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Entry version 122 (02 Jun 2021)
Sequence version 3 (15 Jul 1998)
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Protein

RNA-splicing ligase RtcB

Gene

rtcB

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

GTP-dependent RNA ligase that is involved in tRNA splicing and RNA repair (PubMed:21224389, PubMed:21757685, PubMed:22045815, PubMed:22730297, PubMed:22474365, PubMed:26858100).

Joins RNA with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends (PubMed:21224389, PubMed:21757685, PubMed:22045815, PubMed:22730297, PubMed:22474365, PubMed:26858100).

Also acts as a DNA ligase in case of DNA damage by splicing 'dirty' DNA breaks, characterized by 3'-phosphate (or cyclic-phosphate) and 5'-hydroxy ends that cannot be sealed by classical DNA ligases (PubMed:24218597).

7 Publications

Miscellaneous

Ligation proceeds through 3 nucleotidyl transfer steps, with 2',3'-cyclic phosphate termini being hydrolyzed to 3'-P termini in a step that precedes 3'-P activation with GMP. In the first nucleotidyl transfer step, RtcB reacts with GTP to form a covalent RtcB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3'-P; in the third step, the 5'-OH from the opposite RNA strand attacks the activated 3'-P to form a 3',5'-phosphodiester bond and release GMP (PubMed:22474365, PubMed:26858100). Acts as a DNA ligase by attaching a GMP nucleotide to a DNA 3'-P to form a 'capped' 3' end structure, DNA3'pp5'G. When a suitable DNA 5'-OH end is available, RtcB catalyzes attack of the 5'-OH on DNA3'pp5'G to form a 3'-5' phosphodiester splice junction (PubMed:24218597).3 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

Mn2+2 PublicationsNote: Binds 2 manganese ions per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<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 bindingi75Manganese 1By similarity1
Metal bindingi78Manganese 1By similarity1
Metal bindingi78Manganese 2By similarity1
Metal bindingi168Manganese 1; via tele nitrogenBy similarity1
Metal bindingi185Manganese 2; via tele nitrogenBy similarity1
Metal bindingi281Manganese 2; via tele nitrogenBy similarity1
<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 sitei320GMPBy 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 sitei337GMP-histidine intermediate1 Publication1
Binding sitei407GMPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi167 – 171GMPBy similarity5
Nucleotide bindingi281 – 282GMPBy similarity2
Nucleotide bindingi313 – 316GMPBy similarity4
Nucleotide bindingi337 – 340GMPBy similarity4

<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 processtRNA processing
LigandGTP-binding, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7751-MONOMER
MetaCyc:G7751-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
6.5.1.4, 2026
6.5.1.8, 2026

<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:
RNA-splicing ligase RtcBCurated (EC:6.5.1.83 Publications)
Alternative name(s):
3'-phosphate/5'-hydroxy nucleic acid ligaseCurated
<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:rtcB1 Publication
Synonyms:yhgL
Ordered Locus Names:b3421, JW3384
<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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<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 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_and_biotech_section">'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>Mutagenesisi75D → A: Almost no guanylation activity. Can ligate pre-guanylated nucleotide substrates. 1 Publication1
Mutagenesisi78C → A: No activity. 1 Publication1
Mutagenesisi167N → A: Retains approximately half of overall wild-type activity. Shows increased nucleotide guanylation activity. 1 Publication1
Mutagenesisi168H → A: Retains approximately half of overall wild-type activity. 1 Publication1
Mutagenesisi185H → A: Almost wild type activity. Is impaired in DNA 3'-phosphate capping. 1 Publication1
Mutagenesisi189R → A: Almost wild type activity. Shows increased nucleotide guanylation activity. 1 Publication1
Mutagenesisi281H → A: Less than 10% of overall wild-type activity. Can ligate pre-guanylated nucleotide substrates. 1 Publication1
Mutagenesisi299K → A: Retains approximately half of overall wild-type activity. 1 Publication1
Mutagenesisi337H → A: No overall activity. Abolishes formation of guanylylated RtcB intermediate. Can ligate pre-guanylated nucleotide substrates. 2 Publications1
Mutagenesisi337H → N or Q: Loss of function. Abolishes formation of guanylylated RtcB intermediate. 1 Publication1
Mutagenesisi341R → A: Less than 10% of overall wild-type activity. Shows increased nucleotide guanylation activity. 1 Publication1
Mutagenesisi345R → A: Almost wild type activity. Is impaired in DNA 3'-phosphate capping. 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_00002151091 – 408RNA-splicing ligase RtcBAdd BLAST408

Proteomic databases

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

More...
PaxDbi
P46850

PRoteomics IDEntifications database

More...
PRIDEi
P46850

2D gel databases

Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital

More...
SWISS-2DPAGEi
P46850

<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

Expression is repressed by RtcR.2 Publications

<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

Monomer.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261188, 7 interactors

Protein interaction database and analysis system

More...
IntActi
P46850, 20 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b3421

<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
P46850

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

<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 RtcB family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG1690, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_022279_1_1_6

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P46850

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P46850

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.90.1860.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001233, RtcB
IPR036025, RtcB-like_sf

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01139, RtcB, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF103365, SSF103365, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01288, UPF0027, 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_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.

P46850-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNYELLTTEN APVKMWTKGV PVEADARQQL INTAKMPFIF KHIAVMPDVH
60 70 80 90 100
LGKGSTIGSV IPTKGAIIPA AVGVDIGCGM NALRTALTAE DLPENLAELR
110 120 130 140 150
QAIETAVPHG RTTGRCKRDK GAWENPPVNV DAKWAELEAG YQWLTQKYPR
160 170 180 190 200
FLNTNNYKHL GTLGTGNHFI EICLDESDQV WIMLHSGSRG IGNAIGTYFI
210 220 230 240 250
DLAQKEMQET LETLPSRDLA YFMEGTEYFD DYLKAVAWAQ LFASLNRDAM
260 270 280 290 300
MENVVTALQS ITQKTVRQPQ TLAMEEINCH HNYVQKEQHF GEEIYVTRKG
310 320 330 340 350
AVSARAGQYG IIPGSMGAKS FIVRGLGNEE SFCSCSHGAG RVMSRTKAKK
360 370 380 390 400
LFSVEDQIRA TAHVECRKDA EVIDEIPMAY KDIDAVMAAQ SDLVEVIYTL

RQVVCVKG
Length:408
Mass (Da):45,222
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:iC0C33BA04542185F
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 conflicti84R → G in AAA58219 (PubMed:9278503).Curated1

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
U18997 Genomic DNA Translation: AAA58219.1
U00096 Genomic DNA Translation: AAC76446.1
AP009048 Genomic DNA Translation: BAE77871.1

Protein sequence database of the Protein Information Resource

More...
PIRi
H65137

NCBI Reference Sequences

More...
RefSeqi
NP_417879.1, NC_000913.3
WP_001105504.1, NZ_SSZK01000008.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC76446; AAC76446; b3421
BAE77871; BAE77871; BAE77871

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947929

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW3384
eco:b3421

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.3516

<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
U18997 Genomic DNA Translation: AAA58219.1
U00096 Genomic DNA Translation: AAC76446.1
AP009048 Genomic DNA Translation: BAE77871.1
PIRiH65137
RefSeqiNP_417879.1, NC_000913.3
WP_001105504.1, NZ_SSZK01000008.1

3D structure databases

SMRiP46850
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4261188, 7 interactors
IntActiP46850, 20 interactors
STRINGi511145.b3421

2D gel databases

SWISS-2DPAGEiP46850

Proteomic databases

PaxDbiP46850
PRIDEiP46850

Genome annotation databases

EnsemblBacteriaiAAC76446; AAC76446; b3421
BAE77871; BAE77871; BAE77871
GeneIDi947929
KEGGiecj:JW3384
eco:b3421
PATRICifig|511145.12.peg.3516

Organism-specific databases

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

More...
EchoBASEi
EB2774

Phylogenomic databases

eggNOGiCOG1690, Bacteria
HOGENOMiCLU_022279_1_1_6
InParanoidiP46850
PhylomeDBiP46850

Enzyme and pathway databases

BioCyciEcoCyc:G7751-MONOMER
MetaCyc:G7751-MONOMER
BRENDAi6.5.1.4, 2026
6.5.1.8, 2026

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P46850

Family and domain databases

Gene3Di3.90.1860.10, 1 hit
InterProiView protein in InterPro
IPR001233, RtcB
IPR036025, RtcB-like_sf
PfamiView protein in Pfam
PF01139, RtcB, 1 hit
SUPFAMiSSF103365, SSF103365, 1 hit
PROSITEiView protein in PROSITE
PS01288, UPF0027, 1 hit

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 nameiRTCB_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: P46850
Secondary accession number(s): P76690, Q2M785
<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: November 1, 1995
Last sequence update: July 15, 1998
Last modified: June 2, 2021
This is version 122 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

Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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