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

cra_locus_5382_iso_5

Organism

Catharanthus roseus

Taxonomic ID

4058

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Gentianales; Apocynaceae; Rauvolfioideae; Vinceae; Catharanthinae; Catharanthus

Family

LBD

Protein Properties

Length: 214aa MW: 23225.6 Da PI: 7.9929

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
cra_locus_5382_iso_5	genome	MPGR	-

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	128.2	3.6e-40	8	109	1	101
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPv 73 +C aCk+lrrkCa+dC++apyf++eq p++fa++hk+FGasnv+k+l ++p ++r +a+ +++yeA+ar++dPv cra_locus_5382_iso_5_len_1050_ver_3 8 PCGACKFLRRKCAADCIFAPYFCSEQgPARFAAIHKVFGASNVSKMLLHVPVHDRCEAVVTIAYEAQARIKDPV 81 7***********************99****************************************** PP DUF260 74 yGavgvilklqqqleqlkaelallkeel 101 yG+v++i++lqqq++ l+a+++++k++l cra_locus_5382_iso_5_len_1050_ver_3 82 YGCVAHIFALQQQVAYLQAQVVQVKAQL 109 ********************999875 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.942	7	109	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	3.0E-38	8	106	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009626	Biological Process	plant-type hypersensitive response
GO:0009627	Biological Process	systemic acquired resistance
GO:0009697	Biological Process	salicylic acid biosynthetic process
GO:0009751	Biological Process	response to salicylic acid
GO:0010167	Biological Process	response to nitrate
GO:0010337	Biological Process	regulation of salicylic acid metabolic process
GO:0042742	Biological Process	defense response to bacterium
GO:0080021	Biological Process	response to benzoic acid
GO:0005634	Cellular Component	nucleus
GO:0005886	Cellular Component	plasma membrane
GO:0004842	Molecular Function	ubiquitin-protein transferase activity
GO:0005515	Molecular Function	protein binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 214 aa Download sequence Send to blast
MANGSGSPCG ACKFLRRKCA ADCIFAPYFC SEQGPARFAA IHKVFGASNV SKMLLHVPVH 60 DRCEAVVTIA YEAQARIKDP VYGCVAHIFA LQQQVAYLQA QVVQVKAQLA QTLMDSSRDN 120 QETGALQWPN NNMAGGIIGS SVFPTIPINY GNPISPQSSI CSIESSMEVP TNGDGFSMQE 180 MNMSPNFHQA YAKKRSSQTD LGELQALALR MMKN

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-37	4	109	7	111	LOB family transfactor Ramosa2.1
5ly0_B	1e-37	4	109	7	111	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional activator (PubMed:19717544, PubMed:22974309). Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19 (PubMed:17259263). Functions in the initiation and emergence of lateral roots, in conjunction with LBD18, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:26059335}.

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:17259263, ECO:0000269\|PubMed:23749813}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_027063574.1	1e-105	LOB domain-containing protein 16-like
Refseq	XP_027110460.1	1e-105	LOB domain-containing protein 16-like
Swissprot	Q9SLB7	4e-77	LBD16_ARATH; LOB domain-containing protein 16
TrEMBL	A0A068U6E5	1e-103	A0A068U6E5_COFCA; Uncharacterized protein
STRING	XP_009617763.1	5e-97	(Nicotiana tomentosiformis)

Publications ? help Back to Top
Bargmann BO,Birnbaum KD,Brenner ED An undergraduate study of two transcription factors that promote lateral root formation. Biochem Mol Biol Educ, 2014 May-Jun. 42(3): p. 237-45 [PMID:24615800] Cabrera J,Fenoll C,Escobar C Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis. Plant Signal Behav, 2015. 10(3): p. e990825 [PMID:25664644] Lee HW, et al. Dimerization in LBD16 and LBD18 Transcription Factors Is Critical for Lateral Root Formation. Plant Physiol., 2017. 174(1): p. 301-311 [PMID:28336771] Olmo R, et al. Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program? Front Plant Sci, 2017. 8: p. 875 [PMID:28603536] Lee K,Seo PJ High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis. Planta, 2017. 246(4): p. 797-802 [PMID:28766014] Jeon E, et al. LBD14/ASL17 Positively Regulates Lateral Root Formation and is Involved in ABA Response for Root Architecture in Arabidopsis. Plant Cell Physiol., 2017. 58(12): p. 2190-2201 [PMID:29040694] Pandey SK,Kim J Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis. Plant Signal Behav, 2018. 13(1): p. e1411450 [PMID:29227192] Xu C, et al. Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration. Nat Plants, 2018. 4(2): p. 108-115 [PMID:29358751] Liu J, et al. The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture. Plant Cell Physiol., 2018. 59(4): p. 734-743 [PMID:29361138] Lee HW, et al. LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis. BMC Plant Biol., 2019. 19(1): p. 46 [PMID:30704405]