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

Thecc1EG014612t1

Common Name

TCM_014612

Organism

Theobroma cacao

Taxonomic ID

3641

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Byttnerioideae; Theobroma

Family

Trihelix

Protein Properties

Length: 1005aa MW: 112016 Da PI: 9.6815

Description

Trihelix family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Thecc1EG014612t1	genome	CGD	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	trihelix	65.3	1.3e-20	912	992	1	86
trihelix 1 rWtkqevlaLiearremeerlrrgklkkplWeevskkmrergferspkqCkekwenlnkrykkikegekkrtsessstcpyfdqle 86 +W+ +ev++Li++r ++++r++ k +++lWee+s ++++g++rsp qCk+ w +l ++y++ k +k++ +++pyf+++ Thecc1EG014612t1 912 KWKPEEVKKLIKMRGKLHSRFQVVKGRMALWEEISTSLMAEGISRSPGQCKSLWTSLVQKYEESKGEKKSH-----KEWPYFEDMS 992 7***********************************************************999999986.....68****96 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
Gene3D	G3DSA:3.60.15.10	1.2E-67	195	445	IPR001279	Metallo-beta-lactamase
SuperFamily	SSF56281	6.89E-71	196	610	IPR001279	Metallo-beta-lactamase
SMART	SM00849	4.6E-26	208	405	IPR001279	Metallo-beta-lactamase
Pfam	PF12706	7.9E-11	220	355	IPR001279	Metallo-beta-lactamase
Pfam	PF07521	1.2E-5	551	582	IPR011108	Zn-dependent metallo-hydrolase, RNA specificity domain
PROSITE profile	PS50090	8.014	905	969	IPR017877	Myb-like domain
Gene3D	G3DSA:1.10.10.60	2.9E-5	908	971	IPR009057	Homeodomain-like
Pfam	PF13837	5.7E-17	910	993	No hit	No description
CDD	cd12203	3.37E-21	911	976	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:0016021	Cellular Component	integral component of membrane
GO:0003677	Molecular Function	DNA binding

Sequence ? help Back to Top
Protein Sequence Length: 1005 aa Download sequence Send to blast
MKKVKKKRRK NLYTCGKNTR GRNLSCFKND KQDISPPYKN LHTFTHSLNF PLPEAQSSPL 60 LLVSKLLHKN AKCSGFNLHC CFFFFVNLKE QMQLGFLGGL SFSYSLYFTS FKPIKAPTKM 120 AASTAHSLCP YGLYCRPNPR HRYISCSVGS PTPLGTRRTK VPRKKSGRLD GARKSMEDSV 180 QRKMEQFYEG TAGPPLRVLP IGGLGEIGMN CMLVGNYDRY ILIDAGVMFP DYDELGVQKI 240 IPDTTFIKKW SHKIEAVVIT HGHEDHIGAL PWVIPALDSH TPIYASSFTM ELIKKRLKEN 300 GIFVPSRLKI FKTRKRFMAG PFEIEPLRVT HSIPDCCGLV LRCADGTILH TGDWKIDESP 360 LDGKIFDRQF LEDLSKEGVT LMMSDSTNVL SPGRTISESS VADALLRHIS AAKGRIITTQ 420 FASNIHRLGS VKAAADLTGR KLVFVGMSLR TYLDAAWKDG KAPIDPSTLV KVEDIDAYAP 480 KDLIIVTTGS QAEPRAALNL ASYGSSHSFK LNKEDVILYS AKVIPGNESR VMKMLNRISE 540 IGSTIVMGKN EGLHTSGHGY RGELEEVLKI VKPQHFLPIH GELLFLKEHE LLGKSTGIRH 600 TTVIKNGEML GVSHLRNRRV LSNGFSSLGK ENLQLMYSDG DKAYGTSTEL CIDERLRIAS 660 DGIIVVSMEI LRPQKIDGIM ENSLKGKIRI TTRCLWLDKG KLLDALHKAA HAALSSCPVN 720 CPLGHMERTV SEVLRKMVRK YSGKRPEVIA IALENPAGVF SDELNERLSG NYNVGFEIPT 780 LRKVVDGHPK RSQPNKIKAE DDSNLHLENT SEQSLEVSDG EVEKLLPEED TTTSSPDSLE 840 RHTPNSEGSD EFWKSFITSS SPVNNLVNDN NGLVPKKEYK SQLKSDGTAS SGDDSEMPSS 900 QPKSSKPAKR NKWKPEEVKK LIKMRGKLHS RFQVVKGRMA LWEEISTSLM AEGISRSPGQ 960 CKSLWTSLVQ KYEESKGEKK SHKEWPYFED MSKVFSDFEA TATK*

Sequence ? help Back to Top

Protein Sequence Length: 1005 aa Download sequence Send to blast

MKKVKKKRRK NLYTCGKNTR GRNLSCFKND KQDISPPYKN LHTFTHSLNF PLPEAQSSPL  60
LLVSKLLHKN AKCSGFNLHC CFFFFVNLKE QMQLGFLGGL SFSYSLYFTS FKPIKAPTKM  120
AASTAHSLCP YGLYCRPNPR HRYISCSVGS PTPLGTRRTK VPRKKSGRLD GARKSMEDSV  180
QRKMEQFYEG TAGPPLRVLP IGGLGEIGMN CMLVGNYDRY ILIDAGVMFP DYDELGVQKI  240
IPDTTFIKKW SHKIEAVVIT HGHEDHIGAL PWVIPALDSH TPIYASSFTM ELIKKRLKEN  300
GIFVPSRLKI FKTRKRFMAG PFEIEPLRVT HSIPDCCGLV LRCADGTILH TGDWKIDESP  360
LDGKIFDRQF LEDLSKEGVT LMMSDSTNVL SPGRTISESS VADALLRHIS AAKGRIITTQ  420
FASNIHRLGS VKAAADLTGR KLVFVGMSLR TYLDAAWKDG KAPIDPSTLV KVEDIDAYAP  480
KDLIIVTTGS QAEPRAALNL ASYGSSHSFK LNKEDVILYS AKVIPGNESR VMKMLNRISE  540
IGSTIVMGKN EGLHTSGHGY RGELEEVLKI VKPQHFLPIH GELLFLKEHE LLGKSTGIRH  600
TTVIKNGEML GVSHLRNRRV LSNGFSSLGK ENLQLMYSDG DKAYGTSTEL CIDERLRIAS  660
DGIIVVSMEI LRPQKIDGIM ENSLKGKIRI TTRCLWLDKG KLLDALHKAA HAALSSCPVN  720
CPLGHMERTV SEVLRKMVRK YSGKRPEVIA IALENPAGVF SDELNERLSG NYNVGFEIPT  780
LRKVVDGHPK RSQPNKIKAE DDSNLHLENT SEQSLEVSDG EVEKLLPEED TTTSSPDSLE  840
RHTPNSEGSD EFWKSFITSS SPVNNLVNDN NGLVPKKEYK SQLKSDGTAS SGDDSEMPSS  900
QPKSSKPAKR NKWKPEEVKK LIKMRGKLHS RFQVVKGRMA LWEEISTSLM AEGISRSPGQ  960
CKSLWTSLVQ KYEESKGEKK SHKEWPYFED MSKVFSDFEA TATK*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5a0t_A	1e-84	196	754	19	560	RIBONUCLEASE J
5a0t_B	1e-84	196	754	19	560	RIBONUCLEASE J
5a0v_A	1e-84	196	754	19	560	RIBONUCLEASE J
5a0v_B	1e-84	196	754	19	560	RIBONUCLEASE J
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	1	9	KKVKKKRRK
2	4	8	KKKRR
3	4	9	KKKRRK
4	5	9	KKRRK

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}.

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_007037950.2	0.0	PREDICTED: ribonuclease J isoform X1
Swissprot	Q84W56	0.0	RNJ_ARATH; Ribonuclease J
TrEMBL	A0A061FYV1	0.0	A0A061FYV1_THECC; RNA-metabolising metallo-beta-lactamase family protein
STRING	EOY22451	0.0	(Theobroma cacao)

Orthologous Group ? help Back to Top
Lineage	Orthologous Group ID	Taxa Number	Gene Number
Malvids	OGEM9539	26	34

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

Link Out ? help Back to Top
Phytozome	Thecc1EG014612t1
Entrez Gene	18605082

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] Motamayor JC, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol., 2013. 14(6): p. r53 [PMID:23731509] 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]