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UniProtKB - P25889 (PREA_ECOLI)

Entry version 166 (29 Sep 2021)
Sequence version 3 (15 Jul 1998)
Previous versions | rss
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Protein

NAD-dependent dihydropyrimidine dehydrogenase subunit PreA

Gene

preA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Involved in pyrimidine base degradation. Catalyzes physiologically the reduction of uracil to 5,6-dihydrouracil (DHU) by using NADH as a specific cosubstrate. It also catalyzes the reverse reaction and the reduction of thymine to 5,6-dihydrothymine (DHT).

2 Publications

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

[4Fe-4S] clusterCuratedNote: Binds 2 [4Fe-4S] clusters.Curated

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

  1. KM=38 µM for uracil (at pH 6 and 30 degrees Celsius)1 Publication
  2. KM=87 µM for thymidine (at pH 6 and 30 degrees Celsius)1 Publication
  3. KM=130 µM for DHT (at pH 11 and 30 degrees Celsius)1 Publication
  4. KM=160 µM for DHU (at pH 11 and 30 degrees Celsius)1 Publication
  1. Vmax=0.18 µmol/min/mg enzyme toward DHT (at pH 11 and 30 degrees Celsius)1 Publication
  2. Vmax=0.26 µmol/min/mg enzyme toward thymidine (at pH 6 and 30 degrees Celsius)1 Publication
  3. Vmax=0.43 µmol/min/mg enzyme toward uracil (at pH 6 and 30 degrees Celsius)1 Publication
  4. Vmax=0.44 µmol/min/mg enzyme toward DHU (at pH 11 and 30 degrees Celsius)1 Publication
  5. Vmax=0.67 µmol/min/mg enzyme toward fluorouracil (at pH 6 and 30 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei76SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei137NucleophileBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi344Iron-sulfur 1 (4Fe-4S)Sequence analysis1
Metal bindingi347Iron-sulfur 1 (4Fe-4S)Sequence analysis1
Metal bindingi350Iron-sulfur 1 (4Fe-4S)Sequence analysis1
Metal bindingi354Iron-sulfur 2 (4Fe-4S)Sequence analysis1
Metal bindingi378Iron-sulfur 2 (4Fe-4S)Sequence analysis1
Metal bindingi381Iron-sulfur 2 (4Fe-4S)Sequence analysis1
Metal bindingi384Iron-sulfur 2 (4Fe-4S)Sequence analysis1
Metal bindingi388Iron-sulfur 1 (4Fe-4S)Sequence analysis1

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

Complete GO annotation on QuickGO ...

GO - Biological processi

Complete GO annotation on QuickGO ...

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionOxidoreductase
Ligand4Fe-4S, Iron, Iron-sulfur, Metal-binding, NAD

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...BioCyci		EcoCyc:EG11289-MONOMER
MetaCyc:EG11289-MONOMER

SABIO-RK: Biochemical Reaction Kinetics Database

More...SABIO-RKi		P25889

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
NAD-dependent dihydropyrimidine dehydrogenase subunit PreA (EC:1.3.1.1)
Short name:
DPD
Alternative name(s):
Dihydrothymine dehydrogenase
Dihydrouracil dehydrogenase
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:preA
Synonyms:yeiA
Ordered Locus Names:b2147, JW2134
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia ›
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001691481 – 411NAD-dependent dihydropyrimidine dehydrogenase subunit PreAAdd BLAST411

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...jPOSTi		P25889

PaxDb, a database of protein abundance averages across all three domains of life

More...PaxDbi		P25889

PRoteomics IDEntifications database

More...PRIDEi		P25889

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

<p>This subsection of the 'Expression' section reports the experimentally proven effects of inducers and repressors (usually chemical compounds or environmental factors) on the level of protein (or mRNA) expression (up-regulation, down-regulation, constitutive expression).<p><a href='/help/induction' target='_top'>More...</a></p>Inductioni

Transcriptionally regulated by IscS.1 Publication

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Heterotetramer of 2 PreA and 2 PreT subunits.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...BioGRIDi		4259170, 34 interactors
853281, 1 interactor

ComplexPortal: manually curated resource of macromolecular complexes

More...ComplexPortali		CPX-5561, NAD-dependent dihydropyrimidine dehydrogenase complex

Database of interacting proteins

More...DIPi		DIP-11915N

Protein interaction database and analysis system

More...IntActi		P25889, 2 interactors

STRING: functional protein association networks

More...STRINGi		511145.b2147

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...SMRi		P25889

Database of comparative protein structure models

More...ModBasei		Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini335 – 3674Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd BLAST33
Domaini369 – 3984Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd BLAST30

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni134 – 136Substrate bindingBy similarity3
Regioni201 – 202Substrate bindingBy similarity2

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the dihydropyrimidine dehydrogenase family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0167, Bacteria
COG1146, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_042042_4_2_6

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		P25889

Database for complete collections of gene phylogenies

More...PhylomeDBi		P25889

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.20.20.70, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR017896, 4Fe4S_Fe-S-bd
IPR017900, 4Fe4S_Fe_S_CS
IPR013785, Aldolase_TIM
IPR005720, Dihydroorotate_DH
IPR044512, DPYD

The PANTHER Classification System

More...PANTHERi		PTHR43073, PTHR43073, 2 hits

Pfam protein domain database

More...Pfami		View protein in Pfam
PF01180, DHO_dh, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01037, pyrD_sub1_fam, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS00198, 4FE4S_FER_1, 1 hit
PS51379, 4FE4S_FER_2, 2 hits

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P25889-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MLTKDLSITF CGVKFPNPFC LSSSPVGNCY EMCAKAYDTG WGGVVFKTIG 
        60         70         80         90        100
FFIANEVSPR FDHLVKEDTG FIGFKNMEQI AEHPLEENLA ALRRLKEDYP 
       110        120        130        140        150
DKVLIASIMG ENEQQWEELA RLVQEAGADM IECNFSCPQM TSHAMGSDVG 
       160        170        180        190        200
QSPELVEKYC RAVKRGSTLP MLAKMTPNIG DMCEVALAAK RGGADGIAAI 
       210        220        230        240        250
NTVKSITNID LNQKIGMPIV NGKSSISGYS GKAVKPIALR FIQQMRTHPE 
       260        270        280        290        300
LRDFPISGIG GIETWEDAAE FLLLGAATLQ VTTGIMQYGY RIVEDMASGL 
       310        320        330        340        350
SHYLADQGFD SLQEMVGLAN NNIVPAEDLD RSYIVYPRIN LDKCVGCGRC 
       360        370        380        390        400
YISCYDGGHQ AMEWSEKTRT PHCNTEKCVG CLLCGHVCPV GCIELGEVKF 
       410 
KKGEKEHPVT L
Length:411
Mass (Da):45,069
Last modified:July 15, 1998 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iF44F5F7BA8FAD23C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti389 – 411PVGCI…HPVTL → RWVVLSSGK in M59444 (PubMed:1719366).CuratedAdd BLAST23

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...EMBLi

GenBank nucleotide sequence database

More...GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC75208.2
AP009048 Genomic DNA Translation: BAE76624.1
M59444 Genomic DNA No translation available.

NCBI Reference Sequences

More...RefSeqi		NP_416652.4, NC_000913.3
WP_000956071.1, NZ_SSZK01000011.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		AAC75208; AAC75208; b2147
BAE76624; BAE76624; BAE76624

Database of genes from NCBI RefSeq genomes

More...GeneIDi		949037

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		ecj:JW2134
eco:b2147

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|1411691.4.peg.95

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC75208.2
AP009048 Genomic DNA Translation: BAE76624.1
M59444 Genomic DNA No translation available.
RefSeqiNP_416652.4, NC_000913.3
WP_000956071.1, NZ_SSZK01000011.1

3D structure databases

SMRiP25889
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4259170, 34 interactors
853281, 1 interactor
ComplexPortaliCPX-5561, NAD-dependent dihydropyrimidine dehydrogenase complex
DIPiDIP-11915N
IntActiP25889, 2 interactors
STRINGi511145.b2147

Proteomic databases

jPOSTiP25889
PaxDbiP25889
PRIDEiP25889

Genome annotation databases

EnsemblBacteriaiAAC75208; AAC75208; b2147
BAE76624; BAE76624; BAE76624
GeneIDi949037
KEGGiecj:JW2134
eco:b2147
PATRICifig|1411691.4.peg.95

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...EchoBASEi		EB1266

Phylogenomic databases

eggNOGiCOG0167, Bacteria
COG1146, Bacteria
HOGENOMiCLU_042042_4_2_6
InParanoidiP25889
PhylomeDBiP25889

Enzyme and pathway databases

BioCyciEcoCyc:EG11289-MONOMER
MetaCyc:EG11289-MONOMER
SABIO-RKiP25889

Miscellaneous databases

Protein Ontology

More...PROi		PR:P25889

Family and domain databases

Gene3Di3.20.20.70, 1 hit
InterProiView protein in InterPro
IPR017896, 4Fe4S_Fe-S-bd
IPR017900, 4Fe4S_Fe_S_CS
IPR013785, Aldolase_TIM
IPR005720, Dihydroorotate_DH
IPR044512, DPYD
PANTHERiPTHR43073, PTHR43073, 2 hits
PfamiView protein in Pfam
PF01180, DHO_dh, 1 hit
TIGRFAMsiTIGR01037, pyrD_sub1_fam, 1 hit
PROSITEiView protein in PROSITE
PS00198, 4FE4S_FER_1, 1 hit
PS51379, 4FE4S_FER_2, 2 hits

MobiDB: a database of protein disorder and mobility annotations

More...MobiDBi		Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPREA_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P25889
Secondary accession number(s): P76441, Q2MAT2
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 1, 1992
Last sequence update: July 15, 1998
Last modified: September 29, 2021
This is version 166 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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