PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sopim11g065840.0.1
Organism
Solanum pimpinellifolium
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family MYB
Protein Properties Length: 354aa    MW: 39459.8 Da    PI: 6.5077
Description MYB family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sopim11g065840.0.1genomeCSHLView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Myb_DNA-binding46.58.4e-153279148
                        TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHHT CS
     Myb_DNA-binding  1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqkyl 48
                        +g W++eEde+l ++    G g+W+ +ar  g+ R++k+c++rw +yl
  Sopim11g065840.0.1 32 KGLWSPEEDEKLMHYMLTNGQGCWSDVARNAGLQRCGKSCRLRWINYL 79
                        678*******************************************97 PP
2Myb_DNA-binding50.26e-1685129147
                         TSSS-HHHHHHHHHHHHHTTTT-HHHHHHHHTTTS-HHHHHHHHHHH CS
     Myb_DNA-binding   1 rgrWTteEdellvdavkqlGggtWktIartmgkgRtlkqcksrwqky 47 
                         rg+++++E+e +++++  lG++ W+ Ia++++ gRt++++k++w++ 
  Sopim11g065840.0.1  85 RGAFSPQEEEHIIHLHSILGNR-WSQIAARLP-GRTDNEIKNFWNST 129
                         89********************.*********.***********986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5129416.5862779IPR017930Myb domain
SuperFamilySSF466895.86E-2830126IPR009057Homeodomain-like
SMARTSM007171.4E-103181IPR001005SANT/Myb domain
PfamPF002491.7E-133279IPR001005SANT/Myb domain
Gene3DG3DSA:1.10.10.601.2E-223386IPR009057Homeodomain-like
CDDcd001678.79E-93579No hitNo description
PROSITE profilePS5129424.88280134IPR017930Myb domain
SMARTSM007171.1E-1484132IPR001005SANT/Myb domain
PfamPF002491.6E-1485129IPR001005SANT/Myb domain
CDDcd001674.15E-1087130No hitNo description
Gene3DG3DSA:1.10.10.605.6E-2687135IPR009057Homeodomain-like
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:2000652Biological Processregulation of secondary cell wall biogenesis
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 354 aa     Download sequence    Send to blast
MRKPEFSSSS SSSSAKNNNN NNNNNTNVKL RKGLWSPEED EKLMHYMLTN GQGCWSDVAR  60
NAGLQRCGKS CRLRWINYLR PDLKRGAFSP QEEEHIIHLH SILGNRWSQI AARLPGRTDN  120
EIKNFWNSTL KKRLKNSSSS STPSPNASDS SSDHPSKELN MGVTQQGFMP MLKHNLMSMY  180
MDSTTSPSSS SIALNTINID PLPTLEHTLI NMPNGFNAPS YLSTTQPCLV QGGNIVSANG  240
GNLFYGNNHG IFGGNLSMEG HELYVPPLEN VSIEYQNVEN GNFSHHQNNN NPNNMTNLIN  300
TSHNFNTCSN IKVENFGGIG NYWEGDDLKV GEWDLEELMK DVSPFPFLDF QVE*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1a5j_A6e-26301345108B-MYB
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtTranscription factor that acts as molecular switch in the NAC012/SND1-mediated transcriptional network regulating secondary wall biosynthesis. Is directly activated by NAC012/SND1 and its close homologs, including NAC043/NST1, NAC066/NST2, NAC101/VND6 and NAC030/VND7. Is required for functional expression of a number of secondary wall-associated transcription factors and secondary wall biosynthetic genes involved in cellulose, xylan and lignin synthesis. Functions redundantly with MYB46 in the transcriptional regulatory cascade leading to secondary wall formation in fibers and vessels (PubMed:19808805). Transcription activator that binds to the DNA consensus sequence 5'-ACC[AT]A[AC][TC]-3', designated as the secondary wall MYB-responsive element (SMRE). Regulates directly numerous transcription factors and a number of genes involved in secondary wall biosynthesis that contain SMRE elements in their promoters (PubMed:22197883). {ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:22197883}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00336DAPTransfer from AT3G08500Download
Motif logo
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankHG9755230.0HG975523.1 Solanum lycopersicum chromosome ch11, complete genome.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004251366.10.0transcription factor MYB83
SwissprotQ9C6U18e-86MYB83_ARATH; Transcription factor MYB83
TrEMBLA0A3Q7JNQ00.0A0A3Q7JNQ0_SOLLC; Uncharacterized protein
STRINGSolyc11g065840.1.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA12242154
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G08500.12e-77myb domain protein 83
Publications ? help Back to Top
  1. Vargas L, et al.
    Improving total saccharification yield of Arabidopsis plants by vessel-specific complementation of caffeoyl shikimate esterase (cse) mutants.
    Biotechnol Biofuels, 2016. 9: p. 139
    [PMID:27390589]
  2. Piya S,Kihm C,Rice JH,Baum TJ,Hewezi T
    Cooperative Regulatory Functions of miR858 and MYB83 during Cyst Nematode Parasitism.
    Plant Physiol., 2017. 174(3): p. 1897-1912
    [PMID:28512179]