-terminal domain
#> 46 GDSL-like Lipase/Acylhydrolase
#> 144 Glycosyl hydrolase family 3 N terminal domain
#> 170 Glycosyl hydrolase family 98 C-terminal domain
#> 224 Methane monooxygenase, hydrolase gamma chain
#> 231 Linear amide C-N hydrolases, choloylglycine hydrolase family
#> 356 1-carboxybiuret hydrolase subunit AtzG-like
#> 362 Glycosyl hydrolase family 12
#> 411 Glycosyl hydrolase family 52
#> 470 Glycosyl hydrolase family 65, N-terminal domain
#> 610 Glycosyl-hydrolase 97 N-terminal
#> 648 Glycosyl hydrolase family 3 C-terminal domain
#> 667 GxGYxYP putative glycoside hydrolase C-terminal domain
#> 788 Glycosyl hydrolase-like 10
#> 793 Acetyl-CoA hydrolase/transferase N-terminal domain
#> 827 Phosphoenolpyruvate hydrolase-like
#> 897 N,N dimethylarginine dimethylhydrolase, eukaryotic
#> 930 Glycosyl hydrolase family 63 N-terminal domain
#> 978 Alpha/beta hydrolase of unknown function (DUF1057)
#> 980 Ubiquitin carboxyl-terminal hydrolase
#> 1101 Glycosyl hydrolase family 99
#> 1226 Glycoside hydrolase 131 catalytic N-terminal domain
#> 1278 S-adenosyl-L-homocysteine hydrolase, NAD binding domain
#> 1303 GTP cyclohydrolase I
#> 1311 Glycosyl hydrolase family 80 of chitosanase A
#> 1322 GTP cyclohydrolase N terminal
#> 1343 Glycosyl hydrolase family 26
#> 1352 3HB-oligomer hydrolase (3HBOH)
#> 1417 GDSL-like Lipase/Acylhydrolase
#> 1519 L-2-amino-thiazoline-4-carboxylic acid hydrolase
#> 1583 Nucleotide hydrolase
#> 1584 ADP-ribosylglycohydrolase
#> 1667 Glycosyl hydrolase family 53
#> 1689 Beta-lactamase hydrolase-like protein, phosphatase-like domain
#> 1700 DAPG hydrolase PhiG domain
#> 1928 Glycosyl hydrolases family 15
#> 1931 Poly-gamma-glutamate hydrolase
#> 1993 Glycosyl hydrolases family 16
#> 2006 Glycosyl hydrolase family 49 N-terminal Ig-like domain
#> 2047 Glycosyl hydrolase family 48
#> 2114 Glycosyl hydrolase family 36 N-terminal domain
#> 2131 beta-glucosidase 2, glycosyl-hydrolase family 116 N-term
#> 2190 Glycosyl hydrolase family 59
#> 2247 O-Glycosyl hydrolase family 30
#> 2340 Glycosyl hydrolase family 79, N-terminal domain
#> 2378 Glycosyl hydrolases family 25
#> 2491 Glycosyl hydrolases family 17
#> 2532 Succinylarginine dihydrolase
#> 2552 3-keto-disaccharide hydrolase
#> 2582 Alpha/beta hydrolase domain containing 18
#> 2618 Alpha/beta hydrolase domain
#> 2619 Glycosyl-hydrolase 97 C-terminal, oligomerisation
#> 2647 Glycosyl hydrolases family 18
#> 2673 Ubiquitin carboxyl-terminal hydrolase
#> 2868 Glycosyl hydrolase family 76
#> 3098 Glycosyl hydrolase 36 superfamily, catalytic domain
#> 3153 Creatinine amidohydrolase
#> 3171 Glycosyl hydrolase 108
#> 3185 Glycosyl hydrolases family 38 N-terminal domain
#> 3480 Alpha/beta hydrolase family
#> 3509 Hydrolase of X-linked nucleoside diphosphate N terminal
#> 3515 Glycosyl hydrolases related to GH101 family, GH129
#> 3652 haloacid dehalogenase-like hydrolase
#> 3658 Glycoside hydrolase family 2 C-terminal domain 5
#> 3832 Bacterial Glycosyl hydrolase family 3 C-terminal domain
#> 3922 Glycosyl hydrolase family 45
#> 4000 Sucrose-6-phosphate phosphohydrolase C-terminal
#> 4046 Glycoside hydrolase 97
#> 4078 Steryl acetyl hydrolase
#> 4143 Glycosyl hydrolase family 115
#> 4146 Limonene-1,2-epoxide hydrolase catalytic domain
#> 4157 Glycosyl hydrolase family 79 C-terminal beta domain
#> 4172 Glycoside hydrolase family 5 C-terminal domain
#> 4178 Glycoside-hydrolase family GH114
#> 4193 Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
#> 4302 Glycosyl hydrolase catalytic core
#> 4314 Inosine-uridine preferring nucleoside hydrolase
#> 4320 Nicotine adenine dinucleotide glycohydrolase (NADase)
#> 4326 GTP cyclohydrolase II
#> 4327 GTP cyclohydrolase III
#> 4429 Glycosyl hydrolase family 67 middle domain
#> 4459 Platelet-activating factor acetylhydrolase, isoform II
#> 4524 Zn-finger in ubiquitin-hydrolases and other protein
#> 4547 Phosphoribosyl-ATP pyrophosphohydrolase
#> 4610 Peptidyl-tRNA hydrolase PTH2
#> 4658 Glycoside hydrolase family 44
#> 4660 IMP cyclohydrolase-like protein
#> 4781 alpha/beta hydrolase fold
#> 4865 Hypothetical glycosyl hydrolase family 15
#> 4917 Glycosyl hydrolases family 2, sugar binding domain
#> 4963 Glycosyl hydrolase family 30 beta sandwich domain
#> 4994 Glycosyl hydrolase family 98
#> 5028 Hypothetical glycosyl hydrolase 6
#> 5126 Ubiquitin carboxyl-terminal hydrolase 47 C-terminal
#> 5328 Glycosyl hydrolase family 20, domain 2
#> 5366 Cellulase (glycosyl hydrolase family 5)
#> 5390 Dienelactone hydrolase family
#> 5490 Glycosyl hydrolases family 32 C terminal
#> 5628 Glycosyl hydrolase 101 beta sandwich domain
#> 5705 Hypothetical glycosyl hydrolase family 13
#> 5801 Glycosyl hydrolase family 67 N-terminus
#> 6030 Haloacid dehalogenase-like hydrolase
#> 6102 Glycosyl hydrolase family 66
#> 6130 Alpha/beta hydrolase
#> 6132 Glucan 1,4-alpha-maltotetraohydrolase, domain C
#> 6141 Glycosyl hydrolase family 20, catalytic domain
#> 6154 Serine hydrolase (FSH1)
#> 6164 Glycosyl hydrolases family 2, TIM barrel domain
#> 6204 GTP cyclohydrolase I feedback regulatory protein (GFRP)
#> 6233 Alpha/beta hydrolase family
#> 6237 haloacid dehalogenase-like hydrolase
#> 6754 Hydroxyacylglutathione hydrolase C-terminus
#> 6755 Glycosyl hydrolase family 59 central domain
#> 6763 Glycosyl hydrolase family 62
#> 6802 Glycosyl-hydrolase family 116, catalytic region
#> 6880 Glycosyl hydrolases family 35
#> 6967 Glycosyl hydrolases family 8
#> 6981 Abhydrolase family
#> 7028 Glycosyl hydrolase family 1
#> 7165 Glycosyl hydrolase family 46
#> 7255 Glycosyl hydrolase family 71
#> 7278 Ubiquitin carboxyl-terminal hydrolases
#> 7435 Lipid-binding putative hydrolase
#> 7500 Protein N-terminal asparagine amidohydrolase
#> 7576 Amidohydrolase
#> 7620 Glycosyl hydrolases family 11
#> 7686 Glycosyl hydrolase family 92 N-terminal domain
#> 7694 Glycosyl hydrolase family 65 central catalytic domain
#> 7697 Acetyl-CoA hydrolase/transferase C-terminal domain
#> 7756 Ubiquitin carboxyl-terminal hydrolase, family 1
#> 7948 Type I GTP cyclohydrolase folE2
#> 8047 Zn-dependent metallo-hydrolase RNA specificity domain
#> 8106 Glycosyl hydrolase family 30 TIM-barrel domain
#> 8178 Glycosyl hydrolases family 43
#> 8189 Peptidoglycan hydrolase LytB WW-like domain
#> 8397 Glycosyl hydrolase family 67 C-terminus
#> 8484 Peptidyl-tRNA hydrolase
#> 8561 Glycosyl hydrolase family 70
#> 8636 BAAT / Acyl-CoA thioester hydrolase C terminal
#> 8652 Glycosyl hydrolase family 81 C-terminal domain
#> 8694 haloacid dehalogenase-like hydrolase
#> 8978 Amidohydrolase family
#> 9013 Leukotriene A4 hydrolase, C-terminal
#> 9050 Glycosyl hydrolases family 38 C-terminal beta sandwich domain
#> 9124 Glycosyl hydrolase family 57
#> 9176 Cell Wall Hydrolase
#> 9192 Sucrose-6F-phosphate phosphohydrolase
#> 9217 Lipid-droplet associated hydrolase
#> 9506 Glycosyl hydrolase family 65, C-terminal domain
#> 9716 Hypothetical glycoside hydrolase 5
#> 9724 Glycosyl hydrolase family 63 C-terminal domain
#> 9729 Glycosyl hydrolases family 38 C-terminal sub-domain
#> 9732 Glycosyl hydrolase family 85
#> 9766 Glycosyl hydrolases family 28
#> 9805 Glycoside Hydrolase 20C C-terminal domain
#> 9980 Family 4 glycosyl hydrolase C-terminal domain
#> 9991 Glycosyl hydrolase family 81 N-terminal domain
#> 10035 Glycosyl hydrolase family 36 C-terminal domain
#> 10057 N-terminal of ubiquitin carboxyl-terminal hydrolase 37
#> 10089 Cyclohydrolase (MCH)
#> 10090 Glycosyl hydrolase family 49
#> 10203 GDSL-like Lipase/Acylhydrolase family
#> 10273 Amidohydrolase family
#> 10336 Fumarylacetoacetate (FAA) hydrolase family
#> 10408 Glycosyl hydrolases family 39
#> 10445 Glycosyl hydrolases family 2
#> 10481 S-adenosyl-L-homocysteine hydrolase
#> 10559 N-formylglutamate amidohydrolase
#> 10619 Glycosyl hydrolases family 32 N-terminal domain
#> 10626 Alpha/beta hydrolase of unknown function (DUF1400)
#> 10659 Alpha/beta hydrolase domain
#> 10842 Fungal chitosanase of glycosyl hydrolase group 75
#> 10878 Alpha/beta-hydrolase family
#> 11021 SGNH hydrolase-like domain, acetyltransferase AlgX
#> 11038 Amidohydrolase ring-opening protein (Amido_AtzD_TrzD)
#> 11073 Carbon-nitrogen hydrolase
#> 11088 Glycosyl hydrolase family 10
#> 11215 alpha/beta hydrolase fold
#> 11263 Uncharacterized alpha/beta hydrolase domain (DUF2235)
#> 11385 P-loop containing NTP hydrolase pore-1
#> 11420 MazG nucleotide pyrophosphohydrolase domain
#> 11586 Glycosyl hydrolases family 6
#> 11683 Glycosyl hydrolase family 7
#> 11693 Glycosyl hydrolase family 47
#> 11700 Glycosyl hydrolase family 14
#> 11838 Glycosyl hydrolases family 38 C-terminal domain 1
#> 11913 Glycosyl hydrolase family 9
#> 11916 Family 4 glycosyl hydrolase
#> 11935 Phosphohydrolase-associated domain
#> 12016 Nudix hydrolase domain
#> 12044 Glycosyl hydrolase family 65, N-terminal domain
#> 12103 dATP/dGTP pyrophosphohydrolase
#> 12158 Haloacid dehalogenase-like hydrolase
#> 12201 Glycosyl hydrolases family 38 C-terminal domain
#> 12302 Partial alpha/beta-hydrolase lipase region
#> 12343 Deoxyribohydrolase (DRHyd) domain of the ASK signalosome
#> 12352 LexA-binding, inner membrane-associated putative hydrolase
#> 12441 Epoxide hydrolase N terminus
#> 12459 Gylcosyl hydrolase family 115 C-terminal domain
#> 12516 Serine hydrolase
#> 12597 7TM receptor with intracellular HD hydrolase
#> 12653 Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
#> 12724 Phosphoribosyl-AMP cyclohydrolase
#> 12727 Putative glycosyl hydrolase domain
#> 12854 Acyl-CoA thioester hydrolase/BAAT N-terminal region
#> 13003 Alpha/beta hydrolase of unknown function (DUF900)
#> 13019 Glycosyl Hydrolase Family 88
#> 13065 Alpha/beta hydrolase of unknown function (DUF915)
#> 13075 GDSL-like Lipase/Acylhydrolase family
#> 13085 Bacteriophage peptidoglycan hydrolase
#> 13161 Glycosyl hydrolase family 92 catalytic domain
#> 13247 Glycosyl hydrolase family 31 C-terminal domain
#> 13258 Cellulose-binding Sde182, nucleoside hydrolase-like domain
#> 13270 Ubiquitin carboxyl-terminal hydrolase 38-like, N-terminal domain
#> 13290 Rv2525c-like, glycoside hydrolase-like domain
#> 13388 Glycoside hydrolase 123, catalytic domain
#> 13426 Glycoside hydrolase family 18, BT1044-like
#> 13471 Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain
#> 13519 Glycosyl hydrolase 109, C-terminal domain
#> 13526 Poly (ADP-ribose) glycohydrolase (PARG), helical domain
#> 13529 Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold
#> 13651 Glycosyl hydrolase family 134
#> 13658 Poly (ADP-ribose) glycohydrolase (PARG), Macro domain fold
#> 13875 Glycosyl hydrolases family 31 TIM-barrel domain
#> 13941 Glycosyl hydrolase family 78 alpha-rhamnosidase N-terminal domain
#> 14018 N-sulphoglucosamine sulphohydrolase, C-terminal