ライフサイエンスコーパス: Pfam

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

2 Pfam contains multiple alignments and hidden Markov mode

3 Pfam homology and domain boundary annotations in the tar

4 Pfam is a collection of multiple alignments and profile

5 Pfam is a comprehensive collection of protein domains an

6 Pfam is a database of protein families that currently co

7 Pfam is a large collection of protein domains and famili

8 Pfam is a large collection of protein families and domai

9 Pfam is a large collection of protein multiple sequence

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 on the web in the UK, the USA, France

15 Pfam is available on the World Wide Web in the UK at htt

16 Pfam is available on the WWW in the UK at http://www.san

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

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

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

20 Pfam protein domains are often thought of as evolutionar

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

22 Pfam search results have been calculated for the entire

23 Pfam term enrichment analysis revealed 172 protein famil

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

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

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

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

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

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

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

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

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

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

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

39 and for searching a protein sequence against Pfam.

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

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

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

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

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

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

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

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

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

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

50 Bfam, which can be searched by PDB codes and Pfam identifiers.

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

52 for canonical gene families such as COG and Pfam.

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

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

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

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

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

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

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

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

61 695 superfamilies/families in CATH, SCOP and Pfam, respectively.

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

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

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

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

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

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

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

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

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

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

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

73 m, available at http://ipfam.org, catalogues Pfam domain interactions based on known 3D structures th

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

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

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

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

78 ies used in this study and the corresponding Pfam families is available at http://www.sanger.ac.uk/Us

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

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

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

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

83 s derived from the protein families database Pfam.

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

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

86 tp site ftp://ftp.sanger.ac.uk/pub/databases/Pfam/database_files/.

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

88 rabidopsis were selected based on diagnostic Pfam domains.

89 annotation coverage of functionally diverse Pfam families is demonstrated.

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

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

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

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

94 e assembled ligand sets associated with each Pfam domain.

95 am/ and in the US at http://genome.wustl.edu/Pfam/ Pfam 2.0 matches one or more domains in 50% of Swi

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

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

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

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

100 For Pfam, PSSMs iteratively constructed from seeds based on

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

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

103 n the str and stl families is available from Pfam; alignments of all translations are available at ht

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

122 milies not currently annotated as related in Pfam.

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

124 ith different binding modes within one large Pfam family.

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

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

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

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

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

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

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

132 Release 2.0 of Pfam contains 527 manually verified families which are a

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

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

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

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

137 teins belonging to the Transthyretin clan of Pfam.

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

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

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

141 -4 to d-fructose 6-phosphate via a member of Pfam family PF08013, another previously unknown reaction

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

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

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

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

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

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

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

149 These genes were classified based on Pfam motifs.

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

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

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

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

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

155 d in the US at http://genome.wustl.edu/Pfam/ Pfam 2.0 matches one or more domains in 50% of Swissprot

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

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

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

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

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

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

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

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

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

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

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

167 amilies sets of approximately 100 randomised Pfam protein domains.

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

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

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

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

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

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

174 are/Pfam/, in Sweden at http://www.cgr.ki.se/Pfam/ and in the US at http://pfam.wustl.edu/.

175 c.uk/Software/Pfam/ and http://www.cgr.ki.se/Pfam/, and in the US at http://pfam.wustl.edu/.

176 are/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in France at http://pfam.jouy.inra.fr/ and in the

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

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

179 om isolate genomes for clusters with similar Pfam composition.

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

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

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

183 n Europe at http://www.sanger.ac.uk/Software/Pfam/ and http://www.cgr.ki.se/Pfam/, and in the US at h

184 n the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgb.ki.se/Pfam/, in Franc

185 n the UK at http://www.sanger.ac.uk/Software/Pfam/, in Sweden at http://www.cgr.ki.se/Pfam/ and in th

186 browsing at http://www.sanger.ac.uk/Software/Pfam/iPfam/; the source-data for iPfam is freely availab

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

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

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

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

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

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

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

194 The Pfam assignment data in PDBfam are available at http://d

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

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

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

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

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

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

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

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

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

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

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

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

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

208 several domains of unknown function from the Pfam database.

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

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

211 erring the parent domain alignments from the Pfam family.

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

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

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

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

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

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

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

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

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

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

222 tution matrices on protein alignments in the Pfam database.

223 422 of the protein families collected in the Pfam database.

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

225 6 models of protein domains contained in the Pfam v5.4 database verifies the theoretical predictions:

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

227 Release 3.1 is a major update of the Pfam database and contains 1313 families which are avail

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

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

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

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

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

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

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

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

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

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

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

239 sed on functional domains referencing to the Pfam database.

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

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

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

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

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

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

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

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

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

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

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

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

252 Here, we describe the changes to Pfam content.

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

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

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

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

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

258 ide Web in the UK at http://www.sanger.ac.uk/Pfam/ and in the US at http://genome.wustl.edu/Pfam/ Pfa

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

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

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

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

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

264 hod that combines SwissProt annotations with Pfam multiple alignments.

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

266 e a rapidly growing class of families within Pfam.