ライフサイエンスコーパス: Pfam

1 Pfam and corresponding DPAM-AI domains are at

2 Pfam clans are described in detail, together with the ne

3 Pfam contains multiple alignments and hidden Markov mode

4 Pfam homology and domain boundary annotations in the tar

5 Pfam is a collection of multiple alignments and profile

6 Pfam is a comprehensive collection of protein domains an

7 Pfam is a database of protein families that currently co

8 Pfam is a large collection of protein domains and famili

9 Pfam is a large collection of protein families and domai

10 Pfam is a large collection of protein multiple sequence

11 Pfam is a widely used database of protein families and d

12 Pfam is a widely used database of protein families, curr

13 Pfam is available on the web in the UK, the USA, France

14 Pfam is available via servers in the UK, the USA and Swe

15 Pfam is freely available for browsing and download at

16 Pfam is now based not only on the UniProtKB sequence dat

17 Pfam is possibly the most well known protein family data

18 Pfam protein domains are often thought of as evolutionar

19 Pfam provides similar coverage of ECOD with family class

20 Pfam release 24.0 contains 11,912 families, of which a l

21 Pfam search results have been calculated for the entire

22 Pfam term enrichment analysis revealed 172 protein famil

23 Pfam, available via servers in the UK and the USA, is a

24 Pfam-B, the automatically-generated supplement to Pfam,

25 systematic large-scale study of nearly 2,000 Pfam protein families with sufficient sequence informati

26 We identified 311 proteins and 112 Pfam families, corresponding to 2910 domains, as disease

27 We detected over-representation in 13 Pfam terms including HSP, ALDH and ubiquitin families in

28 By applying our algorithm to 138 Pfam families with at least one member of known structur

29 of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe.

30 39), DUF399 (domain of unknown function 399; Pfam ID: PF04187) and MARTX toxins that contribute to ho

31 unique domain-domain interactions among 4036 Pfam domains, out of which 4349 are inferred from PDB en

32 The pipeline is extended to a set of 417 Pfam families, built on the combination of Tara with oth

33 Of the 5721 Pfam families that lack experimental structures, 2801 ha

34 as diseasesusceptible and 32 proteins and 67 Pfam families (10,783 domains) as diseaseresistant based

35 iota was reflected by identification of 8298 Pfam and 3670 COG protein families.

36 ins in SWISS-PROT-35 and SP-TrEMBL-5 match a Pfam family.

37 F0-ATPase-regulatory proteins representing a Pfam protein family of 246 sequences from 219 species (P

38 ts: A neutral nucleotide model compared to a Pfam domain encoding model (PSILC(nuc/dom)); A protein c

39 /dom)); A protein coding model compared to a Pfam domain encoding model (PSILC(prot/dom)).

40 ssification of pseudogenes than dN/dS when a Pfam domain alignment is available.

41 and recurrent somatic variants differ across Pfam domains.

42 and for searching a protein sequence against Pfam.

43 he protein families data base of alignments (Pfam) analysis suggested the wit3.0 peptide sequence sha

44 e three-dimensional structure models for all Pfam-A sequence families with average length under 150 r

45 Today, for about half of all Pfam domain families no structure is known, but unfortun

46 transcription factor-family curation of all Pfam domains, incorporated the Gene Ontology classificat

47 nabled the linking between authorship of all Pfam entries with the corresponding authors' ORCID ident

48 Applied to all Pfam domains without known structures, confident models

49 modelling of discontinuous domains allowing Pfam domain definitions to be closer to those found in s

50 heir UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public

51 to other databases, such as ArrayExpress and Pfam, entries from which are also cited widely in the li

52 B database are, however, still available and Pfam annotations for individual UniProtKB sequences can

53 Two annotation schemes, i.e. MapMan BIN and Pfam, at two sparsity thresholds, i.e. top 100 (stringen

54 sequence-only (Superfamily, PDBAA BLAST and Pfam) and sequence-structure-based (SAM-T02, 3D-PSSM, mG

55 yme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phyloge

56 rotein families remain to be classified, and Pfam continues working toward comprehensive coverage of

57 ies directly using RPS-BLAST against COG and Pfam databases and indirectly via proxygenes that are id

58 for canonical gene families such as COG and Pfam.

59 esentatives of the exhaustive databases, and Pfam-A and Superfamily as databases that predefine famil

60 domain classifications such as InterPro and Pfam, and other ontologies such as mammalian phenotype a

61 ce databases include UniProtKB, InterPro and Pfam, while wwPDB and RCSB cover protein structure.

62 n information from Superfamily, InterPro and Pfam; three-dimensional structures at the Protein Data B

63 CBI-nr, Araport11, SwissProt, COG, KEGG, and Pfam databases.

64 wn so far are provided with links to PDB and Pfam databases.

65 t represented in PROSITE, Blocks, PRINTS and Pfam databases.

66 Merged annotations from PRINTS, PROSITE and Pfam form the InterPro core.

67 me structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a fl

68 us sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence

69 695 superfamilies/families in CATH, SCOP and Pfam, respectively.

70 ift type, nonsense-mediated decay status and Pfam domain interruptions.

71 egions, more than 80% overlap with annotated Pfam domains, including all of the 15 known drug targets

72 he first representative structure of another Pfam family called the YARHG domain [Pfam:PF13308].

73 ignificant developments in such databases as Pfam, MetaCyc, UniProt, ELM and PDBe.

74 ion of the sequence family databases such as Pfam and Interpro with the structure-oriented databases

75 rowsed using classification systems, such as Pfam, Gene Ontology annotation, mpstruc or the Transport

76 rences to other biological resources such as Pfam, SCOP, CATH, GO, InterPro and the NCBI taxonomy dat

77 We apply this to the task of assigning Pfam domains to sequences and structures in the Protein

78 annotated often enough to prompt curators at Pfam to create a spurious protein family.

79 H, PubMed, Ensembl, Homologene and automatic Pfam domain assignments based on HMM profiles.

80 By bridging the gap between sequence-based Pfam and structure-based ECOD domain classifications, ou

81 We also discuss the mapping between Pfam and known 3D structures.

82 ysis to other databases: Reactome, BioCarta, Pfam, PID and SMART, finding additional hits in ErbB and

83 where FunFHMMer performs better than BLAST, Pfam and CDD.

84 teins with at least one domain classified by Pfam as belonging to the Pseudouridine synthase and Arch

85 ve procedure to that of the HMMs provided by Pfam and SUPERFAMILY, curated ensembles of multiple alig

86 review of the features that are provided by Pfam over and above the basic family data.

87 r with associated data including SCOP, CATH, Pfam, SWISSPROT, InterPro, GO terms, Protein Quaternary

88 ein family and domain databases include COG, Pfam, SMART and Panther.

89 h alignment data from the public collections Pfam and SMART, as well as with contributions from colle

90 Furthermore, we also connected Pfam entries to the Sequence Ontology (SO) through mappi

91 These results show that genes containing Pfam domains associated with duplication resistance in A

92 rches against a reference library containing Pfam-annotated UniProt sequences and random synthetic se

93 cid sequences that matches the corresponding Pfam family seed alignment, an alignment of DNA sequence

94 Currently Pfam matches 72% of known protein sequences, but for pro

95 he structure's key reference, citation data, Pfam domain diagrams, topology diagrams and protein-prot

96 Each report also contains expression data, Pfam domain information and an associated Mouse Mutant P

97 s derived from the protein families database Pfam.

98 29 families of the protein families database Pfam.

99 e method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucl

100 f HMMs is taken from two existing databases (Pfam and SUPERFAMILY), and is limited to models that exc

101 Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of

102 rabidopsis were selected based on diagnostic Pfam domains.

103 annotation coverage of functionally diverse Pfam families is demonstrated.

104 another Pfam family called the YARHG domain [Pfam:PF13308].

105 ble protein family databases (Blocks + DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE,

106 vel highly conserved protein domain, DUF162 [Pfam: PF02589], can be mapped to two proteins: LutB and

107 cterized Pfam protein family called DUF4424 [Pfam:PF14415].

108 e assembled ligand sets associated with each Pfam domain.

109 WssF belongs to a newly established Pfam family and is predicted to provide acyl groups to W

110 proteins, but also in erythromycin esterase (Pfam ID: PF05139), DUF399 (domain of unknown function 39

111 ther domain enrichment approaches exploiting Pfam families, but benefits from more functionally coher

112 open reading frame, kinase) protein family (Pfam 00480) is a large collection of bacterial polypepti

113 embers of an uncharacterized protein family (Pfam PF08000), which provide compelling evidence for the

114 For Pfam, PSSMs iteratively constructed from seeds based on

115 (max 6.6%) for species, 9.0% (max 28.7%) for Pfam protein domains and 9.4% (max 22.9%) for PANTHER ge

116 stimate that more than 4000 contact maps for Pfam families of unknown structure have more than 50% of

117 m Prints not present in PROSITE, blocks from Pfam-A not present in PROSITE or Prints, and so on for P

118 data from DisProt and independent data from Pfam to validate the above observations that rely on the

119 UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, K

120 All data used are downloaded from Pfam, GLASS and IUPHAR/BPS and the data from reference.

121 CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at

122 and DIP; functional domain information from Pfam; protein fingerprints from PRINTS; protein family a

123 We have annotated representatives from Pfam families to improve coverage of diverse sequences a

124 gent query domains, originally selected from Pfam, and full-length proteins containing their homologo

125 ered (overall, 82.9% of sequences taken from Pfam) and the alignment of amino acid sequences restrict

126 s that encodes a domain of unknown function (Pfam: PF10070) and a putative cation transporter (Pfam:

127 protein family (domain of unknown function; Pfam families PF07005 and PF17042) and (ii) discovered n

128 ce polymorphisms) and family resources (e.g. Pfam and eggNog) and displayed on the Gene3D website.

129 ffects accumulation of transcripts for genes/Pfam domains involved in ribosome biogenesis, photosynth

130 For complete genomes Pfam currently matches up to half of the proteins.

131 f ROK glucokinases and non-ROK glucokinases (Pfam 02685), revealing the primary sequence elements sha

132 nzyme Commission (E.C.), Gene Ontology (GO), Pfam, and InterPro].

133 sing the NCBI taxonomy database, IntEnz, GO, Pfam, InterPro, SCOP, CATH, PubMed, Ensembl, Homologene

134 163 OSC genes were investigated to identify Pfam domains significantly enriched in these regions.

135 g of protein domains that had annotations in Pfam, but not in CATH.

136 ltritol to d-tagatose via a dehydrogenase in Pfam family PF00107, a previously unknown reaction; 2) p

137 A recent development in Pfam has enabled the grouping of related families into c

138 r the past 2 years the number of families in Pfam has doubled and now stands at 6190 (version 10.0).

139 ions: (i) for all protein domain families in Pfam, the fixation of genes horizontally transferred is

140 integral membrane proteins, cereal genes in Pfam family PF02458 emerged as candidates for the ferulo

141 se to d-tagatose 6-phosphate via a kinase in Pfam family PF00294, a previously orphan EC number; and

142 uently scored more remotely related Pfams in Pfam clans higher than closely related Pfams, thus, lead

143 milies not currently annotated as related in Pfam.

144 e have expanded this coverage by integrating Pfam and SUPERFAMILY domain annotations, and we now reso

145 domain boundaries, their classification into Pfam clans, as well as their functional annotation.

146 es: in particular, about 81% of medium-large Pfam families and 72% of ECOD families can be mapped to

147 ith different binding modes within one large Pfam family.

148 arge protein families (including the largest Pfam alignment containing 27000 HIV GP120 glycoprotein s

149 ilies to the Wikipedia community, by linking Pfam families to relevant Wikipedia pages and encouragin

150 to provide CATH annotations for 4.62 million Pfam domains.

151 iants (DGV), dbGaP, DrugBank, KEGG, miRBase, Pfam, Reactome, SEED, TCDB and UniProt.

152 o the frequency of occurrence in the modeled Pfam families, suggesting the significant role of the Ta

153 high sensitivity, Uniclust contains 17% more Pfam domain annotations than UniProt.

154 using protein regions that match two or more Pfam families not currently annotated as related in Pfam

155 At this site contact predictions for most Pfam families are also available.

156 shold, (iii) recognition of FDRs in Multiple Pfam enzyme families, and (iv) recognition of multiple P

157 sters constituted of protein regions with no Pfam annotation, which are therefore candidates for repr

158 n uncovered a considerable fraction (15%) of Pfam domains containing multiple structural and evolutio

159 The latest version (4.3) of Pfam contains 1815 families.

160 The latest version (6.6) of Pfam contains 3071 families, which match 69% of proteins

161 antial phylogenetic separations (1.1-9.7% of Pfam families surveyed at three taxonomic ranges studied

162 The primary changes of Pfam since release 2.1 are that we now use the more adva

163 teins belonging to the Transthyretin clan of Pfam.

164 sed coverage in our dataset via inclusion of Pfam domains.

165 Protein Data Bank structures at the level of Pfam domains and amino acid residues.

166 lent domains, and conversely the majority of Pfam domains sampled by our data play no currently estab

167 -4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction

168 Improvements to the range of Pfam web tools and the first set of Pfam web services th

169 The current release of Pfam (22.0) contains 9318 protein families.

170 parsimony approach to compare repertoires of Pfam domains and their combinations, we show that indepe

171 In contrast, in a non-redundant sample of Pfam-AB, only 1% of four-amino acid word clumps (4.7% of

172 range of Pfam web tools and the first set of Pfam web services that allow programmatic access to the

173 represents the first eukaryotic structure of Pfam family PF03937 and reveals a conserved surface regi

174 We describe the use of Pfam protein motif models and the HMMER program to predi

175 These genes were classified based on Pfam motifs.

176 ade using a new algorithm based primarily on Pfam domain occurrence patterns in mitochondrial and non

177 ene Ontology Annotation projects; updates on Pfam, SMART and InterPro domain databases; update papers

178 arch options allow search by UniProt code or Pfam domain identifier, and results can be filtered by d

179 , originally described by either TIGRFAMs or Pfam entries.

180 and RNA polymerase I, as well as many other Pfam families that had not previously been classified.

181 While most other Pfam-searching web servers set a limit of one sequence p

182 , diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY

183 sequences of protein family domains (Pfams), Pfam functions and clan information, we develop a deep l

184 nd Genomes (KEGG) annotations, and potential Pfam domains were assigned to each transcript isoform.

185 omplementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.

186 lgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.

187 s and functional sites from PROSITE, PRINTS, Pfam and ProDom.

188 ember databases, currently--PROSITE, PRINTS, Pfam, ProDom and SMART.

189 ignature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PA

190 oteins was predicted with pattern profilers (Pfam, Prosite, TMHMM, and pSORT), and by examining queri

191 ent; and integration with PROSITE, profiles, Pfam and ProDom, as part of the international InterPro p

192 PROSITE, Pfam, PRINTS, ProDom, SMART and TIGRFAMs have been manua

193 Currently, it includes PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIRSF and SUPERFA

194 r a library containing 5,092 nuclear protein Pfam domains across varied contexts.

195 ported as being homologues of TraB proteins (Pfam ID: PF01963), a widely distributed family of unknow

196 amilies sets of approximately 100 randomised Pfam protein domains.

197 o expert annotations of domain-like regions (Pfam-A) and completing through cuts based on termini of

198 at generates a dynamic 2D network of related Pfam domain architectures.

199 The current release (Pfam 29.0) includes 16 295 entries and 559 clans.

200 ures are the first examples of the Rep_trans Pfam family providing insights into the replication of n

201 tion features important updates on the EBI's Pfam, PDBe and PRIDE databases, as well as a variety of

202 and annotations on domains (taken from SCOP, Pfam and InterPro) and RNAs (from Rfam) as well.

203 ct 4,248 profiles from 120 randomly selected Pfam-A families.

204 e frequently found to consist of known short Pfam domains, e.g., leucine-rich repeats, tetratricopept

205 om isolate genomes for clusters with similar Pfam composition.

206 Since Pfam has many community contributors, we recently enable

207 for the presence of protease cleavage sites, Pfam domains, glycosylation sites, signal peptides, tran

208 domain alignment collections, such as SMART, Pfam and COG, we have continued an effort to update, and

209 Gene Ontology terms, KEGG pathways and SMART/Pfam domains for each group.

210 Some Pfam entries (1.6%) which have no matches to reference p

211 istory of each seed sequence in the spurious Pfam protein family (PF10695, 'Cw-hydrolase') uncovered

212 ences, but for proteins with known structure Pfam matches 95%, which we believe represents the likely

213 In addition to secondary structure, Pfam multiple sequence alignments now contain active sit

214 esponding three-dimensional (3D) structures, Pfam domains, and protein-protein interaction interfaces

215 available, have been utilised to ensure that Pfam families correspond with structural domains, and to

216 he most significant of these changes is that Pfam is now primarily based on the UniProtKB reference p

217 nce databases the fraction of sequences that Pfam matches is reduced, suggesting that continued addit

218 The Pfam database can be searched in local, glocal or merged

219 The Pfam family DUF4424 adopts a 19-stranded beta-sandwich f

220 mic DNA can be directly searched against the Pfam library using the Wise2 package.

221 f Orthologous Groups (COGs) of genes and the Pfam system.

222 ting Intolerant from Tolerant (SIFT) and the Pfam-based LogR.E-value method, we have identified featu

223 ting Intolerant From Tolerant (SIFT) and the Pfam-based LogR.E-value metric.

224 thus, leading to erroneous assignment at the Pfam family level.

225 method precludes definitive conclusions, the Pfam models provide the only tertiary structure informat

226 s of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and

227 relevant Wikipedia pages and encouraging the Pfam and Wikipedia communities to improve and expand tho

228 a grouping of activity classes following the Pfam-A specifications of protein domains.

229 iple sequence alignment as obtained from the Pfam database (a database of protein families and conser

230 ces, and protein family annotations from the Pfam database for approximately 86%.

231 several domains of unknown function from the Pfam database.

232 ilies based on the protein families from the Pfam database.

233 o >13,000 manually curated families from the Pfam database.

234 erring the parent domain alignments from the Pfam family.

235 , using 1750 gene trees constructed from the Pfam protein family database, that it appears to be a pr

236 le bioactivities to protein domains from the Pfam-A collection of protein families.

237 in the database by adding families from the Pfam-A, ProDom and Domo databases to those from PROSITE

238 We continue to improve the Pfam website and add new visualizations, such as the 'su

239 the domain of unknown function DUF28 in the Pfam and PALI databases for which there was no structura

240 enome that contain a domain described in the Pfam database as domain of unknown function 579 (DUF579)

241 known relationships between families in the Pfam database as well as detect novel distant relationsh

242 JIP60 are conserved in 815 plant RIPs in the Pfam database that were identified by HUMMR as containin

243 We observed that some domains in the Pfam database were found almost exclusively in proteins

244 manually curated inclusion thresholds in the Pfam database, especially on the subset of families that

245 amilies ( approximately 8,000) listed in the Pfam database.

246 tution matrices on protein alignments in the Pfam database.

247 422 of the protein families collected in the Pfam database.

248 ition-specific scoring functions used in the Pfam models, the score statistics of hybrid alignment ob

249 6 models of protein domains contained in the Pfam v5.4 database verifies the theoretical predictions:

250 nces that contain the coding sequence of the Pfam alignment when they can be recovered (overall, 82.9

251 s in close correspondence to the ones of the Pfam and ECOD resources: in particular, about 81% of med

252 nces derived from the seed alignments of the Pfam database of amino acid alignments of families of ho

253 Search of the Pfam database predicts the presence of IgA1 protease and

254 s intended for genome-scale searching of the Pfam database without having to install this database an

255 des fragilis respectively are members of the Pfam family PF12985 (DUF3869).

256 dd to the functionality and usability of the Pfam resource.

257 equence Ontology (SO) through mapping of the Pfam type definitions to SO terms.

258 The new method, MITOPRED, is based on the Pfam domain occurrence patterns and the amino acid compo

259 Based on this we have renamed the Pfam families representing the two domains found in the

260 Methodology improvements for searching the Pfam collection locally as well as via the web are descr

261 hmmpfam, the program used for searching the Pfam HMM database.

262 ion was compared to a proteome data set, the Pfam domain database, and the genomes of six other fungi

263 s that will be of particular interest to the Pfam community.

264 sed on functional domains referencing to the Pfam database.

265 Here, we use the Pfam protein family database to examine a set of candida

266 Sequence analysis using the Pfam server identified a low stringency match to a fatty

267 domain linkers had been delineated using the Pfam-A database.

268 Comparison with the Pfam classification highlights significant overlap and p

269 ead relying on direct collaboration with the Pfam sequence family database to inform our classificati

270 t of bioactivities stored in ChEMBL with the Pfam-A domain most likely to mediate small molecule bind

271 n interaction data was integrated within the Pfam database and website, but it has now been migrated

272 e resource called iPfam is hosted within the Pfam UK website.

273 as defined by profiles contained within the Pfam-A database.

274 In the last two years the Pfam database has undergone a substantial reorganisation

275 ly permits authors to claim credit for their Pfam curation and link them to their ORCID record.

276 These Pfam families match 63% of proteins in SWISS-PROT 37 and

277 More than half of these Pfam families contain DPAM domains that can be confident

278 references and pointers to related TIGRFAMs, Pfam and InterPro models.

279 oups) and KO (KEGG Orthology) in addition to Pfam domains; (iii) information on intronless genes are

280 e heuristic to map small molecule binding to Pfam domains.

281 Here, we describe the changes to Pfam content.

282 HMMER3 has necessitated numerous changes to Pfam that are described in detail.

283 TIGRFAMs is thus complementary to Pfam, whose models typically achieve broad coverage acro

284 ower fold, added several protein families to Pfam database(2) and experimentally demonstrated that on

285 Small molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactiv

286 lust sequences are annotated with matches to Pfam, SCOP domains, and proteins in the PDB, using our H

287 B, the automatically-generated supplement to Pfam, has been removed.

288 PF10070) and a putative cation transporter (Pfam: PF00361).

289 n illustration, trRosetta was applied to two Pfam families with unknown structures, for which the pre

290 We analyze a previously uncharacterized Pfam protein family called DUF4424 [Pfam:PF14415].

291 than a thousand structurally uncharacterized Pfam families to achieve reasonable structural annotatio

292 between the member databases (MSD, UniProt, Pfam, Interpro, SCOP and CATH).

293 updated version to 26,219 among 5140 unique Pfam domains, a 23% increase compared to 20,513 unique D

294 of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-s

295 kground information, domain architecture via Pfam links, a list of all sequences and an assessment of

296 o 6000 amino acids with AlphaFold, visualize Pfam annotations, and dock ligands with AutoDock Vina an

297 hod that combines SwissProt annotations with Pfam multiple alignments.

298 This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. co

299 e a rapidly growing class of families within Pfam.

300 definition of tandem repeat families within Pfam.