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Entry version 71 (13 Feb 2019)
Sequence version 2 (11 Sep 2007)
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Protein

Phytochrome B

Gene

PHYB

Organism
Oryza sativa subsp. indica (Rice)
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

Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region. Photoconversion of Pr to Pfr induces an array of morphogenic responses, whereas reconversion of Pfr to Pr cancels the induction of those responses. Pfr controls the expression of a number of nuclear genes including those encoding the small subunit of ribulose-bisphosphate carboxylase, chlorophyll A/B binding protein, protochlorophyllide reductase, rRNA, etc. It also controls the expression of its own gene(s) in a negative feedback fashion.

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 sitei364Phytochromobilin chromophore (covalent; via 1 link)By similarity1

<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 functionPhotoreceptor protein, Receptor
Biological processSensory transduction, Transcription, Transcription regulation
LigandChromophore

<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:
Phytochrome B
<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:PHYB
Synonyms:PHYB1
ORF Names:OsI_010955
<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>OrganismiOryza sativa subsp. indica (Rice)
<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 identifieri39946 [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 lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
<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
  • UP000007015 <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 3

<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_00003008601 – 1171Phytochrome BAdd BLAST1171

<p>This subsection of the <a href="http://www.uniprot.org/help/ptm_processing_section">PTM/processing</a> section describes post-translational modifications (PTMs). This subsection <strong>complements</strong> the information provided at the sequence level or describes modifications for which <strong>position-specific data is not yet available</strong>.<p><a href='/help/post-translational_modification' target='_top'>More...</a></p>Post-translational modificationi

Contains one covalently linked phytochromobilin chromophore.By similarity

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
A2XFW2

<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.

GO - Molecular functioni

<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
A2XFW2

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

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">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>Domaini259 – 442GAFAdd BLAST184
Domaini661 – 732PAS 1PROSITE-ProRule annotationAdd BLAST72
Domaini795 – 866PAS 2PROSITE-ProRule annotationAdd BLAST72
Domaini943 – 1161Histidine kinasePROSITE-ProRule annotationAdd BLAST219

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes the position of regions of compositional bias within the protein and the particular amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi39 – 51Poly-GlyAdd BLAST13

<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 phytochrome family.Curated

Keywords - Domaini

Repeat

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG410YKN2 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000272703

Family and domain databases

Conserved Domains Database

More...
CDDi
cd00075 HATPase_c, 1 hit
cd00082 HisKA, 1 hit
cd00130 PAS, 2 hits

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.450.40, 1 hit
3.30.565.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR003018 GAF
IPR029016 GAF-like_dom_sf
IPR003594 HATPase_C
IPR036890 HATPase_C_sf
IPR005467 His_kinase_dom
IPR003661 HisK_dim/P
IPR036097 HisK_dim/P_sf
IPR000014 PAS
IPR035965 PAS-like_dom_sf
IPR013654 PAS_2
IPR013767 PAS_fold
IPR016132 Phyto_chromo_attachment
IPR013516 Phyto_chromo_BS
IPR001294 Phytochrome
IPR012129 Phytochrome_A-E
IPR013515 Phytochrome_cen-reg

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01590 GAF, 1 hit
PF02518 HATPase_c, 1 hit
PF00512 HisKA, 1 hit
PF00989 PAS, 2 hits
PF08446 PAS_2, 1 hit
PF00360 PHY, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF000084 Phytochrome, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR01033 PHYTOCHROME

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00065 GAF, 1 hit
SM00387 HATPase_c, 1 hit
SM00388 HisKA, 1 hit
SM00091 PAS, 2 hits

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47384 SSF47384, 1 hit
SSF55785 SSF55785, 3 hits
SSF55874 SSF55874, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00229 sensory_box, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS50109 HIS_KIN, 1 hit
PS50112 PAS, 2 hits
PS00245 PHYTOCHROME_1, 1 hit
PS50046 PHYTOCHROME_2, 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.

A2XFW2-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MASGSRATPT RSPSSARPAA PRHQHHHSQS SGGSTSRAGG GGGGGGGGGG
60 70 80 90 100
GAAAAESVSK AVAQYTLDAR LHAVFEQSGA SGRSFDYTQS LRASPTPSSE
110 120 130 140 150
QQIAAYLSRI QRGGHIQPFG CTLAVADDSS FRLLAYSENT ADLLDLSPHH
160 170 180 190 200
SVPSLDSSAV PPPVSLGADA RLLFAPSSAV LLERAFAARE ISLLNPLWIH
210 220 230 240 250
SRVSSKPFYA ILHRIDVGVV IDLEPARTED PALSIAGAVQ SQKLAVRAIS
260 270 280 290 300
RLQALPGGDV KLLCDTVVEH VRELTGYDRV MVYRFHEDEH GEVVAESRRN
310 320 330 340 350
NLEPYIGLHY PATDIPQASR FLFRQNRVRM IADCHAAPVR VIQDPALTQP
360 370 380 390 400
LCLVGSTLRS PHGCHAQYMA NMGSIASLVM AVIISSGGDD DHNISRGSIP
410 420 430 440 450
SAMKLWGLVV CHHTSPRCIP FPLRYACEFL MQAFGLQLNM ELQLAHQLSE
460 470 480 490 500
KHILRTQTLL CDMLLRDSPT GIVTQSPSIM DLVKCDGAAL YYHGKYYPLG
510 520 530 540 550
VTPTEVQIKD IIEWLTMCHG DSTGLSTDSL ADAGYPGAAA LGDAVSGMAV
560 570 580 590 600
AYITPSDYLF WFRSHTAKEI KWGGAKHHPE DKDDGQRMHP RSSFKAFLEV
610 620 630 640 650
VKSRSLPWEN AEMDAIHSLQ LILRDSFRDS AEGTSNSKAI VNGQVQLGEL
660 670 680 690 700
ELRGIDELSS VAREMVRLIE TATVPIFAVD TDGCINGWNA KVAELTGLSV
710 720 730 740 750
EEAMGKSLVN DLIFKESEET VNKLLSRALR GDEDKNVEIK LKTFGPEQSK
760 770 780 790 800
GPIFVIVNAC SSRDYTKNIV GVCFVGQDVT GQKVVMDKFI NIQGDYKAIV
810 820 830 840 850
HNPNPLIPPI FASDENTCCS EWNTAMEKLT GWSRGEVVGK LLVGEVFGNC
860 870 880 890 900
CRLKGPDALT KFMIVLHNAI GGQDCEKFPF SFFDKNGKYV QALLTANTRS
910 920 930 940 950
RMDGEAIGAF CFLQIASPEL QQAFEIQRHH EKKCYARMKE LAYIYQEIKN
960 970 980 990 1000
PLNGIRFTNS LLEMTDLKDD QRQFLETSTA CEKQMSKIVK DASLQSIEDG
1010 1020 1030 1040 1050
SLVLEKGEFS LGSVMNAVVS QVMIQLRERD LQLIRDIPDE IKEASAYGDQ
1060 1070 1080 1090 1100
YRIQQVLCDF LLSMVRFAPA ENGWVEIQVR PNIKQNSDGT DTMLFPFRFA
1110 1120 1130 1140 1150
CPGEGLPPEI VQDMFSNSRW TTQEGIGLSI CRKILKLMGG EVQYIRESER
1160 1170
SFFHIVLELP QPQQAASRGT S
Length:1,171
Mass (Da):128,451
Last modified:September 11, 2007 - 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:iB5DFBD9D230C3A08
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 conflicti206K → N in CAA40795 (PubMed:2005872).Curated1
Sequence conflicti245A → V in CAA40795 (PubMed:2005872).Curated1
Sequence conflicti366A → G in CAA40795 (PubMed:2005872).Curated1
Sequence conflicti457Q → G in CAA40795 (PubMed:2005872).Curated1
Sequence conflicti540A → D in CAA40795 (PubMed:2005872).Curated1
Sequence conflicti762S → T in CAA40795 (PubMed:2005872).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
X57563 Genomic DNA Translation: CAA40795.2
CM000128 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...
PIRi
S14065

<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
X57563 Genomic DNA Translation: CAA40795.2
CM000128 Genomic DNA No translation available.
PIRiS14065

3D structure databases

ProteinModelPortaliA2XFW2
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PRIDEiA2XFW2

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG410YKN2 LUCA
HOGENOMiHOG000272703

Family and domain databases

CDDicd00075 HATPase_c, 1 hit
cd00082 HisKA, 1 hit
cd00130 PAS, 2 hits
Gene3Di3.30.450.40, 1 hit
3.30.565.10, 1 hit
InterProiView protein in InterPro
IPR003018 GAF
IPR029016 GAF-like_dom_sf
IPR003594 HATPase_C
IPR036890 HATPase_C_sf
IPR005467 His_kinase_dom
IPR003661 HisK_dim/P
IPR036097 HisK_dim/P_sf
IPR000014 PAS
IPR035965 PAS-like_dom_sf
IPR013654 PAS_2
IPR013767 PAS_fold
IPR016132 Phyto_chromo_attachment
IPR013516 Phyto_chromo_BS
IPR001294 Phytochrome
IPR012129 Phytochrome_A-E
IPR013515 Phytochrome_cen-reg
PfamiView protein in Pfam
PF01590 GAF, 1 hit
PF02518 HATPase_c, 1 hit
PF00512 HisKA, 1 hit
PF00989 PAS, 2 hits
PF08446 PAS_2, 1 hit
PF00360 PHY, 1 hit
PIRSFiPIRSF000084 Phytochrome, 1 hit
PRINTSiPR01033 PHYTOCHROME
SMARTiView protein in SMART
SM00065 GAF, 1 hit
SM00387 HATPase_c, 1 hit
SM00388 HisKA, 1 hit
SM00091 PAS, 2 hits
SUPFAMiSSF47384 SSF47384, 1 hit
SSF55785 SSF55785, 3 hits
SSF55874 SSF55874, 1 hit
TIGRFAMsiTIGR00229 sensory_box, 1 hit
PROSITEiView protein in PROSITE
PS50109 HIS_KIN, 1 hit
PS50112 PAS, 2 hits
PS00245 PHYTOCHROME_1, 1 hit
PS50046 PHYTOCHROME_2, 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 nameiPHYB_ORYSI
<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: A2XFW2
Secondary accession number(s): P25764, Q84LN8
<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: September 11, 2007
Last sequence update: September 11, 2007
Last modified: February 13, 2019
This is version 71 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 programPlant 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
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