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Protein

Riboflavin biosynthesis protein RibBA

Gene

ribBA

Organism
Mycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)
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>
-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 conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate.UniRule annotation
Catalyzes the conversion of GTP to 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and pyrophosphate.UniRule annotation

<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

Protein has several cofactor binding sites:

<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: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
This subpathway is part of the pathway riboflavin 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 2-hydroxy-3-oxobutyl phosphate from D-ribulose 5-phosphate, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Pathwayi: riboflavin biosynthesis

This protein is involved in step 1 of the subpathway that synthesizes 5-amino-6-(D-ribitylamino)uracil from GTP.UniRule annotation
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Riboflavin biosynthesis protein RibBA (ribBA)
  2. Riboflavin biosynthesis protein RibD (ribG)
  3. Riboflavin biosynthesis protein RibD (ribG)
  4. no protein annotated in this organism
This subpathway is part of the pathway riboflavin 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 5-amino-6-(D-ribitylamino)uracil from GTP, the pathway riboflavin biosynthesis and in Cofactor biosynthesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ 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 bindingi29Magnesium or manganese 1UniRule annotation1
Metal bindingi29Magnesium or manganese 2UniRule annotation1
<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 sitei33D-ribulose 5-phosphateUniRule annotation1
<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>Sitei127Essential for DHBP synthase activityUniRule annotation1
Metal bindingi144Magnesium or manganese 2UniRule annotation1
Binding sitei165D-ribulose 5-phosphateUniRule annotation1
Sitei165Essential for DHBP synthase activityUniRule annotation1
Metal bindingi264Zinc; catalyticUniRule annotation1
Metal bindingi275Zinc; catalyticUniRule annotation1
Metal bindingi277Zinc; catalyticUniRule annotation1
Binding sitei280GTPUniRule annotation1
Binding sitei325GTPUniRule annotation1
<p>This subsection of the ‘Function’ 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 sitei337Proton acceptor; for GTP cyclohydrolase activityUniRule annotation1
Active sitei339Nucleophile; for GTP cyclohydrolase activityUniRule annotation1
Binding sitei360GTPUniRule annotation1
Binding sitei365GTPUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Function’ 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 bindingi259 – 263GTPUniRule annotation5
Nucleotide bindingi303 – 305GTPUniRule annotation3

<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 functionHydrolase, Lyase, Multifunctional enzyme
Biological processRiboflavin biosynthesis
LigandGTP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
MAVI262316:G1G0E-1196-MONOMER

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

More...
UniPathwayi
UPA00275;UER00399

UPA00275;UER00400

<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:
Riboflavin biosynthesis protein RibBAUniRule annotation
Including the following 2 domains:
3,4-dihydroxy-2-butanone 4-phosphate synthaseUniRule annotation (EC:4.1.99.12UniRule annotation)
Short name:
DHBP synthaseUniRule annotation
GTP cyclohydrolase-2UniRule annotation (EC:3.5.4.25UniRule annotation)
Alternative name(s):
GTP cyclohydrolase IIUniRule annotation
<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:ribBAUniRule annotation
Ordered Locus Names:MAP_1140
<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>OrganismiMycobacterium paratuberculosis (strain ATCC BAA-968 / K-10)
<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 identifieri262316 [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 lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium avium complex (MAC)
<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
  • UP000000580 <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 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_10000674251 – 425Riboflavin biosynthesis protein RibBAAdd BLAST425

<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
262316.MAP1140

<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

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

More...
ProteinModelPortali
Q741F1

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

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SMRi
Q741F1

Database of comparative protein structure models

More...
ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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

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>Regioni1 – 204DHBP synthaseAdd BLAST204
Regioni28 – 29D-ribulose 5-phosphate bindingUniRule annotation2
Regioni141 – 145D-ribulose 5-phosphate bindingUniRule annotation5
Regioni205 – 425GTP cyclohydrolase IIAdd BLAST221

<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

In the N-terminal section; belongs to the DHBP synthase family.UniRule annotation
In the C-terminal section; belongs to the GTP cyclohydrolase II family.UniRule annotation

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105C66 Bacteria
COG0108 LUCA
COG0807 LUCA

KEGG Orthology (KO)

More...
KOi
K14652

Identification of Orthologs from Complete Genome Data

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OMAi
GCTTGIS

Database of Orthologous Groups

More...
OrthoDBi
POG091H008U

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00641 GTP_cyclohydro2, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

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Gene3Di
3.40.50.10990, 1 hit

HAMAP database of protein families

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HAMAPi
MF_00179 RibA, 1 hit
MF_00180 RibB, 1 hit
MF_01283 RibBA, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR017945 DHBP_synth_RibB-like_a/b_dom
IPR000422 DHBP_synthase_RibB
IPR032677 GTP_cyclohydro_II
IPR000926 RibA
IPR036144 RibA-like_sf
IPR016299 Riboflavin_synth_RibBA

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00926 DHBP_synthase, 1 hit
PF00925 GTP_cyclohydro2, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF142695 SSF142695, 1 hit
SSF55821 SSF55821, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00505 ribA, 1 hit
TIGR00506 ribB, 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.

Q741F1-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTRLDSVERA VADIAAGKAV IVIDDEDREN EGDLIFAAEK ATPEMVAFMV
60 70 80 90 100
RYTSGYLCVP LDGAICDRLG LLPMYAVNQD KHGTAYTVTV DARNGVGTGI
110 120 130 140 150
SASDRATTMR LLADPTSIAE DFTRPGHVVP LRAKDGGVLR RPGHTEAAVD
160 170 180 190 200
LARMAGLQPA GAICEIVSQK DEGSMAQTDE LRVFADEHDL AMITIADLIE
210 220 230 240 250
WRRKHEKHIE RIAEARIPTR HGEFRAIGYT SIYEEVEHVA LVRGEIAGPN
260 270 280 290 300
SDGDDVLVRV HSECLTGDVF GSRRCDCGPQ LDAAMAMVAR EGRGIVLYMR
310 320 330 340 350
GHEGRGIGLM HKLQAYQLQD AGEDTVDANL KLGLPADARD YGIGAQILVD
360 370 380 390 400
LGVRSMRLLT NNPAKRVGLD GYGLHIIERV PLPVRTNAEN IRYLMTKRDK
410 420
MGHDLAGLDD FHESVHLPGE FGGAL
Length:425
Mass (Da):46,281
Last modified:July 5, 2004 - 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:iCBC99068A07B9A82
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

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DDBJi
Links Updated
AE016958 Genomic DNA Translation: AAS03457.1

NCBI Reference Sequences

More...
RefSeqi
WP_003877629.1, NC_002944.2

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAS03457; AAS03457; MAP_1140

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
2720077

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
mpa:MAP_1140

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|262316.17.peg.1199

<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
AE016958 Genomic DNA Translation: AAS03457.1
RefSeqiWP_003877629.1, NC_002944.2

3D structure databases

ProteinModelPortaliQ741F1
SMRiQ741F1
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi262316.MAP1140

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAS03457; AAS03457; MAP_1140
GeneIDi2720077
KEGGimpa:MAP_1140
PATRICifig|262316.17.peg.1199

Phylogenomic databases

eggNOGiENOG4105C66 Bacteria
COG0108 LUCA
COG0807 LUCA
KOiK14652
OMAiGCTTGIS
OrthoDBiPOG091H008U

Enzyme and pathway databases

UniPathwayi
UPA00275;UER00399

UPA00275;UER00400

BioCyciMAVI262316:G1G0E-1196-MONOMER

Family and domain databases

CDDicd00641 GTP_cyclohydro2, 1 hit
Gene3Di3.40.50.10990, 1 hit
HAMAPiMF_00179 RibA, 1 hit
MF_00180 RibB, 1 hit
MF_01283 RibBA, 1 hit
InterProiView protein in InterPro
IPR017945 DHBP_synth_RibB-like_a/b_dom
IPR000422 DHBP_synthase_RibB
IPR032677 GTP_cyclohydro_II
IPR000926 RibA
IPR036144 RibA-like_sf
IPR016299 Riboflavin_synth_RibBA
PfamiView protein in Pfam
PF00926 DHBP_synthase, 1 hit
PF00925 GTP_cyclohydro2, 1 hit
SUPFAMiSSF142695 SSF142695, 1 hit
SSF55821 SSF55821, 1 hit
TIGRFAMsiTIGR00505 ribA, 1 hit
TIGR00506 ribB, 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 nameiRIBBA_MYCPA
<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: Q741F1
<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: February 5, 2008
Last sequence update: July 5, 2004
Last modified: December 5, 2018
This is version 97 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 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
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