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

Aco005756.1

Organism

Ananas comosus

Taxonomic ID

4615

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Bromeliaceae; Ananas

Family

LBD

Protein Properties

Length: 827aa MW: 90698 Da PI: 6.4095

Description

LBD family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
Aco005756.1	genome	JGI	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	DUF260	119	2.7e-37	87	186	1	100
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeqpkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallk 98 aCaaCk++rrkC++dC+lapyfpa+q+++f n+h+lFG+sn+lk+++ l+ +r++am++++y++++ra d v G+++++l+l++q+e ael+l+ Aco005756.1 87 ACAACKYQRRKCNPDCTLAPYFPADQQRQFLNAHRLFGVSNILKIIRGLDSRKRDEAMRTIIYQSNVRAMDSVGGCYRIVLELERQVELYTAELQLVL 184 7*********************************************************************************************9987 PP DUF260 99 ee 100 ++ Aco005756.1 185 QQ 186 76 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
PROSITE profile	PS50891	23.499	86	187	IPR004883	Lateral organ boundaries, LOB
Pfam	PF03195	9.4E-36	87	183	IPR004883	Lateral organ boundaries, LOB
Pfam	PF12265	3.4E-9	381	440	IPR022052	Histone-binding protein RBBP4, N-terminal
Gene3D	G3DSA:2.130.10.10	1.7E-43	443	556	IPR015943	WD40/YVTN repeat-like-containing domain
SuperFamily	SSF50978	2.0E-39	462	558	IPR017986	WD40-repeat-containing domain
SMART	SM00320	430	463	502	IPR001680	WD40 repeat
SMART	SM00320	0.2	517	557	IPR001680	WD40 repeat
Pfam	PF00400	0.038	523	557	IPR001680	WD40 repeat
SuperFamily	SSF50978	2.0E-39	593	797	IPR017986	WD40-repeat-containing domain
Gene3D	G3DSA:2.130.10.10	1.7E-43	595	819	IPR015943	WD40/YVTN repeat-like-containing domain
SMART	SM00320	5.1E-5	598	638	IPR001680	WD40 repeat
Pfam	PF00400	0.12	603	638	IPR001680	WD40 repeat
PROSITE profile	PS50082	9.071	605	647	IPR001680	WD40 repeat
PROSITE profile	PS50294	16.823	605	739	IPR017986	WD40-repeat-containing domain
SMART	SM00320	6.3E-6	643	683	IPR001680	WD40 repeat
PROSITE profile	PS50082	9.506	650	683	IPR001680	WD40 repeat
Pfam	PF00400	0.032	651	683	IPR001680	WD40 repeat
SMART	SM00320	2.3E-4	692	730	IPR001680	WD40 repeat
Pfam	PF00400	0.003	693	730	IPR001680	WD40 repeat
SMART	SM00320	3.2	749	796	IPR001680	WD40 repeat

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0006281	Biological Process	DNA repair
GO:0009826	Biological Process	unidimensional cell growth
GO:0009908	Biological Process	flower development
GO:0009965	Biological Process	leaf morphogenesis
GO:0010090	Biological Process	trichome morphogenesis
GO:0010224	Biological Process	response to UV-B
GO:0005730	Cellular Component	nucleolus
GO:0005829	Cellular Component	cytosol
GO:0005515	Molecular Function	protein binding
GO:0046872	Molecular Function	metal ion binding

Sequence ? help Back to Top
Protein Sequence Length: 827 aa Download sequence Send to blast
MSINPNPNPN PNPNPNATSN HHHHPLLVVG PSSSSSSSHP HPHPHPHPPP PHPHHPSSSS 60 SSSFQTLAPS SSSSSSSRLS GGQSNSACAA CKYQRRKCNP DCTLAPYFPA DQQRQFLNAH 120 RLFGVSNILK IIRGLDSRKR DEAMRTIIYQ SNVRAMDSVG GCYRIVLELE RQVELYTAEL 180 QLVLQQLAVC RAQAQAAAAA APLSAELGLN VAADVDDGVV YNNNLFGNNN FVPIAPHQQQ 240 QQQQYYNYFC YDSDGENSTR FNNNVIVNFN NENNFGNIGD NVEDALVSSS INFQQEQMQK 300 QLEEVKLEEL DVKPLVDVFE AGQSFIRENE EEQLKSSASS LCRAKMAEKE DLNTMEHVQE 360 HDLKGAASLF TLTNGSSSAI EYTQWKSLVP VLYDWLANHN LVWPSLSCRK DGGRSLSRRR 420 TRIASTDGSV PNTLVIANCE VVKPRVAAAE HISQFNEEAR SPFVKKFKTI IHPGEVNRIR 480 ELPQNSKIVA THTDSPDVLI WDVEAQPNRH AVLGAAESRP DLILTGHKEN AEFALAMCPT 540 EPFVLSGGKD KSVVLWSIQD HISTLAESAS KSPVSPGSSG SKQVVGKSGT EKSSDTPTIG 600 PRGVYQGHGD TVEDVQFCPS SAQEFCSVGD DSCLIFWDAR VGTSPVVKVE KAHNADLHCV 660 DWNPHDMNLI LTGSADTSVR MFDRRNLTSG GVGSPIHKFE GHKAAVLCWS PDKATIFGSA 720 AEDGFLNIWD HEKVGKKKER TGTRTSNTPP GLFFQHAGHR DKVVDFHWNA YDPWTIVSVS 780 DDGESTGGGG TLQIWRMSDL IYRPEEEVLA ELEKFKAHLA SCTPKA*

Sequence ? help Back to Top

Protein Sequence Length: 827 aa Download sequence Send to blast

MSINPNPNPN PNPNPNATSN HHHHPLLVVG PSSSSSSSHP HPHPHPHPPP PHPHHPSSSS  60
SSSFQTLAPS SSSSSSSRLS GGQSNSACAA CKYQRRKCNP DCTLAPYFPA DQQRQFLNAH  120
RLFGVSNILK IIRGLDSRKR DEAMRTIIYQ SNVRAMDSVG GCYRIVLELE RQVELYTAEL  180
QLVLQQLAVC RAQAQAAAAA APLSAELGLN VAADVDDGVV YNNNLFGNNN FVPIAPHQQQ  240
QQQQYYNYFC YDSDGENSTR FNNNVIVNFN NENNFGNIGD NVEDALVSSS INFQQEQMQK  300
QLEEVKLEEL DVKPLVDVFE AGQSFIRENE EEQLKSSASS LCRAKMAEKE DLNTMEHVQE  360
HDLKGAASLF TLTNGSSSAI EYTQWKSLVP VLYDWLANHN LVWPSLSCRK DGGRSLSRRR  420
TRIASTDGSV PNTLVIANCE VVKPRVAAAE HISQFNEEAR SPFVKKFKTI IHPGEVNRIR  480
ELPQNSKIVA THTDSPDVLI WDVEAQPNRH AVLGAAESRP DLILTGHKEN AEFALAMCPT  540
EPFVLSGGKD KSVVLWSIQD HISTLAESAS KSPVSPGSSG SKQVVGKSGT EKSSDTPTIG  600
PRGVYQGHGD TVEDVQFCPS SAQEFCSVGD DSCLIFWDAR VGTSPVVKVE KAHNADLHCV  660
DWNPHDMNLI LTGSADTSVR MFDRRNLTSG GVGSPIHKFE GHKAAVLCWS PDKATIFGSA  720
AEDGFLNIWD HEKVGKKKER TGTRTSNTPP GLFFQHAGHR DKVVDFHWNA YDPWTIVSVS  780
DDGESTGGGG TLQIWRMSDL IYRPEEEVLA ELEKFKAHLA SCTPKA*

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
2xyi_A	2e-55	381	806	24	417	PROBABLE HISTONE-BINDING PROTEIN CAF1
3c99_A	2e-55	381	806	26	419	Chromatin assembly factor 1 p55 subunit
3c9c_A	2e-55	381	806	26	419	Chromatin assembly factor 1 p55 subunit
Search in ModeBase

Functional Description ? help Back to Top
Source	Description
UniProt	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of the flowering autonomous pathway which positively regulates flowering by promoting transcriptional repression of the flowering repressor FLC. May promote histone deacetylation at the FLC locus leading to the formation of repressive chromatin structures. Also negatively regulates cold-responsive genes. {ECO:0000269\|PubMed:12548286, ECO:0000269\|PubMed:14593187, ECO:0000269\|PubMed:14745447, ECO:0000269\|PubMed:14745450}.

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_020099061.1	0.0	WD-40 repeat-containing protein MSI4-like
Swissprot	O22607	0.0	MSI4_ARATH; WD-40 repeat-containing protein MSI4
STRING	XP_008795452.1	0.0	(Phoenix dactylifera)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT3G13850.1	3e-35	LOB domain-containing protein 22

Link Out ? help Back to Top
Phytozome	Aco005756.1

Publications ? help Back to Top
Díaz-Sala C,Garrido G,Sabater B Age-related loss of rooting capability in Arabidopsis thaliana and its reversal by peptides containing the Arg-Gly-Asp (RGD) motif. Physiol Plant, 2002. 114(4): p. 601-607 [PMID:11975735] Lee JH, et al. Characterization of Arabidopsis and rice DWD proteins and their roles as substrate receptors for CUL4-RING E3 ubiquitin ligases. Plant Cell, 2008. 20(1): p. 152-67 [PMID:18223036] Zhang Y, et al. Arabidopsis DDB1-CUL4 ASSOCIATED FACTOR1 forms a nuclear E3 ubiquitin ligase with DDB1 and CUL4 that is involved in multiple plant developmental processes. Plant Cell, 2008. 20(6): p. 1437-55 [PMID:18552200] Bäurle I,Dean C Differential interactions of the autonomous pathway RRM proteins and chromatin regulators in the silencing of Arabidopsis targets. PLoS ONE, 2008. 3(7): p. e2733 [PMID:18628965] Campi M,D'Andrea L,Emiliani J,Casati P Participation of chromatin-remodeling proteins in the repair of ultraviolet-B-damaged DNA. Plant Physiol., 2012. 158(2): p. 981-95 [PMID:22170978] Honda H, et al. Purification and characterization of two phospho-β-galactosidases, LacG1 and LacG2, from Lactobacillus gasseri ATCC33323(T). J. Gen. Appl. Microbiol., 2012. 58(1): p. 11-7 [PMID:22449746] Xu Y, et al. A matrix protein silences transposons and repeats through interaction with retinoblastoma-associated proteins. Curr. Biol., 2013. 23(4): p. 345-50 [PMID:23394836] Lee J,Amasino RM Two FLX family members are non-redundantly required to establish the vernalization requirement in Arabidopsis. Nat Commun, 2013. 4: p. 2186 [PMID:23864009] Kenzior A,Folk WR Arabidopsis thaliana MSI4/FVE associates with members of a novel family of plant specific PWWP/RRM domain proteins. Plant Mol. Biol., 2015. 87(4-5): p. 329-39 [PMID:25600937] Luo M, et al. Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis. Plant J., 2015. 82(6): p. 925-36 [PMID:25922987] Kang MY, et al. Negative regulatory roles of DE-ETIOLATED1 in flowering time in Arabidopsis. Sci Rep, 2015. 5: p. 9728 [PMID:25962685] Kang MY,Kwon HY,Kim NY,Sakuraba Y,Paek NC CONSTITUTIVE PHOTOMORPHOGENIC 10 (COP10) Contributes to Floral Repression under Non-Inductive Short Days in Arabidopsis. Int J Mol Sci, 2015. 16(11): p. 26493-505 [PMID:26556345] Yu CW,Chang KY,Wu K Genome-Wide Analysis of Gene Regulatory Networks of the FVE-HDA6-FLD Complex in Arabidopsis. Front Plant Sci, 2016. 7: p. 555 [PMID:27200029] Feng P, et al. Chloroplast retrograde signal regulates flowering. Proc. Natl. Acad. Sci. U.S.A., 2016. 113(38): p. 10708-13 [PMID:27601637] Cheng JZ,Zhou YP,Lv TX,Xie CP,Tian CE Research progress on the autonomous flowering time pathway in Arabidopsis. Physiol Mol Biol Plants, 2017. 23(3): p. 477-485 [PMID:28878488] Liu C,Wang B,Li Z,Peng Z,Zhang J TsNAC1 Is a Key Transcription Factor in Abiotic Stress Resistance and Growth. Plant Physiol., 2018. 176(1): p. 742-756 [PMID:29122985] Sang S,Chen Y,Yang Q,Wang P Arabidopsis inositol polyphosphate multikinase delays flowering time through mediating transcriptional activation of FLOWERING LOCUS C. J. Exp. Bot., 2017. 68(21-22): p. 5787-5800 [PMID:29161428] Zhou JX, et al. Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time. J Integr Plant Biol, 2018. 60(5): p. 362-368 [PMID:29314758] Kenzior AL,Folk WR AtMSI4 and RbAp48 WD-40 repeat proteins bind metal ions. FEBS Lett., 1998. 440(3): p. 425-9 [PMID:9872415]