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

XP_009595179.1

Organism

Nicotiana tomentosiformis

Taxonomic ID

4098

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana

Family

Protein Properties

Length: 858aa MW: 94450.4 Da PI: 6.3328

Description

B3 family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
XP_009595179.1	genome	NCBI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	B3	59.9	4.5e-19	338	437	1	98
EEEE-..-HHHHTT-EE--HHH.HTT..---..--SEEEEEETTS-EEEEEE....EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE. CS B3 1 ffkvltpsdvlksgrlvlpkkfaeeh..ggkkeesktltledesgrsWevkliy..rkksgryvltkGWkeFvkangLkegDfvvFkldgrsefe 91 f+kvl+ sd+++ grlvlpk +ae++ +++ + ++++d +g++W++++++ +++s++yvl+ G + +L++gD+v+F++++ +++ XP_009595179.1 338 FEKVLSASDAGRIGRLVLPKACAEAYfpPINQSDGLPIRIQDIKGKEWTFQFRFwpNNNSRMYVLE-GVTPCIQNMQLQAGDTVTFSRID-PGGK 430 99************************556666778***********99899999999.*******************887.7887 PP .EEEEE- CS B3 92 lvvkvfr 98 lv+++++ XP_009595179.1 431 LVMGFRK 437 8888776 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:2.40.330.10	1.6E-29	335	441	IPR015300	DNA-binding pseudobarrel domain
SuperFamily	SSF101936	6.02E-21	335	438	IPR015300	DNA-binding pseudobarrel domain
CDD	cd10017	6.38E-24	336	437	No hit	No description
Pfam	PF02362	2.2E-16	338	437	IPR003340	B3 DNA binding domain
PROSITE profile	PS50863	11.237	338	439	IPR003340	B3 DNA binding domain
SMART	SM01019	3.1E-22	338	438	IPR003340	B3 DNA binding domain
PROSITE profile	PS51050	14.538	562	612	IPR011124	Zinc finger, CW-type
Pfam	PF07496	4.8E-12	567	609	IPR011124	Zinc finger, CW-type

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0010030	Biological Process	positive regulation of seed germination
GO:0045892	Biological Process	negative regulation of transcription, DNA-templated
GO:2000034	Biological Process	regulation of seed maturation
GO:0005634	Cellular Component	nucleus
GO:0005739	Cellular Component	mitochondrion
GO:0003677	Molecular Function	DNA binding
GO:0008270	Molecular Function	zinc ion binding

Sequence ? help Back to Top
Protein Sequence Length: 858 aa Download sequence Send to blast
MGFLDLEILN MGSMICMNEV CRKTTSSEWK KGWSLKSGGF ANLCYNCGSA FENLSFCETF 60 HMGDSGWREC KMCGKHLHCG CIASKYLFEY LDFGGVGCIS CARCLDDHSM RPMQVPADDF 120 RDSAFGTNFI QPLHVEKGVD KTNFDKGRLP TVNNIMEISE PGQPFQSQKD ENNVSLGKTK 180 QEKVLPVGDV STCFSNLNQQ SIASLFREQD NSKPNQGVKE MYDTTNQPSL DFSLSTPVGC 240 SSSGLSFPDG GVEGREHEKT PFQQGLRTRH ILLKPLKPSP SFGSDSNKEL PSQTRIARPP 300 AEGRGGRNQL LPRYWPRITD QELCQLSGDL NSAIVPLFEK VLSASDAGRI GRLVLPKACA 360 EAYFPPINQS DGLPIRIQDI KGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ NMQLQAGDTV 420 TFSRIDPGGK LVMGFRKATN SVETQDPQSS HLPDGSGSAD TSFTGLTENL NNGGRTSADS 480 VHRQVPVSEK KKTTNIGSKN KRLLMHADDA MELRITWEES QELLRPPPTT QPTILVIEDC 540 EFEAYDEPPV FGKQTIFTSR PSGDQEQWAQ CDSCSKWRRL PMHVLLPPKW TCSDNIWDSN 600 RCSCSAPEEI KAKELEAFFR VSKGHKRQKI AGKNEDCEPS GLNALATVAV LGDSISDLGE 660 PLVGATTKHP RHRPGCTCIV CIQPPSGKGK HQPTCKCNAC LSAERRFKTL MLRKKKKQSE 720 REAEVAQAKD QVPPKDGSET DGASGAELMM QTSHSENERN TNGDHMEKVG AGKGQLDLNC 780 HPNREDEMLI EAAAGISMTS LINAADLPLD MYQTQNGLAT LDKCLLSLAT AGSEGQQPDN 840 GCVRPADAQV QENNGDNG

Sequence ? help Back to Top

Protein Sequence Length: 858 aa Download sequence Send to blast

MGFLDLEILN MGSMICMNEV CRKTTSSEWK KGWSLKSGGF ANLCYNCGSA FENLSFCETF  60
HMGDSGWREC KMCGKHLHCG CIASKYLFEY LDFGGVGCIS CARCLDDHSM RPMQVPADDF  120
RDSAFGTNFI QPLHVEKGVD KTNFDKGRLP TVNNIMEISE PGQPFQSQKD ENNVSLGKTK  180
QEKVLPVGDV STCFSNLNQQ SIASLFREQD NSKPNQGVKE MYDTTNQPSL DFSLSTPVGC  240
SSSGLSFPDG GVEGREHEKT PFQQGLRTRH ILLKPLKPSP SFGSDSNKEL PSQTRIARPP  300
AEGRGGRNQL LPRYWPRITD QELCQLSGDL NSAIVPLFEK VLSASDAGRI GRLVLPKACA  360
EAYFPPINQS DGLPIRIQDI KGKEWTFQFR FWPNNNSRMY VLEGVTPCIQ NMQLQAGDTV  420
TFSRIDPGGK LVMGFRKATN SVETQDPQSS HLPDGSGSAD TSFTGLTENL NNGGRTSADS  480
VHRQVPVSEK KKTTNIGSKN KRLLMHADDA MELRITWEES QELLRPPPTT QPTILVIEDC  540
EFEAYDEPPV FGKQTIFTSR PSGDQEQWAQ CDSCSKWRRL PMHVLLPPKW TCSDNIWDSN  600
RCSCSAPEEI KAKELEAFFR VSKGHKRQKI AGKNEDCEPS GLNALATVAV LGDSISDLGE  660
PLVGATTKHP RHRPGCTCIV CIQPPSGKGK HQPTCKCNAC LSAERRFKTL MLRKKKKQSE  720
REAEVAQAKD QVPPKDGSET DGASGAELMM QTSHSENERN TNGDHMEKVG AGKGQLDLNC  780
HPNREDEMLI EAAAGISMTS LINAADLPLD MYQTQNGLAT LDKCLLSLAT AGSEGQQPDN  840
GCVRPADAQV QENNGDNG

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
6j9a_A	5e-69	316	445	2	131	B3 domain-containing transcription repressor VAL1
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Transcriptional repressor of gene expression involved in embryonic pathways, such as LEC1, ABI3, and FUS3. Repressor of the sugar-inducible genes involved in the seed maturation program in seedlings. Plays an essential role in regulating the transition from seed maturation to seedling growth. Functionally redundant with VAL2/HSL1. {ECO:0000269\|PubMed:15894743, ECO:0000269\|PubMed:17158584, ECO:0000269\|PubMed:17267611}.

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

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_009595179.1	0.0	PREDICTED: B3 domain-containing transcription repressor VAL1-like isoform X2
Swissprot	Q6Z3U3	0.0	Y7797_ORYSJ; B3 domain-containing protein Os07g0679700
Swissprot	Q8W4L5	0.0	VAL1_ARATH; B3 domain-containing transcription repressor VAL1
TrEMBL	A0A1J6I6X9	0.0	A0A1J6I6X9_NICAT; B3 domain-containing protein
STRING	XP_009595178.1	0.0	(Nicotiana tomentosiformis)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT2G30470.1	0.0	high-level expression of sugar-inducible gene 2

Publications ? help Back to Top
Kikuchi S, et al. Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science, 2003. 301(5631): p. 376-9 [PMID:12869764] Jia H,McCarty DR,Suzuki M Distinct roles of LAFL network genes in promoting the embryonic seedling fate in the absence of VAL repression. Plant Physiol., 2013. 163(3): p. 1293-305 [PMID:24043445] Schneider A, et al. Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developing Arabidopsis thaliana embryos. Plant J., 2016. 85(2): p. 305-19 [PMID:26678037] Chhun T, et al. HSI2 Repressor Recruits MED13 and HDA6 to Down-Regulate Seed Maturation Gene Expression Directly During Arabidopsis Early Seedling Growth. Plant Cell Physiol., 2016. 57(8): p. 1689-706 [PMID:27335347] Qüesta JI,Song J,Geraldo N,An H,Dean C Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization. Science, 2016. 353(6298): p. 485-8 [PMID:27471304] Yuan W, et al. A cis cold memory element and a trans epigenome reader mediate Polycomb silencing of FLC by vernalization in Arabidopsis. Nat. Genet., 2016. 48(12): p. 1527-1534 [PMID:27819666] Merini W, et al. The Arabidopsis Polycomb Repressive Complex 1 (PRC1) Components AtBMI1A, B, and C Impact Gene Networks throughout All Stages of Plant Development. Plant Physiol., 2017. 173(1): p. 627-641 [PMID:27837089] Li C,Cui Y A DNA element that remembers winter. Nat. Genet., 2016. 48(12): p. 1451-1452 [PMID:27898079] Chen N,Veerappan V,Abdelmageed H,Kang M,Allen RD HSI2/VAL1 Silences AGL15 to Regulate the Developmental Transition from Seed Maturation to Vegetative Growth in Arabidopsis. Plant Cell, 2018. 30(3): p. 600-619 [PMID:29475938] Sasnauskas G,Kauneckaite K,Siksnys V Structural basis of DNA target recognition by the B3 domain of Arabidopsis epigenome reader VAL1. Nucleic Acids Res., 2018. 46(8): p. 4316-4324 [PMID:29660015] Wu B, et al. Structural insight into the role of VAL1 B3 domain for targeting to FLC locus in Arabidopsis thaliana. Biochem. Biophys. Res. Commun., 2018. 501(2): p. 415-422 [PMID:29733847]