PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

PlantRegMap/PlantTFDB v5.0

Plant Transcription Factor Database

Transcription Factor Information

Basic Information | Signature Domain | Sequence |

Basic Information? help Back to Top

TF ID

Phvul.003G110100.1

Common Name

PHAVU_003G110100g

Organism

Phaseolus vulgaris

Taxonomic ID

3885

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus

Family

ARR-B

Protein Properties

Length: 680aa MW: 74210.4 Da PI: 6.0455

Description

ARR-B family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Phvul.003G110100.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	G2-like	90.4	1.6e-28	213	266	1	55
G2-like 1 kprlrWtpeLHerFveaveqLGGsekAtPktilelmkvkgLtlehvkSHLQkYRl 55 kpr++W+ eLH++Fv av+qL G++kA+Pk+ilelm+v+gLt+e+v+SHLQkYRl Phvul.003G110100.1 213 KPRVVWSVELHQQFVAAVDQL-GIDKAVPKKILELMNVPGLTRENVASHLQKYRL 266 79*****************.******************************8 PP
2	Response_reg	76.3	1.1e-25	35	143	1	109
EEEESSSHHHHHHHHHHHHHTTCEEEEEESSHHHHHHHHHHHH..ESEEEEESSCTTSEHHHHHHHHHHHTTTSEEEEEESTTTHHHHHHH CS Response_reg 1 vlivdDeplvrellrqalekegyeevaeaddgeealellkekd..pDlillDiempgmdGlellkeireeepklpiivvtahgeeedalea 89 vl+vdD+p+ +++l+++l+ y ev+ + +e al ll+e++ +D+++ D+ mp+mdG++ll++i e +lp+i+++a + ++ + + Phvul.003G110100.1 35 VLVVDDDPTCLMILEKMLRTCLY-EVTKCNRAETALSLLRENKngFDIVISDVHMPDMDGFKLLEHIGLEM-DLPVIMMSADDGKSVVMKG 123 89*******************.***********999999******************6654.8************** PP HHTTESEEEESS--HHHHHH CS Response_reg 90 lkaGakdflsKpfdpeelvk 109 + Ga d+l Kp+ +e+l + Phvul.003G110100.1 124 VTHGACDYLIKPVRIEALKN 143 **************9986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PIRSF	PIRSF036392	2.2E-185	12	671	IPR017053	Response regulator B-type, plant
SuperFamily	SSF52172	2.99E-35	32	155	IPR011006	CheY-like superfamily
Gene3D	G3DSA:3.40.50.2300	2.1E-42	32	173	No hit	No description
SMART	SM00448	1.8E-30	33	145	IPR001789	Signal transduction response regulator, receiver domain
PROSITE profile	PS50110	42.514	34	149	IPR001789	Signal transduction response regulator, receiver domain
Pfam	PF00072	5.4E-23	35	143	IPR001789	Signal transduction response regulator, receiver domain
CDD	cd00156	3.45E-27	36	148	No hit	No description
SuperFamily	SSF46689	6.63E-20	210	270	IPR009057	Homeodomain-like
PROSITE profile	PS51294	11.518	210	269	IPR017930	Myb domain
Gene3D	G3DSA:1.10.10.60	5.3E-30	212	271	IPR009057	Homeodomain-like
TIGRFAMs	TIGR01557	7.3E-25	213	266	IPR006447	Myb domain, plants
Pfam	PF00249	2.9E-7	215	265	IPR001005	SANT/Myb domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006355	Biological Process	regulation of transcription, DNA-templated
GO:0009414	Biological Process	response to water deprivation
GO:0009873	Biological Process	ethylene-activated signaling pathway
GO:0010082	Biological Process	regulation of root meristem growth
GO:0010119	Biological Process	regulation of stomatal movement
GO:0010150	Biological Process	leaf senescence
GO:0010380	Biological Process	regulation of chlorophyll biosynthetic process
GO:0031537	Biological Process	regulation of anthocyanin metabolic process
GO:0080022	Biological Process	primary root development
GO:0080036	Biological Process	regulation of cytokinin-activated signaling pathway
GO:0080113	Biological Process	regulation of seed growth
GO:0005634	Cellular Component	nucleus
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 680 aa Download sequence Send to blast
MNLSNGKGSM STVTTTAVMK SGDAVSDQFP AGLRVLVVDD DPTCLMILEK MLRTCLYEVT 60 KCNRAETALS LLRENKNGFD IVISDVHMPD MDGFKLLEHI GLEMDLPVIM MSADDGKSVV 120 MKGVTHGACD YLIKPVRIEA LKNIWQHVVR KKKNEWKDAE QSGSAEEGDR QPKASDEADY 180 SSSANEGSWR NSKKRRDEEE EAEDRDDTST LKKPRVVWSV ELHQQFVAAV DQLGIDKAVP 240 KKILELMNVP GLTRENVASH LQKYRLYLRR LSGVSQHQNN LNNSFLGSQE ATFGTISSIN 300 GIDLQTLAVT GQLPAQSLAT LQAAGLGRST AKTGVPMPLM DQRNLFSFEN PRVRFGEGQQ 360 QHLSSSKPMN LLLGIPTNME PKQLANLHQS TQSIASLNMR VNASATQGNP LMMQMPQSQP 420 RGQMLSENTG PRVPRLPSSL GQPTVSNGIS NGFLGRNGIA GNNRGPAYNP VPPNSSLLSF 480 PMNQSSEVSV NNSLPLGSSP GISSITTKGS FQEEVTSGIK ATGGFPSYDI FNELHHQKSH 540 DWEITNPSLT YSASHHANPL QGNIDVSPSV LVHQGFSSTQ QNGQSRDATL IGKAMFSLGE 600 GSEQDNLQNA VQHLHPLLVD NSIRVKAERI PDASSQTNLF PDHYVQEDLM SALLKQQEGM 660 GPAESEFEFD AYSLDNIPV*

Sequence ? help Back to Top

Protein Sequence Length: 680 aa Download sequence Send to blast

MNLSNGKGSM STVTTTAVMK SGDAVSDQFP AGLRVLVVDD DPTCLMILEK MLRTCLYEVT  60
KCNRAETALS LLRENKNGFD IVISDVHMPD MDGFKLLEHI GLEMDLPVIM MSADDGKSVV  120
MKGVTHGACD YLIKPVRIEA LKNIWQHVVR KKKNEWKDAE QSGSAEEGDR QPKASDEADY  180
SSSANEGSWR NSKKRRDEEE EAEDRDDTST LKKPRVVWSV ELHQQFVAAV DQLGIDKAVP  240
KKILELMNVP GLTRENVASH LQKYRLYLRR LSGVSQHQNN LNNSFLGSQE ATFGTISSIN  300
GIDLQTLAVT GQLPAQSLAT LQAAGLGRST AKTGVPMPLM DQRNLFSFEN PRVRFGEGQQ  360
QHLSSSKPMN LLLGIPTNME PKQLANLHQS TQSIASLNMR VNASATQGNP LMMQMPQSQP  420
RGQMLSENTG PRVPRLPSSL GQPTVSNGIS NGFLGRNGIA GNNRGPAYNP VPPNSSLLSF  480
PMNQSSEVSV NNSLPLGSSP GISSITTKGS FQEEVTSGIK ATGGFPSYDI FNELHHQKSH  540
DWEITNPSLT YSASHHANPL QGNIDVSPSV LVHQGFSSTQ QNGQSRDATL IGKAMFSLGE  600
GSEQDNLQNA VQHLHPLLVD NSIRVKAERI PDASSQTNLF PDHYVQEDLM SALLKQQEGM  660
GPAESEFEFD AYSLDNIPV*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
1irz_A	1e-22	212	272	4	64	ARR10-B
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins. Involved in the expression of nuclear genes for components of mitochondrial complex I. Promotes cytokinin-mediated leaf longevity. Involved in the ethylene signaling pathway in an ETR1-dependent manner and in the cytokinin signaling pathway. {ECO:0000269\|PubMed:11370868, ECO:0000269\|PubMed:11574878, ECO:0000269\|PubMed:15282545, ECO:0000269\|PubMed:16407152}.
UniProt	Transcriptional activator that binds specifically to the DNA sequence 5'-[AG]GATT-3'. Functions as a response regulator involved in His-to-Asp phosphorelay signal transduction system. Phosphorylation of the Asp residue in the receiver domain activates the ability of the protein to promote the transcription of target genes. Could directly activate some type-A response regulators in response to cytokinins. Regulates SHY2 by binding to its promoter (PubMed:19039136). Involved in the root-meristem size determination through the regulation of cell differentiation (PubMed:17363254). {ECO:0000269\|PubMed:11574878, ECO:0000269\|PubMed:11691951, ECO:0000269\|PubMed:17363254, ECO:0000269\|PubMed:19039136}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00054	PBM	Transfer from AT4G16110	Download

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Phvul.003G110100.1

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Down-regulated by gibberellin. {ECO:0000269\|PubMed:20605455}.

Regulation -- PlantRegMap ? help Back to Top
Source	Upstream Regulator	Target Gene
PlantRegMap	Retrieve	Retrieve

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AP015034	0.0	AP015034.1 Vigna angularis var. angularis DNA, chromosome 1, almost complete sequence, cultivar: Shumari.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_007154337.1	0.0	hypothetical protein PHAVU_003G110100g
Swissprot	Q940D0	0.0	ARR1_ARATH; Two-component response regulator ARR1
Swissprot	Q9ZWJ9	0.0	ARR2_ARATH; Two-component response regulator ARR2
TrEMBL	V7CBR1	0.0	V7CBR1_PHAVU; Two-component response regulator
STRING	XP_007154337.1	0.0	(Phaseolus vulgaris)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF3958	34	58

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G16110.1	0.0	response regulator 2

Link Out ? help Back to Top
Phytozome	Phvul.003G110100.1
Entrez Gene	18634558

Publications ? help Back to Top
Bürkle L,Meyer S,Dortay H,Lehrach H,Heyl A In vitro recombination cloning of entire cDNA libraries in Arabidopsis thaliana and its application to the yeast two-hybrid system. Funct. Integr. Genomics, 2005. 5(3): p. 175-83 [PMID:15714319] Moubayidin L, et al. Spatial coordination between stem cell activity and cell differentiation in the root meristem. Dev. Cell, 2013. 26(4): p. 405-15 [PMID:23987513] Takahashi N, et al. Cytokinins control endocycle onset by promoting the expression of an APC/C activator in Arabidopsis roots. Curr. Biol., 2013. 23(18): p. 1812-7 [PMID:24035544] Kurepa J,Li Y,Perry SE,Smalle JA Ectopic expression of the phosphomimic mutant version of Arabidopsis response regulator 1 promotes a constitutive cytokinin response phenotype. BMC Plant Biol., 2014. 14: p. 28 [PMID:24423196] Cortleven A, et al. A novel protective function for cytokinin in the light stress response is mediated by the Arabidopsis histidine kinase2 and Arabidopsis histidine kinase3 receptors. Plant Physiol., 2014. 164(3): p. 1470-83 [PMID:24424319] Ge XM, et al. Heterotrimeric G protein mediates ethylene-induced stomatal closure via hydrogen peroxide synthesis in Arabidopsis. Plant J., 2015. 82(1): p. 138-50 [PMID:25704455] Takahashi N,Umeda M Cytokinins promote onset of endoreplication by controlling cell cycle machinery. Plant Signal Behav, 2014. 9(8): p. e29396 [PMID:25763620] Marín-de la Rosa N, et al. Genome Wide Binding Site Analysis Reveals Transcriptional Coactivation of Cytokinin-Responsive Genes by DELLA Proteins. PLoS Genet., 2015. 11(7): p. e1005337 [PMID:26134422] D'Alessandro S,Golin S,Hardtke CS,Lo Schiavo F,Zottini M The co-chaperone p23 controls root development through the modulation of auxin distribution in the Arabidopsis root meristem. J. Exp. Bot., 2015. 66(16): p. 5113-22 [PMID:26163704] Jiang L, et al. Strigolactones spatially influence lateral root development through the cytokinin signaling network. J. Exp. Bot., 2016. 67(1): p. 379-89 [PMID:26519957] Moubayidin L, et al. A SCARECROW-based regulatory circuit controls Arabidopsis thaliana meristem size from the root endodermis. Planta, 2016. 243(5): p. 1159-68 [PMID:26848984] Muraro D, et al. A multi-scale model of the interplay between cell signalling and hormone transport in specifying the root meristem of Arabidopsis thaliana. J. Theor. Biol., 2016. 404: p. 182-205 [PMID:27157127] Cortleven A, et al. Cytokinin Regulates the Etioplast-Chloroplast Transition through the Two-Component Signaling System and Activation of Chloroplast-Related Genes. Plant Physiol., 2016. 172(1): p. 464-78 [PMID:27388681] Kobayashi K, et al. Shoot Removal Induces Chloroplast Development in Roots via Cytokinin Signaling. Plant Physiol., 2017. 173(4): p. 2340-2355 [PMID:28193764] Arnaud D, et al. Cytokinin-Mediated Regulation of Reactive Oxygen Species Homeostasis Modulates Stomatal Immunity in Arabidopsis. Plant Cell, 2017. 29(3): p. 543-559 [PMID:28254779] Zhang TQ, et al. A Two-Step Model for de Novo Activation of WUSCHEL during Plant Shoot Regeneration. Plant Cell, 2017. 29(5): p. 1073-1087 [PMID:28389585] Kushwah S,Laxmi A The interaction between glucose and cytokinin signaling in controlling Arabidopsis thaliana seedling root growth and development. Plant Signal Behav, 2017. 12(5): p. e1312241 [PMID:28467152] Meng WJ, et al. Type-B ARABIDOPSIS RESPONSE REGULATORs Specify the Shoot Stem Cell Niche by Dual Regulation of WUSCHEL. Plant Cell, 2017. 29(6): p. 1357-1372 [PMID:28576846] Kobayashi K,Iwase A Simultaneous but spatially different regulation of non-photosynthetic callus formation and photosynthetic root development after shoot removal. Plant Signal Behav, 2017. 12(6): p. e1338999 [PMID:28594268] Liu B,De Storme N,Geelen D Cold interferes with male meiotic cytokinesis in Arabidopsis thaliana independently of the AHK2/3-AHP2/3/5 cytokinin signaling module. Cell Biol. Int., 2017. 41(8): p. 879-889 [PMID:28618065] Zhang F,May A,Irish VF Type-B ARABIDOPSIS RESPONSE REGULATORs Directly Activate WUSCHEL. Trends Plant Sci., 2017. 22(10): p. 815-817 [PMID:28886911] Yan Z, et al. Type B Response Regulators Act As Central Integrators in Transcriptional Control of the Auxin Biosynthesis Enzyme TAA1. Plant Physiol., 2017. 175(3): p. 1438-1454 [PMID:28931628] Rong XF, et al. Type-B ARRs Control Carpel Regeneration Through Mediating AGAMOUS Expression in Arabidopsis. Plant Cell Physiol., 2018. 59(4): p. 756-764 [PMID:29186581] Bustillo-Avendaño E, et al. Regulation of Hormonal Control, Cell Reprogramming, and Patterning during De Novo Root Organogenesis. Plant Physiol., 2018. 176(2): p. 1709-1727 [PMID:29233938] Waldie T,Leyser O Cytokinin Targets Auxin Transport to Promote Shoot Branching. Plant Physiol., 2018. 177(2): p. 803-818 [PMID:29717021] Takatsuka H,Higaki T,Umeda M Actin Reorganization Triggers Rapid Cell Elongation in Roots. Plant Physiol., 2018. 178(3): p. 1130-1141 [PMID:30185441]