PlantTFDB - Plant Transcription Factor Database @ CBI, PKU

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Cucurbitales; Cucurbitaceae; Benincaseae; Citrullus

Family

Trihelix

Protein Properties

Length: 697aa MW: 77353.6 Da PI: 7.5846

Description

Trihelix family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Cla019268	genome	ICuGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	trihelix	54.6	2.8e-17	620	684	1	65
trihelix 1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkik 65 +W+ +e+++Li++r e++ r++ ++ +++lWee+s+ m++ g++rsp qCk+ w +l ++++ + Cla019268 620 KWKPEEIKKLIKLRGELHARFQVARGRMALWEEISNGMSADGINRSPGQCKSLWASLVQKFEVCS 684 7************************************************************9876 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.60.15.10	7.7E-68	37	287	IPR001279	Metallo-beta-lactamase
SuperFamily	SSF56281	2.23E-58	38	367	IPR001279	Metallo-beta-lactamase
SMART	SM00849	2.0E-24	50	247	IPR001279	Metallo-beta-lactamase
Pfam	PF12706	9.9E-11	62	197	IPR001279	Metallo-beta-lactamase
PROSITE profile	PS50090	7.909	613	677	IPR017877	Myb-like domain
Gene3D	G3DSA:1.10.10.60	1.0E-5	615	679	IPR009057	Homeodomain-like
Pfam	PF13837	1.5E-12	618	683	No hit	No description
CDD	cd12203	1.22E-21	619	681	No hit	No description

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009658	Biological Process	chloroplast organization
GO:0009942	Biological Process	longitudinal axis specification
GO:0060918	Biological Process	auxin transport
GO:0009507	Cellular Component	chloroplast
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 697 aa Download sequence Send to blast
SKVPRKRPGR LEGARRSMED SVQRKMEQFY EGSDGPPLRV LPIGGLGEIG MNCMLVGNYD 60 RYILIDAGVM FPDHDELGVQ KIIPDTTFIK RWSHKIEAVV ITHGHEDHIG ALPWVIPALD 120 SHTPIYASSF TVELIKKRLK ENGIFVPSRL KVFKMKKRFT AGPFEIEPIR VTHSIPDCCG 180 LVLRCADGII LHTGDWKIDE SPLDGKVFDR ETLEELSKEG VTLMMSDSTN VLSPGRTISE 240 SVVADALLRR ISAAKGRVIT TQFASNIHRL GSVKAAADLT GRKLVFVGMS LRTYLDAAWK 300 DGKAPIDPST LVKVEDIDAY APKDLLIVTT GSQAEPRAAL NLASYGSSHS LKLSKEDMIL 360 YSAKPFCFEL QTPLPPMWDY LVMEILRPQS VDGSNETGIR GKLRITTRCL WLDKGKLLDA 420 LHKAAHAALS SCPVNCPLAH MERTVAELLR KMVRKYSGKR PEVIVMAVEN PGGVLSEELG 480 ARLSGKSNTG FGMSALRKAV DGQPTKSHVN STRPDGNDDL HSEESQGYYL EPGRLLPEDD 540 YDTSSSNLTE TQSFDNEGLE DFWRPFITPS SPAKELAKDN EGSVQQSKNM LEITNEREEV 600 SDDKSLKTSN SDVKPLKRNK WKPEEIKKLI KLRGELHARF QVARGRMALW EEISNGMSAD 660 GINRSPGQCK SLWASLVQKF EVCSSVSTFN FELALPL

Sequence ? help Back to Top

Protein Sequence Length: 697 aa Download sequence Send to blast

SKVPRKRPGR LEGARRSMED SVQRKMEQFY EGSDGPPLRV LPIGGLGEIG MNCMLVGNYD  60
RYILIDAGVM FPDHDELGVQ KIIPDTTFIK RWSHKIEAVV ITHGHEDHIG ALPWVIPALD  120
SHTPIYASSF TVELIKKRLK ENGIFVPSRL KVFKMKKRFT AGPFEIEPIR VTHSIPDCCG  180
LVLRCADGII LHTGDWKIDE SPLDGKVFDR ETLEELSKEG VTLMMSDSTN VLSPGRTISE  240
SVVADALLRR ISAAKGRVIT TQFASNIHRL GSVKAAADLT GRKLVFVGMS LRTYLDAAWK  300
DGKAPIDPST LVKVEDIDAY APKDLLIVTT GSQAEPRAAL NLASYGSSHS LKLSKEDMIL  360
YSAKPFCFEL QTPLPPMWDY LVMEILRPQS VDGSNETGIR GKLRITTRCL WLDKGKLLDA  420
LHKAAHAALS SCPVNCPLAH MERTVAELLR KMVRKYSGKR PEVIVMAVEN PGGVLSEELG  480
ARLSGKSNTG FGMSALRKAV DGQPTKSHVN STRPDGNDDL HSEESQGYYL EPGRLLPEDD  540
YDTSSSNLTE TQSFDNEGLE DFWRPFITPS SPAKELAKDN EGSVQQSKNM LEITNEREEV  600
SDDKSLKTSN SDVKPLKRNK WKPEEIKKLI KLRGELHARF QVARGRMALW EEISNGMSAD  660
GINRSPGQCK SLWASLVQKF EVCSSVSTFN FELALPL

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5a0t_A	1e-62	38	363	19	340	RIBONUCLEASE J
5a0t_B	1e-62	38	363	19	340	RIBONUCLEASE J
5a0v_A	1e-62	38	363	19	340	RIBONUCLEASE J
5a0v_B	1e-62	38	363	19	340	RIBONUCLEASE J
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Essential 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
UniProt	INDUCTION: By light. {ECO:0000269\|PubMed:25871650}.

Annotation -- Protein ? help Back to Top
Source	Hit ID	E-value	Description
Refseq	XP_015866975.1	0.0	uncharacterized protein LOC107404538
Swissprot	Q84W56	0.0	RNJ_ARATH; Ribonuclease J
TrEMBL	A0A1S3CLZ6	0.0	A0A1S3CLZ6_CUCME; ribonuclease J isoform X1
TrEMBL	A0A1S3CN32	0.0	A0A1S3CN32_CUCME; ribonuclease J isoform X2
STRING	XP_008464473.1	0.0	(Cucumis melo)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Fabids	OGEF5099	34	50

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G63420.1	0.0	Trihelix family protein

Publications ? help Back to Top
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] 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]