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

Lus10038823

Organism

Linum usitatissimum

Taxonomic ID

4006

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Linaceae; Linum

Family

bHLH

Protein Properties

Length: 982aa MW: 108858 Da PI: 9.9682

Description

bHLH family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Lus10038823	genome	BGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	HLH	38.5	2e-12	74	124	2	55
HHHHHHHHHHHHHHHHHHHHHHHCTSCCC...TTS-STCHHHHHHHHHHHHHHH CS HLH 2 rrahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 r++h +Er+RR+++N+ + Lr+l+P+ + k+ + a+i +v+YI++Lq Lus10038823 74 RMSHITVERNRREQMNEHLGVLRSLMPSF---YVKRGDQASIIGGVVDYINELQ 124 89************************9...9******************9 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50888	14.335	72	123	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF47459	1.19E-15	73	146	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
CDD	cd00083	1.07E-10	74	127	No hit	No description
Pfam	PF00010	1.5E-9	74	124	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
Gene3D	G3DSA:4.10.280.10	1.2E-11	74	125	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SMART	SM00353	3.8E-9	78	129	IPR011598	Myc-type, basic helix-loop-helix (bHLH) domain
SuperFamily	SSF88946	8.79E-30	669	816	IPR013325	RNA polymerase sigma factor, region 2
Gene3D	G3DSA:1.10.601.10	5.9E-24	687	703	No hit	No description
Gene3D	G3DSA:1.10.601.10	5.9E-24	741	816	No hit	No description
TIGRFAMs	TIGR02937	2.1E-24	745	969	IPR014284	RNA polymerase sigma-70 like domain
Pfam	PF04542	1.5E-9	749	815	IPR007627	RNA polymerase sigma-70 region 2
PRINTS	PR00046	1.8E-11	776	789	IPR000943	RNA polymerase sigma-70
PRINTS	PR00046	1.8E-11	800	808	IPR000943	RNA polymerase sigma-70
SuperFamily	SSF88659	1.48E-8	820	872	IPR013324	RNA polymerase sigma factor, region 3/4
Gene3D	G3DSA:1.10.10.10	1.9E-11	822	874	IPR011991	Winged helix-turn-helix DNA-binding domain
Pfam	PF04539	3.0E-11	835	895	IPR007624	RNA polymerase sigma-70 region 3
SuperFamily	SSF88659	2.8E-17	908	979	IPR013324	RNA polymerase sigma factor, region 3/4
CDD	cd06171	2.41E-7	910	968	No hit	No description
Gene3D	G3DSA:1.10.10.10	7.3E-21	913	980	IPR011991	Winged helix-turn-helix DNA-binding domain
Pfam	PF04545	3.9E-14	916	969	IPR007630	RNA polymerase sigma-70 region 4
PRINTS	PR00046	1.8E-11	920	932	IPR000943	RNA polymerase sigma-70
PRINTS	PR00046	1.8E-11	941	956	IPR000943	RNA polymerase sigma-70
PRINTS	PR00046	1.8E-11	956	967	IPR000943	RNA polymerase sigma-70

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006352	Biological Process	DNA-templated transcription, initiation
GO:0009658	Biological Process	chloroplast organization
GO:0010114	Biological Process	response to red light
GO:0010207	Biological Process	photosystem II assembly
GO:0010218	Biological Process	response to far red light
GO:0045893	Biological Process	positive regulation of transcription, DNA-templated
GO:0071483	Biological Process	cellular response to blue light
GO:0005739	Cellular Component	mitochondrion
GO:0009507	Cellular Component	chloroplast
GO:0001053	Molecular Function	plastid sigma factor activity
GO:0003677	Molecular Function	DNA binding
GO:0003700	Molecular Function	transcription factor activity, sequence-specific DNA binding
GO:0003899	Molecular Function	DNA-directed RNA polymerase activity
GO:0046983	Molecular Function	protein dimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 982 aa Download sequence Send to blast
MSEYFLEGCS EFGGSGADDL FAIFESLDRA NNTHTAGKEE EEGQQQPKSK KRKIAAAAAG 60 SGGCDDDVEV GGDRMSHITV ERNRREQMNE HLGVLRSLMP SFYVKRGDQA SIIGGVVDYI 120 NELQQILGSL ETKKQRKLYS TDVSSPQLPV VANNPRPSQL ISPRKSPLSP KPPSTIINLP 180 PISPRTPQPT SPYIDIVPTT TKRTSFLPSP TGSSNSSSNV MMINGGMGII SCNNNNNNND 240 VVANCKSAIA DVEVKFSGPH LILKTVSPRI PGQAVKIIAA LKDLSLEILH VNVDTVEESL 300 LVNFFTIKIG IECQLSAEEL AQQIQQTFFL PRHPPPKRHR MTTVKVCLMN LYPSAAVSTL 360 FFFDCRFEIV GCCNGLFCIA NSVRWRATQL ILWNPSTLET KVLPKSINGF EFDSEHRFFF 420 LSIPTTSAAG NSPEFESPVN LRAKISTGFL PVGRIGEFVR GTSLCQSVYE MALSVMGVVT 480 VSSSASRTPV GITARISSNG SSSSSSSSLS SSSSLPSRRS VIVAFKIDKL DHIASSLVSP 540 DSKAKKGRPR KVKGTPVVPT LDNLDYYNEA AAKLETLYKL SPPSSDVEEE EEVGTRERKR 600 KARDGLKAGR VVVRNWEKKP KRLSLDGRVA LKKINHGNVG CGKRRSVVNK DDDEEVGKIE 660 ELVRQYTGST SMASLDWKKM KIPPVLTSSE HTWLFNLMQP MKAVMQLKDE LQKTMGKVPT 720 DVQLADAANS TVFEIRRQLE TGQAARNKLI KHNLRLVLFV INKYFSDFAN SSRFQDLCQA 780 GAQGLITAID RFEPKRKLKL STYGLFWIRH SIIRSMTVSS FIHVPFGLES IRADIQKKKL 840 QLLVELQREP NDEEIAERVG ISMERYREVI RAGRPVLSLH SRNPVTQVEL INEIADMNGG 900 ENRRRPALLR LALDDVLDSL KPKESLVIRQ RYGLDGKGDR SLSEIAANLN ISREMVRKHE 960 VKALMKLKHP ARVDHLRQYV V*

Sequence ? help Back to Top

Protein Sequence Length: 982 aa Download sequence Send to blast

MSEYFLEGCS EFGGSGADDL FAIFESLDRA NNTHTAGKEE EEGQQQPKSK KRKIAAAAAG  60
SGGCDDDVEV GGDRMSHITV ERNRREQMNE HLGVLRSLMP SFYVKRGDQA SIIGGVVDYI  120
NELQQILGSL ETKKQRKLYS TDVSSPQLPV VANNPRPSQL ISPRKSPLSP KPPSTIINLP  180
PISPRTPQPT SPYIDIVPTT TKRTSFLPSP TGSSNSSSNV MMINGGMGII SCNNNNNNND  240
VVANCKSAIA DVEVKFSGPH LILKTVSPRI PGQAVKIIAA LKDLSLEILH VNVDTVEESL  300
LVNFFTIKIG IECQLSAEEL AQQIQQTFFL PRHPPPKRHR MTTVKVCLMN LYPSAAVSTL  360
FFFDCRFEIV GCCNGLFCIA NSVRWRATQL ILWNPSTLET KVLPKSINGF EFDSEHRFFF  420
LSIPTTSAAG NSPEFESPVN LRAKISTGFL PVGRIGEFVR GTSLCQSVYE MALSVMGVVT  480
VSSSASRTPV GITARISSNG SSSSSSSSLS SSSSLPSRRS VIVAFKIDKL DHIASSLVSP  540
DSKAKKGRPR KVKGTPVVPT LDNLDYYNEA AAKLETLYKL SPPSSDVEEE EEVGTRERKR  600
KARDGLKAGR VVVRNWEKKP KRLSLDGRVA LKKINHGNVG CGKRRSVVNK DDDEEVGKIE  660
ELVRQYTGST SMASLDWKKM KIPPVLTSSE HTWLFNLMQP MKAVMQLKDE LQKTMGKVPT  720
DVQLADAANS TVFEIRRQLE TGQAARNKLI KHNLRLVLFV INKYFSDFAN SSRFQDLCQA  780
GAQGLITAID RFEPKRKLKL STYGLFWIRH SIIRSMTVSS FIHVPFGLES IRADIQKKKL  840
QLLVELQREP NDEEIAERVG ISMERYREVI RAGRPVLSLH SRNPVTQVEL INEIADMNGG  900
ENRRRPALLR LALDDVLDSL KPKESLVIRQ RYGLDGKGDR SLSEIAANLN ISREMVRKHE  960
VKALMKLKHP ARVDHLRQYV V*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
4ljz_F	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4ljz_L	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4lk0_F	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4lk0_L	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4xsx_F	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4xsx_L	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4xsy_F	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4xsy_L	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4xsz_F	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
4xsz_L	1e-31	732	980	267	520	RNA polymerase sigma factor RpoD
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	73	84	RMSHITVERNRR

Functional Description ? help Back to Top
Source	Description
UniProt	Essential protein. Sigma factors are initiation factors that promote the attachment of plastid-encoded RNA polymerase (PEP) to specific initiation sites (e.g. psbA and psbD) and are then released. Essential for blue light-mediated transcription of psbD, which encodes the photosystem II reaction center protein D2. Plays a role in reproduction. Required during female gametophyte development (PubMed:21123745). {ECO:0000269\|PubMed:12805603, ECO:0000269\|PubMed:14976253, ECO:0000269\|PubMed:18532976, ECO:0000269\|PubMed:21123745}.

Cis-element ? help Back to Top
Source	Link
PlantRegMap	Lus10038823

Regulation -- Description ? help Back to Top
Source	Description
UniProt	INDUCTION: Induced by blue light illumination (470 nm), especially after dark adaptation. Induction is mediated through both cryptochrome 1 and cryptochrome 2 at lower light intensities and mainly through cryptochrome 1 at higher light intensities. {ECO:0000269\|PubMed:10946105, ECO:0000269\|PubMed:11959137, ECO:0000269\|PubMed:14976253, ECO:0000269\|PubMed:18532976}.

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_002513587.1	0.0	RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
Swissprot	Q9ZNX9	0.0	SIGE_ARATH; RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
TrEMBL	B9RIL8	0.0	B9RIL8_RICCO; RNA polymerase sigma factor rpoD, putative
STRING	Lus10038823	0.0	(Linum usitatissimum)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT5G53210.1	2e-35	bHLH family protein

Link Out ? help Back to Top
Phytozome	Lus10038823

Publications ? help Back to Top
Hakimi MA,Privat I,Valay JG,Lerbs-Mache S Evolutionary conservation of C-terminal domains of primary sigma(70)-type transcription factors between plants and bacteria. J. Biol. Chem., 2000. 275(13): p. 9215-21 [PMID:10734058] Allison LA The role of sigma factors in plastid transcription. Biochimie, 2000 Jun-Jul. 82(6-7): p. 537-48 [PMID:10946105] Fujiwara M,Nagashima A,Kanamaru K,Tanaka K,Takahashi H Three new nuclear genes, sigD, sigE and sigF, encoding putative plastid RNA polymerase sigma factors in Aarabidopsis thaliana. FEBS Lett., 2000. 481(1): p. 47-52 [PMID:10984613] Tsunoyama Y,Morikawa K,Shiina T,Toyoshima Y Blue light specific and differential expression of a plastid sigma factor, Sig5 in Arabidopsis thaliana. FEBS Lett., 2002. 516(1-3): p. 225-8 [PMID:11959137] Yao J,Roy-Chowdhury S,Allison LA AtSig5 is an essential nucleus-encoded Arabidopsis sigma-like factor. Plant Physiol., 2003. 132(2): p. 739-47 [PMID:12805603] Kubis S, et al. The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins. Plant Cell, 2003. 15(8): p. 1859-71 [PMID:12897258] Tsunoyama Y, et al. Blue light-induced transcription of plastid-encoded psbD gene is mediated by a nuclear-encoded transcription initiation factor, AtSig5. Proc. Natl. Acad. Sci. U.S.A., 2004. 101(9): p. 3304-9 [PMID:14976253] Ishizaki Y, et al. A nuclear-encoded sigma factor, Arabidopsis SIG6, recognizes sigma-70 type chloroplast promoters and regulates early chloroplast development in cotyledons. Plant J., 2005. 42(2): p. 133-44 [PMID:15807777] Schweer J,Loschelder H,Link G A promoter switch that can rescue a plant sigma factor mutant. FEBS Lett., 2006. 580(28-29): p. 6617-22 [PMID:17118361] Onda Y,Yagi Y,Saito Y,Takenaka N,Toyoshima Y Light induction of Arabidopsis SIG1 and SIG5 transcripts in mature leaves: differential roles of cryptochrome 1 and cryptochrome 2 and dual function of SIG5 in the recognition of plastid promoters. Plant J., 2008. 55(6): p. 968-78 [PMID:18532976] Yu F, et al. ANK6, a mitochondrial ankyrin repeat protein, is required for male-female gamete recognition in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A., 2010. 107(51): p. 22332-7 [PMID:21123745] 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] Davey MP, et al. The UV-B photoreceptor UVR8 promotes photosynthetic efficiency in Arabidopsis thaliana exposed to elevated levels of UV-B. Photosyn. Res., 2012. 114(2): p. 121-31 [PMID:23161229] Noordally ZB, et al. Circadian control of chloroplast transcription by a nuclear-encoded timing signal. Science, 2013. 339(6125): p. 1316-9 [PMID:23493713] Börner T,Aleynikova AY,Zubo YO,Kusnetsov VV Chloroplast RNA polymerases: Role in chloroplast biogenesis. Biochim. Biophys. Acta, 2015. 1847(9): p. 761-9 [PMID:25680513] Yamburenko MV,Zubo YO,Börner T Abscisic acid affects transcription of chloroplast genes via protein phosphatase 2C-dependent activation of nuclear genes: repression by guanosine-3'-5'-bisdiphosphate and activation by sigma factor 5. Plant J., 2015. 82(6): p. 1030-41 [PMID:25976841] Xiao D, et al. SENESCENCE-SUPPRESSED PROTEIN PHOSPHATASE Directly Interacts with the Cytoplasmic Domain of SENESCENCE-ASSOCIATED RECEPTOR-LIKE KINASE and Negatively Regulates Leaf Senescence in Arabidopsis. Plant Physiol., 2015. 169(2): p. 1275-91 [PMID:26304848] Mellenthin M,Ellersiek U,Börger A,Baier M Expression of the Arabidopsis Sigma Factor SIG5 Is Photoreceptor and Photosynthesis Controlled. Plants (Basel), 2014. 3(3): p. 359-91 [PMID:27135509] Belbin FE, et al. Integration of light and circadian signals that regulate chloroplast transcription by a nuclear-encoded sigma factor. New Phytol., 2017. 213(2): p. 727-738 [PMID:27716936] Zhao P, et al. ATHB17 enhances stress tolerance by coordinating photosynthesis associated nuclear gene and ATSIG5 expression in response to abiotic stress. Sci Rep, 2017. 7: p. 45492 [PMID:28358040]