Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

UniProtKB - B5YKK8 (B5YKK8_THEYD)

Entry version 76 (07 Oct 2020)
Sequence version 1 (25 Nov 2008)
Previous versions | rss
Add a publicationFeedback
Protein

D-3-phosphoglycerate dehydrogenase

Gene

serA

Organism
Thermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)
Status
Unreviewed-Annotation score:

Annotation score:2 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>-Protein inferred from homologyi <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

Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L-serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.ARBA annotation

<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 <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: L-serine biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.UniRule annotationARBA annotation
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. D-3-phosphoglycerate dehydrogenase (serA)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

<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 functionOxidoreductaseUniRule annotationImported
Biological processAmino-acid biosynthesis, Serine biosynthesisUniRule annotationARBA annotation
LigandNADUniRule annotation

Enzyme and pathway databases

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...UniPathwayi		UPA00135;UER00196

<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:
D-3-phosphoglycerate dehydrogenaseUniRule annotation (EC:1.1.1.95UniRule 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:serAImported
Ordered Locus Names:THEYE_A0937Imported
<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>OrganismiThermodesulfovibrio yellowstonii (strain ATCC 51303 / DSM 11347 / YP87)Imported
<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 identifieri289376 [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 lineageiBacteria › Nitrospirae › Nitrospirales › Nitrospiraceae › Thermodesulfovibrio ›
<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
  • UP000000718 <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: Chromosome

<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

Protein-protein interaction databases

STRING: functional protein association networks

More...STRINGi		289376.THEYE_A0937

<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%5Fand%5Fdomains%5Fsection">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>Domaini454 – 526ACTInterPro annotationAdd BLAST73

<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 D-isomer specific 2-hydroxyacid dehydrogenase family.UniRule annotationARBA annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...eggNOGi		COG0111, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...HOGENOMi		CLU_019796_8_1_0

InParanoid: Eukaryotic Ortholog Groups

More...InParanoidi		B5YKK8

KEGG Orthology (KO)

More...KOi		K00058

Identification of Orthologs from Complete Genome Data

More...OMAi		NIAGMQV

Database of Orthologous Groups

More...OrthoDBi		1638924at2

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...Gene3Di		3.30.1330.90, 1 hit

Integrated resource of protein families, domains and functional sites

More...InterProi		View protein in InterPro
IPR002912, ACT_dom
IPR029009, ASB_dom_sf
IPR006139, D-isomer_2_OHA_DH_cat_dom
IPR029753, D-isomer_DH_CS
IPR029752, D-isomer_DH_CS1
IPR006140, D-isomer_DH_NAD-bd
IPR036291, NAD(P)-bd_dom_sf
IPR006236, PGDH

Pfam protein domain database

More...Pfami		View protein in Pfam
PF00389, 2-Hacid_dh, 1 hit
PF02826, 2-Hacid_dh_C, 1 hit
PF01842, ACT, 1 hit

Superfamily database of structural and functional annotation

More...SUPFAMi		SSF143548, SSF143548, 1 hit
SSF51735, SSF51735, 1 hit

TIGRFAMs; a protein family database

More...TIGRFAMsi		TIGR01327, PGDH, 1 hit

PROSITE; a protein domain and family database

More...PROSITEi		View protein in PROSITE
PS51671, ACT, 1 hit
PS00065, D_2_HYDROXYACID_DH_1, 1 hit
PS00670, D_2_HYDROXYACID_DH_2, 1 hit
PS00671, D_2_HYDROXYACID_DH_3, 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.

B5YKK8-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MKVLVSDSIS SKGVEILKKA GFEVDVKTGL KPEELKSIIG EYDALIIRSA 
        60         70         80         90        100
TKVTAEIIDA ADKLKVIGRA GTGVDNVDKI AATKKGIVVM NTPGGNTITT 
       110        120        130        140        150
AEHAIAMLFS LARRIPQATA SMKSGKWEKK KFMGVELYNK TIGIIGLGRI 
       160        170        180        190        200
GSEVAKRTQC MGMNVLAYDP FLSDERAEEL GITKTDLDKI FAEADFITIH 
       210        220        230        240        250
TPLTSETKYL INKNTIEKMK KGVYIINCAR GGIVNEKDLY DAIQSGKVAG 
       260        270        280        290        300
AALDVFEKEP PEEGYALITD ERVICTPHLG ASTLEAQENV AVAIAEQVVD 
       310        320        330        340        350
YLINGTIRNA VNFPSIPFDQ VPLIRPYLVL LERMGSFVSQ IFTKSIKQVQ 
       360        370        380        390        400
IEYLGEISNL NTQALTAAAL KGILDPILGE PVNYVNASFI AKERGIEVRE 
       410        420        430        440        450
IKGKEAGDYQ SLVRITLISK DDRAVIAGTL LSRKDPRIVQ INDISMEIIP 
       460        470        480        490        500
EGNMIFLRNH DRPGVIGNIG TLLGQNNINI GHMHFGRKEA GGIAFSVISV 
       510        520 
DATLTDDIIE KIKQLPNVLE VRPVYISVH
Length:529
Mass (Da):57,701
Last modified:November 25, 2008 - 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:iE8DCB1FDFC9821CB
GO

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
CP001147 Genomic DNA Translation: ACI21985.1

NCBI Reference Sequences

More...RefSeqi		WP_012546680.1, NC_011296.1
YP_002248773.1, NC_011296.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...EnsemblBacteriai		ACI21985; ACI21985; THEYE_A0937

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...KEGGi		tye:THEYE_A0937

Pathosystems Resource Integration Center (PATRIC)

More...PATRICi		fig|289376.4.peg.923

<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
CP001147 Genomic DNA Translation: ACI21985.1
RefSeqiWP_012546680.1, NC_011296.1
YP_002248773.1, NC_011296.1

3D structure databases

Database of comparative protein structure models

More...ModBasei		Search...

SWISS-MODEL Interactive Workspace

More...SWISS-MODEL-Workspacei		Submit a new modelling project...

Protein-protein interaction databases

STRINGi289376.THEYE_A0937

Genome annotation databases

EnsemblBacteriaiACI21985; ACI21985; THEYE_A0937
KEGGitye:THEYE_A0937
PATRICifig|289376.4.peg.923

Phylogenomic databases

eggNOGiCOG0111, Bacteria
HOGENOMiCLU_019796_8_1_0
InParanoidiB5YKK8
KOiK00058
OMAiNIAGMQV
OrthoDBi1638924at2

Enzyme and pathway databases

UniPathwayiUPA00135;UER00196

Family and domain databases

Gene3Di3.30.1330.90, 1 hit
InterProiView protein in InterPro
IPR002912, ACT_dom
IPR029009, ASB_dom_sf
IPR006139, D-isomer_2_OHA_DH_cat_dom
IPR029753, D-isomer_DH_CS
IPR029752, D-isomer_DH_CS1
IPR006140, D-isomer_DH_NAD-bd
IPR036291, NAD(P)-bd_dom_sf
IPR006236, PGDH
PfamiView protein in Pfam
PF00389, 2-Hacid_dh, 1 hit
PF02826, 2-Hacid_dh_C, 1 hit
PF01842, ACT, 1 hit
SUPFAMiSSF143548, SSF143548, 1 hit
SSF51735, SSF51735, 1 hit
TIGRFAMsiTIGR01327, PGDH, 1 hit
PROSITEiView protein in PROSITE
PS51671, ACT, 1 hit
PS00065, D_2_HYDROXYACID_DH_1, 1 hit
PS00670, D_2_HYDROXYACID_DH_2, 1 hit
PS00671, D_2_HYDROXYACID_DH_3, 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 nameiB5YKK8_THEYD
<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: B5YKK8
<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/TrEMBL: November 25, 2008
Last sequence update: November 25, 2008
Last modified: October 7, 2020
This is version 76 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 statusiUnreviewed (UniProtKB/TrEMBL)

<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 proteomeImported
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again