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

SMil_00022219-RA_Salv

Organism

Salvia miltiorrhiza

Taxonomic ID

226208

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Salvia

Family

LBD

Protein Properties

Length: 126aa MW: 13096.2 Da PI: 9.3412

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
SMil_00022219-RA_Salv	genome	NDCTCM	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	123.4	1.2e-38	22	110	1	88
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqql 87 +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p ++r+da+ +++yeA+ar+rdPvyG+v++i++lqqq+ SMil_00022219-RA_Salv 22 PCGACKFLRRKCVAGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHIPVQKRPDAVVTICYEAQARLRDPVYGCVAHIFALQQQV 109 7*********************9989*********************************************************9 PP DUF260 88 e 88 SMil_00022219-RA_Salv 110 Y 110 6 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	21.658	21	123	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	5.3E-38	22	110	IPR004883	Lateral organ boundaries, LOB

Sequence ? help Back to Top
Protein Sequence Length: 126 aa Download sequence Send to blast
MSPAGGGGSS SSGGGGAGGG GPCGACKFLR RKCVAGCIFA PYFDSEQGAA HFAAVHKVFG 60 ASNVSKLLLH IPVQKRPDAV VTICYEAQAR LRDPVYGCVA HIFALQQQVY IYILSLSRAP 120 SLRVLI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5ly0_A	1e-36	18	110	7	98	LOB family transfactor Ramosa2.1
5ly0_B	1e-36	18	110	7	98	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}.

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

Annotation -- Nucleotide ? help Back to Top
Source	Hit ID	E-value	Description
GenBank	AC118672	5e-83	AC118672.3 Genomic sequence for Oryza sativa, Nipponbare strain, clone OSJNBb0078P24, from chromosome 3, complete sequence.
GenBank	AC226706	5e-83	AC226706.2 Oryza minuta clone OM__Ba0084M12, complete sequence.
GenBank	AP014959	5e-83	AP014959.1 Oryza sativa Japonica Group DNA, chromosome 3, cultivar: Nipponbare, complete sequence.
GenBank	CP012611	5e-83	CP012611.1 Oryza sativa Indica Group cultivar RP Bio-226 chromosome 3 sequence.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_028109183.1	6e-58	LOB domain-containing protein 18-like
Swissprot	O22131	1e-51	LBD18_ARATH; LOB domain-containing protein 18
TrEMBL	M1AYU8	1e-56	M1AYU8_SOLTU; Uncharacterized protein
STRING	PGSC0003DMT400033253	2e-57	(Solanum tuberosum)
STRING	GSMUA_Achr5P11330_001	3e-56	(Musa acuminata)

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
AT2G45420.1	4e-52	LOB domain-containing protein 18

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]