PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Niben101Scf05750g04002.1
Organism
Nicotiana benthamiana
Taxonomic ID
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 Trihelix
Protein Properties Length: 876aa    MW: 97049.3 Da    PI: 7.542
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Scf05750g04002.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix64.23e-20784864186
                  trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdql 85 
                               rW+++e+++Li++r e+++r+   + +++lWee+s+++ + g++rsp qCk+ w +l ++y++ k  +k+     ++++pyf+++
  Niben101Scf05750g04002.1 784 RWKHDEIQKLIKLRGELHSRFLVVRGRMALWEEISSNLLSSGVNRSPAQCKSLWASLVQKYEESKSDKKS-----QEKWPYFEEM 863
                               8****************************************************************99998.....578******* PP

                  trihelix  86 e 86 
                               +
  Niben101Scf05750g04002.1 864 N 864
                               7 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.108.2E-6276353IPR001279Metallo-beta-lactamase
SuperFamilySSF562812.13E-6877518IPR001279Metallo-beta-lactamase
SMARTSM008495.1E-2289313IPR001279Metallo-beta-lactamase
PfamPF007531.8E-790261IPR001279Metallo-beta-lactamase
PfamPF075215.6E-7461490IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.293777841IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.603.7E-5778843IPR009057Homeodomain-like
PfamPF138372.4E-17782866No hitNo description
CDDcd122032.15E-21783848No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 876 aa     Download sequence    Send to blast
MAAFSAISLC PYKLCHQLKP SKRYISCYTP SSSTIGVHGS KGPRIRPAKP EGAGRSIDDS  60
VQRRMEHFYE GADGPPLRVL PIGGLGEIGM NCMLVGNYDR YILIDAGIMF PGYEDLGVQK  120
IIPDTTFIKK WSHKIEAVVI THGHEDHIGA LPWVIPALDS HTPIFASSFT MEVCYDPMSS  180
LIAFNYTAFP VFTRDMYYVL IKKRLKEFGI FVPSRLKVFK TRRKFTAGPF EVEPITVTHS  240
IPDCSGIVLR CSDGTILHTG DWKIDESPLD GKVFDREGLE ELSKEGVTLM MSDSTNVLSP  300
GRTLSETVVA DSLLRHISAA KGRVITTQFA SNIHRLGSVK AAADLTGRKL VFVGMSLRTY  360
LDAAWKDGKA PIDPSTLVKV EDIDAYAPKD LLIVTTGSQA EPRAALNLAS YGSSHSLKLN  420
KEDIVLYSAK VIPGNETRVM EMLNRISDIG STIVMGKNEL LHTSGHAHRE ELEEVLKIVK  480
PQHFLPIHGE LLFLKEHELL GKSTGIRHTA VIKNGEMLGV SHLRNRKVLS NGFISLGKEN  540
LQLMYSDGDK AFGTAAELCI DERQRIASDG IIVVSMEILR PQSMDGATEK ALKGKIRITT  600
RCLWLDKGKL LDALHKAAHA ALSSCPLSCP LPHMERTVSE VLRKMVRKYS SKRPEVIAIA  660
FENPAGVLAD EINGKLSGKS HIGFGISALR NVMDEDQKGK QASEARAEEG PGYPIDDAAE  720
QVEGVDMDIE RLTHDRGTTS SSNSGDEYST TKEESESSRE ESIQIDSGFP ESMMKSSKPL  780
KRNRWKHDEI QKLIKLRGEL HSRFLVVRGR MALWEEISSN LLSSGVNRSP AQCKSLWASL  840
VQKYEESKSD KKSQEKWPYF EEMNEILSDL EAASQK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A9e-837766219560RIBONUCLEASE J
5a0t_B9e-837766219560RIBONUCLEASE J
5a0v_A9e-837766219560RIBONUCLEASE J
5a0v_B9e-837766219560RIBONUCLEASE J
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtEssential protein required during embryogenesis, especially in initiating and maintaining the organization of shoot apical meristems (SAMs), cotyledons, and hypocotyls (PubMed:15266054, PubMed:25871650). Involved in auxin-mediated pathways during embryogenesis (PubMed:25871650). RNase that has both endonuclease and 5'-3' exonuclease activities. Involved in RNA surveillance to prevent overaccumulation of antisense RNA (PubMed:22033332). Probably involved in maturation of rRNA and in some organisms also mRNA maturation and/or decay (By similarity). {ECO:0000250|UniProtKB:Q72JJ7, ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:22033332, ECO:0000269|PubMed:25871650}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019243537.10.0PREDICTED: uncharacterized protein LOC109223609
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLA0A1J6J4H10.0A0A1J6J4H1_NICAT; Uncharacterized protein
STRINGXP_009774848.10.0(Nicotiana sylvestris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA58742331
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G63420.10.0Trihelix family protein
Publications ? help Back to Top
  1. Bryant N,Lloyd J,Sweeney C,Myouga F,Meinke D
    Identification of nuclear genes encoding chloroplast-localized proteins required for embryo development in Arabidopsis.
    Plant Physiol., 2011. 155(4): p. 1678-89
    [PMID:21139083]
  2. Halpert M,Liveanu V,Glaser F,Schuster G
    The Arabidopsis chloroplast RNase J displays both exo- and robust endonucleolytic activities.
    Plant Mol. Biol., 2019. 99(1-2): p. 17-29
    [PMID:30511330]