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Entry version 102 (07 Oct 2020)
Sequence version 1 (21 Jul 1986)
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Protein

RNA ligase 1

Gene

63

Organism
Enterobacteria phage T4 (Bacteriophage T4)
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 countering a host defense mechanism which, following viral infection, activates the host anticodon nuclease and shuts off viral translation. Repairs 5'-PO4 and 3'-OH groups in the cleaved host tRNA (PubMed:16671895, PubMed:17068206, PubMed:2444436). The nick ligation reaction entails three nucleotidyl transfer steps (PubMed:12766156). In the first step, the RNA ligase reacts with ATP in the absence of nucleic acid to form a covalent ligase-AMP intermediate and release pyrophosphate (PubMed:12766156). In step 2, the ligase-AMP binds to the nicked duplex nucleic acid and transfers the adenylate to the 5'-PO4 terminus to form an adenylylated nicked intermediate (PubMed:12766156). In step 3, the RNA ligase directs the attack of the nick 3'-OH on the 5'-phosphoanhydride linkage, resulting in a repaired 3'-5' phosphodiester and release of AMP (By similarity) (PubMed:12766156).UniRule annotation4 Publications

Caution

An interaction between the carbonyl oxygen of Gly-269 and the magnesium ion may occur.1 Publication

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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

Mg2+UniRule annotation2 PublicationsNote: Binds 2 magnesium ions that perform the catalytic activity via a two-metal mechanism (PubMed:28223499, PubMed:16263720). One of the catalytic Mg2+, which is coordinated by 5 water molecules, engages the lysine nucleophile and the ATP alpha phosphate while the Mg2+ orients the PPi leaving group (PubMed:28223499).UniRule annotation2 Publications

<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>pH dependencei

Optimum pH is 8.0.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei37ATPUniRule annotation1 Publication1
Binding sitei54ATPUniRule annotation1 Publication1
Binding sitei75ATPUniRule annotation1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 sitei99N6-AMP-lysine intermediateUniRule annotation1 Publication1
Binding sitei159ATPUniRule annotation1 Publication1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei159Essential for RNA ligase activityUniRule annotation1 Publication1
Binding sitei240ATPUniRule annotation1 Publication1
Binding sitei242ATPUniRule annotation1 Publication1
Sitei246Essential for RNA ligase activityUniRule annotation1 Publication1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">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 bindingi272Magnesium; catalyticUniRule annotation2 Publications1

<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

GO - Biological processi

<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 functionLigase
Biological processEvasion of bacteria-mediated translation shutoff by virus, Host-virus interaction, RNA repair
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

<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%5Fand%5Ftaxonomy%5Fsection">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:
RNA ligase 1UniRule annotation (EC:6.5.1.3UniRule annotation3 Publications)
Alternative name(s):
Gene product 63
Short name:
gp63
Rnl1UniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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:63
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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>OrganismiEnterobacteria phage T4 (Bacteriophage T4)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 identifieri10665 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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 lineageiVirusesDuplodnaviriaHeunggongviraeUroviricotaCaudoviricetesCaudoviralesMyoviridaeTevenvirinaeTequatrovirus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section only exists in viral entries and indicates the host(s) either as a specific organism or taxonomic group of organisms that are susceptible to be infected by a virus.<p><a href='/help/virus_host' target='_top'>More...</a></p>Virus hostiEscherichia coli [TaxID: 562]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">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
  • UP000009087 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">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: Genome

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology%5Fand%5Fbiotech%5Fsection">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi37Y → A: No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and on tRNA repair. 1 Publication1
Mutagenesisi45W → A: Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and on tRNA repair. 1 Publication1
Mutagenesisi54R → A: 65% loss of adenylyltransferase activity. 70% loss of ligase activity. 1 Publication1
Mutagenesisi75K → A: 95% loss of adenylyltransferase activity. Impaired ligase activity. 1 Publication1
Mutagenesisi77F → A: 90% loss of adenylyltransferase activity. Impaired ligase activity. 1 Publication1
Mutagenesisi99K → A: Complete loss of adenylyltransferase activity and ligase activity. 1 Publication1
Mutagenesisi99K → N: Complete loss of ligase activity. 1 Publication1
Mutagenesisi99K → R: About 50% loss of ligase activity. 1 Publication1
Mutagenesisi100E → Q: No effect on ligase activity. 1 Publication1
Mutagenesisi100E → T: About 50% loss of ligase activity. 1 Publication1
Mutagenesisi101D → N, S or E: Complete loss of ligase activity. 1 Publication1
Mutagenesisi102G → A: Complete loss of adenylyltransferase activity and ligase activity. 1 Publication1
Mutagenesisi119K → A: Increased adenylyltransferase activity. No effect on ligase activity. 1 Publication1
Mutagenesisi159E → A: Complete loss of ligation of 5'-PO4 and 3'-OH termini of the RNA strand and complete loss of tRNA repair. 1 Publication1
Mutagenesisi165N → A: Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair. 1 Publication1
Mutagenesisi179L → A: Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair. 1 Publication1
Mutagenesisi182R → A: Complete loss of ligation. 1 Publication1
Mutagenesisi227E → A: Complete loss of adenylyltransferase activity and ligase activity. 1 Publication1
Mutagenesisi228G → A: Complete loss of adenylyltransferase activity and ligase activity. 1 Publication1
Mutagenesisi230V → A: Partial loss of the ligation of 5'-PO4 and 3'-OH termini of the RNA strand; no effect on tRNA repair. 1 Publication1
Mutagenesisi240K → A: Complete loss of adenylyltransferase activity and ligase activity. 1 Publication1
Mutagenesisi242K → A: Complete loss of adenylyltransferase activity and ligase activity. 1 Publication1
Mutagenesisi246Y → A: Complete loss of ligation of 5'-PO4 and 3'-OH termini of the RNA strand and complete loss of tRNA repair; no effect on adenylyltransferase activity. 1 Publication1
Mutagenesisi272D → A: No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and no effect on tRNA repair. 1 Publication1
Mutagenesisi273D → A: No effect on the ligation of 5'-PO4 and 3'-OH termini of the RNA strand and no effect on tRNA repair. 1 Publication1

<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_00001649761 – 374RNA ligase 1Add BLAST374

<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

Secondary structure

1374
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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SMRi
P00971

Database of comparative protein structure models

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ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

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PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P00971

<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

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>Domaini

The N-terminus contains the nucleotidyltransferase domain (PubMed:17585047). The C-terminus probably confers tRNA specificity (PubMed:17585047).1 Publication

<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 Tequatrovirus RNA ligase 1 family.UniRule annotation

Phylogenomic databases

KEGG Orthology (KO)

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KOi
K18961

Family and domain databases

HAMAP database of protein families

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HAMAPi
MF_04149, RNALIG_T4, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR019039, RNA_ligase_T4-Rnl1_N
IPR012648, Rnl1

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF09511, RNA_lig_T4_1, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR02308, RNA_lig_T4_1, 1 hit

<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%5Flength">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%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">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.

P00971-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQELFNNLME LCKDSQRKFF YSDDVSASGR TYRIFSYNYA SYSDWLLPDA
60 70 80 90 100
LECRGIMFEM DGEKPVRIAS RPMEKFFNLN ENPFTMNIDL NDVDYILTKE
110 120 130 140 150
DGSLVSTYLD GDEILFKSKG SIKSEQALMA NGILMNINHH RLRDRLKELA
160 170 180 190 200
EDGFTANFEF VAPTNRIVLA YQEMKIILLN VRENETGEYI SYDDIYKDAT
210 220 230 240 250
LRPYLVERYE IDSPKWIEEA KNAENIEGYV AVMKDGSHFK IKSDWYVSLH
260 270 280 290 300
STKSSLDNPE KLFKTIIDGA SDDLKAMYAD DEYSYRKIEA FETTYLKYLD
310 320 330 340 350
RALFLVLDCH NKHCGKDRKT YAMEAQGVAK GAGMDHLFGI IMSLYQGYDS
360 370
QEKVMCEIEQ NFLKNYKKFI PEGY
Length:374
Mass (Da):43,509
Last modified:July 21, 1986 - v1
<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:i04388DBA72A8121C
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
X00365 Genomic DNA Translation: CAA25107.1
X04140 Genomic DNA Translation: CAA27760.1
AF158101 Genomic DNA Translation: AAD42514.1
M10160 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...
PIRi
A01202, LQBPR4

NCBI Reference Sequences

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RefSeqi
NP_049839.1, NC_000866.4

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
1258717

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
vg:1258717

<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
X00365 Genomic DNA Translation: CAA25107.1
X04140 Genomic DNA Translation: CAA27760.1
AF158101 Genomic DNA Translation: AAD42514.1
M10160 Genomic DNA No translation available.
PIRiA01202, LQBPR4
RefSeqiNP_049839.1, NC_000866.4

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

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RCSB PDBi

Protein Data Bank Japan

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PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2C5UX-ray2.21A/B1-374[»]
5TT6X-ray2.19A1-374[»]
SMRiP00971
ModBaseiSearch...
PDBe-KBiSearch...

Genome annotation databases

GeneIDi1258717
KEGGivg:1258717

Phylogenomic databases

KOiK18961

Miscellaneous databases

EvolutionaryTraceiP00971

Family and domain databases

HAMAPiMF_04149, RNALIG_T4, 1 hit
InterProiView protein in InterPro
IPR019039, RNA_ligase_T4-Rnl1_N
IPR012648, Rnl1
PfamiView protein in Pfam
PF09511, RNA_lig_T4_1, 1 hit
TIGRFAMsiTIGR02308, RNA_lig_T4_1, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

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 nameiRLIG_BPT4
<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: P00971
<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%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: October 7, 2020
This is version 102 of the entry and version 1 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 programViral 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

3D-structure, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
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