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Protein

Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase

Gene

thiD

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score:

Annotation score:4 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

Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P.By similarity

<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 <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>Pathwayi: thiamine diphosphate biosynthesis

This protein is involved in step 2 and 3 of the subpathway that synthesizes 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole.
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (thiD)
  3. Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (thiD)
This subpathway is part of the pathway thiamine diphosphate biosynthesis, which is itself part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 4-amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-ribosyl)imidazole, the pathway thiamine diphosphate biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ 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 sitei44Substrate1 Publication1

<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

  • ATP binding Source: UniProtKB-KW
  • hydroxymethylpyrimidine kinase activity Source: GO_Central
  • phosphomethylpyrimidine kinase activity Source: GO_Central

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 functionKinase, Transferase
Biological processThiamine biosynthesis
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
SENT99287:STM2146-MONOMER

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

More...
UniPathwayi
UPA00060;UER00137

UPA00060;UER00138

<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:
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase (EC:2.7.1.49By similarity, EC:2.7.4.7By similarity)
Alternative name(s):
Hydroxymethylpyrimidine kinase
Short name:
HMP kinase
Hydroxymethylpyrimidine phosphate kinase
Short name:
HMP-P kinase
Short name:
HMP-phosphate kinase
Short name:
HMPP kinase
<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:thiD
Ordered Locus Names:STM2146
<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>OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
<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 identifieri99287 [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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
<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
  • UP000001014 <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

<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

GO - Cellular componenti

  • cytosol Source: GO_Central

<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

Chemistry databases

Drug and drug target database

More...
DrugBanki
DB02022 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine

<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.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00001920261 – 266Hydroxymethylpyrimidine/phosphomethylpyrimidine kinaseAdd BLAST266

Proteomic databases

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

More...
PaxDbi
P55882

PRoteomics IDEntifications database

More...
PRIDEi
P55882

<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

Homodimer.1 Publication

Protein-protein interaction databases

STRING: functional protein association networks

More...
STRINGi
99287.STM2146

<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

1266
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P55882

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

More...
SMRi
P55882

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P55882

<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 ThiD family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DWF Bacteria
COG0351 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000225275

KEGG Orthology (KO)

More...
KOi
K00941

Identification of Orthologs from Complete Genome Data

More...
OMAi
VKIGMLH

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P55882

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01169 HMPP_kinase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.1190.20, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR004399 HMP/HMP-P_kinase
IPR013749 PM/HMP-P_kinase-1
IPR029056 Ribokinase-like

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF08543 Phos_pyr_kin, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53613 SSF53613, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00097 HMP-P_kinase, 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>.<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.

P55882-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQRINALTIA GTDPSGGAGI QADLKTFSAL GAYGCSVITA LVAQNTCGVQ
60 70 80 90 100
SVYRIEPDFV AAQLDSVFSD VRIDTTKIGM LAETDIVEAV AERLQRHHVR
110 120 130 140 150
NVVLDTVMLA KSGDPLLSPS AIETLRVRLL PQVSLITPNL PEAAALLDAP
160 170 180 190 200
HARTEQEMLA QGRALLAMGC EAVLMKGGHL EDAQSPDWLF TREGEQRFSA
210 220 230 240 250
PRVNTKNTHG TGCTLSAALA ALRPRHRSWG ETVNEAKAWL SAALAQADTL
260
EVGKGIGPVH HFHAWW
Length:266
Mass (Da):28,544
Last modified:January 23, 2002 - v2
<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:iF8B94332E1616368
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 conflicti44Q → E in AAB66492 (PubMed:9244280).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U87940 Genomic DNA Translation: AAB66492.1
AE006468 Genomic DNA Translation: AAL21049.1

NCBI Reference Sequences

More...
RefSeqi
NP_461090.1, NC_003197.2
WP_001188957.1, NC_003197.2

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAL21049; AAL21049; STM2146

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
1253667

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
stm:STM2146

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|99287.12.peg.2271

<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
U87940 Genomic DNA Translation: AAB66492.1
AE006468 Genomic DNA Translation: AAL21049.1
RefSeqiNP_461090.1, NC_003197.2
WP_001188957.1, NC_003197.2

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1JXHX-ray2.30A/B1-266[»]
1JXIX-ray2.64A/B1-266[»]
1LLJmodel-A1-266[»]
ProteinModelPortaliP55882
SMRiP55882
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi99287.STM2146

Chemistry databases

DrugBankiDB02022 4-Amino-5-Hydroxymethyl-2-Methylpyrimidine

Proteomic databases

PaxDbiP55882
PRIDEiP55882

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL21049; AAL21049; STM2146
GeneIDi1253667
KEGGistm:STM2146
PATRICifig|99287.12.peg.2271

Phylogenomic databases

eggNOGiENOG4105DWF Bacteria
COG0351 LUCA
HOGENOMiHOG000225275
KOiK00941
OMAiVKIGMLH
PhylomeDBiP55882

Enzyme and pathway databases

UniPathwayi
UPA00060;UER00137

UPA00060;UER00138

BioCyciSENT99287:STM2146-MONOMER

Miscellaneous databases

EvolutionaryTraceiP55882

Family and domain databases

CDDicd01169 HMPP_kinase, 1 hit
Gene3Di3.40.1190.20, 1 hit
InterProiView protein in InterPro
IPR004399 HMP/HMP-P_kinase
IPR013749 PM/HMP-P_kinase-1
IPR029056 Ribokinase-like
PfamiView protein in Pfam
PF08543 Phos_pyr_kin, 1 hit
SUPFAMiSSF53613 SSF53613, 1 hit
TIGRFAMsiTIGR00097 HMP-P_kinase, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
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 nameiTHID_SALTY
<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: P55882
<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, 1997
Last sequence update: January 23, 2002
Last modified: December 5, 2018
This is version 117 of the entry and version 2 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

3D-structure, Complete proteome, Reference proteome

Documents

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