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 Phvul.009G167400.1
Common NamePHAVU_009G167400g
Organism
Phaseolus vulgaris
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
Family Trihelix
Protein Properties Length: 872aa    MW: 96180.8 Da    PI: 8.7306
Description Trihelix family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Phvul.009G167400.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1trihelix62.69.3e-20779859186
            trihelix   1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 
                         +W+ +ev++Li +r+e+++r++  k +++lWee+s+k+++ g++rsp qCk+ w +l  +y+ ik+ + ++     +++py +++e
  Phvul.009G167400.1 779 KWKTDEVKKLIGIREELHDRFQIVKGRMALWEEISQKLSADGISRSPGQCKSLWTSLVLKYEGIKNEKDSK-----KSWPYIEDME 859
                         7****************************************************************999984.....56*******8 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:3.60.15.101.4E-6676326IPR001279Metallo-beta-lactamase
SuperFamilySSF562814.17E-7177491IPR001279Metallo-beta-lactamase
SMARTSM008499.3E-2489286IPR001279Metallo-beta-lactamase
PfamPF007532.5E-990234IPR001279Metallo-beta-lactamase
PfamPF075219.1E-7432463IPR011108Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profilePS500908.246772836IPR017877Myb-like domain
Gene3DG3DSA:1.10.10.601.4E-4773836IPR009057Homeodomain-like
PfamPF138371.1E-16777861No hitNo description
CDDcd122032.80E-19778843No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009658Biological Processchloroplast organization
GO:0009942Biological Processlongitudinal axis specification
GO:0060918Biological Processauxin transport
GO:0009507Cellular Componentchloroplast
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 872 aa     Download sequence    Send to blast
MAALTSLSLS LRPLSLRRKP TTSISASLSS LPGSTHGSTT KAPRGRARRN EGPRKSMEDS  60
VQRKMEQFYE GSDGPPLRVL PIGGLGEIGM NCMLVGNHDR YILIDAGVMF PDYDELGVQK  120
IIPDTTFIRK WSHKIEALVI THGHEDHIGA LPWVIPALDS NTPIFSSSFT KELINKRLKE  180
HGIFVPSRLK VFRMRKKFVA GPFEIEPIRV THSIPDCCGL VLRCSDGTIL HTGDWKIDET  240
PLDGNVFDRE ALEELSKEGV TLMMSDSTNV LSPGRTISES VVADALLRHI SASNGRVITT  300
QFASNLHRLG SVKAAADLTG RKLVFVGMSL RTYLDAAWKD GKAPIDPSTL VKAEDIDAYA  360
PKDLLIVTTG SQAEPRAALN LASFGSSHAF KLTKEDLVLY SAKVIPGNES RVMKMLNRVS  420
EIGSTIVMGK NEGLHTSGHA YRGELEEVLR IVKPQHFLPI HGELLFLKEH ELLGKSTGIR  480
HTAVIKNGEM LGVTHLRNRK VLSNGFISLG KENLQLKYSD GDRAFGTSTE LFIDERMRIA  540
LDGIIVTSME IFRPKSLGSL APNTLKGKIR ITTRCLWLDK GKLMDALYKS AHAALSSCPV  600
NSPLAHIERT VSEVLRKMVR KYSGKRPEVI SIAIENPASA ITDEINTKLS GKTHAGLGIS  660
TSKRAVDRHE RGNQPTSLQV TDDSIDNVSG AEGYLSEEDN TASGADGDIS ESEDSDEFWK  720
QFITPLPVEK PFGADNAYDS QKEHESNLKK GDSKNTDEAK SEETSTSEPK SSKSVKRNKW  780
KTDEVKKLIG IREELHDRFQ IVKGRMALWE EISQKLSADG ISRSPGQCKS LWTSLVLKYE  840
GIKNEKDSKK SWPYIEDMER IMSDKEAPAT K*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5a0t_A2e-847763519560RIBONUCLEASE J
5a0t_B2e-847763519560RIBONUCLEASE J
5a0v_A2e-847763519560RIBONUCLEASE J
5a0v_B2e-847763519560RIBONUCLEASE 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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPhvul.009G167400.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By light. {ECO:0000269|PubMed:25871650}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0150350.0AP015035.1 Vigna angularis var. angularis DNA, chromosome 2, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007137930.10.0hypothetical protein PHAVU_009G167400g
SwissprotQ84W560.0RNJ_ARATH; Ribonuclease J
TrEMBLV7AWH30.0V7AWH3_PHAVU; Uncharacterized protein
STRINGXP_007137930.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF50993450
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]