PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum

Family

LBD

Protein Properties

Length: 275aa MW: 28090.9 Da PI: 7.7571

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Sme2.5_09999.1_g00001.1	genome	EGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	126.3	1.4e-39	46	146	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqq 85 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p ++r da++++++eA+ar+rdPvyG+v++i +lqq Sme2.5_09999.1_g00001.1 46 PCGACKFLRRKCVAGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHIPVHKRLDAVATICFEAQARLRDPVYGCVAHIINLQQ 131 7*********************9989****************************************************** PP DUF260 86 qleqlkaelallkee 100 q+ +l+ael +l+++ Sme2.5_09999.1_g00001.1 132 QVVNLQAELTYLQAH 146 ********99876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	22.791	45	147	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	1.6E-38	46	144	IPR004883	Lateral organ boundaries, LOB

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010089	Biological Process	xylem development
GO:0010311	Biological Process	lateral root formation
GO:0005634	Cellular Component	nucleus

Sequence ? help Back to Top
Protein Sequence Length: 275 aa Download sequence Send to blast
MSSNNPSSST GGGICGGTSG STSSGGGGCG GGGGGGGGGG GGGGGPCGAC KFLRRKCVAG 60 CIFAPYFDSE QGAAHFAAVH KVFGASNVSK LLLHIPVHKR LDAVATICFE AQARLRDPVY 120 GCVAHIINLQ QQVVNLQAEL TYLQAHLATL ELPTPPPLPP PPPPQQPQTM LQQPSLSIAD 180 LPTAGPSLPA AYDLSSLFDP MVQPSWAMQQ PRPPSPLPLD PRHHFSGGAR ATVDMPPSTG 240 GGGGDLQELA RELLHRHGSP TLPCRESPAL PPQTK

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	4e-36	42	140	7	104	LOB family transfactor Ramosa2.1
5ly0_B	4e-36	42	140	7	104	LOB family transfactor Ramosa2.1
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Functional Description ? help Back to Top
Source	Description
UniProt	Involved in the positive regulation of tracheary element (TE) differentiation. Involved in a positive feedback loop that maintains or promotes NAC030/VND7 expression that regulates TE differentiation-related genes (PubMed:19088331). Functions in the initiation and emergence of lateral roots, in conjunction with LBD16, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Transcriptional activator that directly regulates EXPA14, a gene encoding a cell wall-loosening factor that promotes lateral root emergence. Activates EXPA14 by directly binding to a specific region of its promoter (PubMed:22974309). Transcriptional activator that directly regulates EXPA17, a gene encoding a cell wall-loosening factor that promotes lateral root emergence (PubMed:23872272). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269\|PubMed:19088331, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:22974309, ECO:0000269\|PubMed:23749813, ECO:0000269\|PubMed:23872272, ECO:0000269\|PubMed:26059335}.

Binding Motif ? help Back to Top
Motif ID	Method	Source	Motif file
MP00314	DAP	Transfer from AT2G45420	Download

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: By auxin. {ECO:0000269\|PubMed:15659631, ECO:0000269\|PubMed:19717544, ECO:0000269\|PubMed:23749813}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	HG975513	1e-139	HG975513.1 Solanum lycopersicum chromosome ch01, complete genome.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009604912.1	1e-121	PREDICTED: LOB domain-containing protein 30-like
Refseq	XP_016514578.1	1e-121	PREDICTED: LOB domain-containing protein 30-like
Swissprot	O22131	4e-79	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	A0A1S4DME9	1e-120	A0A1S4DME9_TOBAC; LOB domain-containing protein 30-like
STRING	XP_009604912.1	1e-120	(Nicotiana tomentosiformis)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Asterids	OGEA43	24	669

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT4G00220.1	4e-79	LBD family protein

Publications ? help Back to Top
Heyndrickx KS,Vandepoele K Systematic identification of functional plant modules through the integration of complementary data sources. Plant Physiol., 2012. 159(3): p. 884-901 [PMID:22589469] 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] 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] Pandey SK, et al. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. Plant J., 2018. 95(2): p. 233-251 [PMID:29681137] 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]