PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID evm_27.model.AmTr_v1.0_scaffold00041.18
Common NameAMTR_s00041p00044170, LOC18441516
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; basal Magnoliophyta; Amborellales; Amborellaceae; Amborella
Family LBD
Protein Properties Length: 218aa    MW: 22780.8 Da    PI: 8.3868
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
evm_27.model.AmTr_v1.0_scaffold00041.18genomeTAGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260129.71.2e-40151151100
                                   DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAeara 69 
                                              +C aCk+lrrkC+++Cv+apyf +eq +++fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+
  evm_27.model.AmTr_v1.0_scaffold00041.18  15 PCGACKFLRRKCVSGCVFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHIPAHKRLDAVVTVCYEAQARL 84 
                                              7***********************9989****************************************** PP

                                   DUF260  70 rdPvyGavgvilklqqqleqlkaelallkee 100
                                              rdPvyG+v++i++lqqq+++l+aela+++++
  evm_27.model.AmTr_v1.0_scaffold00041.18  85 RDPVYGCVAHIFALQQQVMNLQAELAYMQAH 115
                                              **************************99986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.99914116IPR004883Lateral organ boundaries, LOB
PfamPF031951.1E-3915113IPR004883Lateral organ boundaries, LOB
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010089Biological Processxylem development
GO:0010311Biological Processlateral root formation
GO:0005634Cellular Componentnucleus
Sequence ? help Back to Top
Protein Sequence    Length: 218 aa     Download sequence    Send to blast
MSSGGGGGGG GGNGPCGACK FLRRKCVSGC VFAPYFDSEQ GAAHFAAVHK VFGASNVSKL  60
LLHIPAHKRL DAVVTVCYEA QARLRDPVYG CVAHIFALQQ QVMNLQAELA YMQAHLSTME  120
LPPPPPPPPA PSQPSAAFMS TSPDLIASSS NSNFDLSALF DHHSHYVIDP ASRFYRSQPD  180
PAVTAGGAAG GELHALAREL LTRRRSSPGP STKALSN*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A2e-37111097104LOB family transfactor Ramosa2.1
5ly0_B2e-37111097104LOB family transfactor Ramosa2.1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved 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
MP00314DAPTransfer from AT2G45420Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: 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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006851815.11e-158LOB domain-containing protein 18
SwissprotO221312e-65LBD18_ARATH; LOB domain-containing protein 18
TrEMBLW1PTE31e-156W1PTE3_AMBTC; Uncharacterized protein
STRINGERN132821e-157(Amborella trichopoda)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP40515100
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45420.13e-64LOB domain-containing protein 18
Publications ? help Back to Top
  1. 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]
  2. Amborella Genome Project
    The Amborella genome and the evolution of flowering plants.
    Science, 2013. 342(6165): p. 1241089
    [PMID:24357323]
  3. 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]
  4. 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]
  5. 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]
  6. 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]