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

RrC4630_p2

Organism

Raphanus raphanistrum

Taxonomic ID

109996

Taxonomic Lineage

cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus

Family

NF-YC

Protein Properties

Length: 686aa MW: 74377.8 Da PI: 6.0074

Description

NF-YC family protein

Gene Model

Gene Model ID	Type	Source	Coding Sequence
RrC4630_p2	genome	MSU	View CDS

Signature Domain? help Back to Top

No.	Domain	Score	E-value	Start	End	HMM Start	HMM End
1	NF-YC	176.1	3.5e-55	58	161	1	101
NF-YC 1 qlksfwekq...iekatdfknhelPlarikkilkadedvkmisaeaPvllskacelfileltlrswlhaeenkrrtlkksdiaaavtrtdifdflvdiv 96 ql++fwe+q iek+tdfknh+lPlarikki+kadedv+misaeaPv++++ace+fileltlrsw+h+eenkrrtl+k+diaaavtrtdifdflvdiv RrC4630_p2 58 QLQVFWENQfkeIEKTTDFKNHSLPLARIKKIMKADEDVRMISAEAPVVFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAVTRTDIFDFLVDIV 156 89****99999********************************************************************************** PP NF-YC 97 prdel 101 pr++l RrC4630_p2 157 PREDL 161 986 PP

Protein Features ? help Back to Top

Database	Entry ID	E-value	Start	End	InterPro ID	Description
SuperFamily	SSF47113	3.02E-31	53	152	IPR009072	Histone-fold
Gene3D	G3DSA:1.10.20.10	4.1E-37	72	144	IPR009072	Histone-fold
Pfam	PF00808	3.2E-21	80	143	IPR003958	Transcription factor CBF/NF-Y/archaeal histone domain
Gene3D	G3DSA:3.90.1300.10	8.2E-86	273	680	IPR023631	Amidase signature domain
SuperFamily	SSF75304	5.49E-86	286	680	IPR023631	Amidase signature domain
Pfam	PF01425	1.9E-51	287	456	IPR023631	Amidase signature domain
PROSITE pattern	PS00571	0	375	406	IPR020556	Amidase, conserved site
Pfam	PF01425	2.8E-5	590	676	IPR023631	Amidase signature domain

Gene Ontology ? help Back to Top
GO Term	GO Category	GO Description
GO:0009684	Biological Process	indoleacetic acid biosynthetic process
GO:0005829	Cellular Component	cytosol
GO:0004040	Molecular Function	amidase activity
GO:0043864	Molecular Function	indoleacetamide hydrolase activity
GO:0046982	Molecular Function	protein heterodimerization activity

Sequence ? help Back to Top
Protein Sequence Length: 686 aa Download sequence Send to blast
MDQQEHAQSG AMNYGSNPYQ TNPMTTTVAG SAGPAAPPGQ LGFHQIHQQQ QQQQLAQQLQ 60 VFWENQFKEI EKTTDFKNHS LPLARIKKIM KADEDVRMIS AEAPVVFARA CEMFILELTL 120 RSWNHTEENK RRTLQKNDIA AAVTRTDIFD FLVDIVPRED LRDEVLGSIP RGTVPEAAAA 180 GYPYGYLPAG TAPIGNPGMV MGNPGGAYPP NPYMGQPIVQ RRGDFREENE RTYQKNFKSL 240 CFIHKKLYLV ILYHLCDLNT EATTVMAMSN DYGAFIEKST ISPTASSSFP SLKGLTFAIK 300 DIFDVEGRVT GFGNPDWLRT HSAATSTAPV VSSLLEAGAT SLGITIMDEM AYSINGENAH 360 YGTPVNPVAS DRVPGGSSSG SAVAVGAGLV DFSIGTDTGG SIRVPASYCG IFGFRPSHGV 420 VSTVGVTPMA QSFDTVGWFA RDTGTLKQVG SVLLQQPDLN ATKPSQLIIA DDCFKLCSVP 480 RDLLVQPLVK SVDKSFGGNT VINKMDLGEY IQENVPSLKH FMTSETQQEF CVPPLMALSS 540 SMRLLQRYEF KVNHGEWVSS VKPEFGPGIS ERIEEAIRVS GEKIDLCRLV KTQLLTALST 600 LLGDNGVLMI PTVPGPPPHL QADVVALESF RSRAFSLLSI AGVSGLCQVS IPLGLHENLP 660 ISVSLVAKHG SDGFLLSLVD CLSKFI

Sequence ? help Back to Top

Protein Sequence Length: 686 aa Download sequence Send to blast

MDQQEHAQSG AMNYGSNPYQ TNPMTTTVAG SAGPAAPPGQ LGFHQIHQQQ QQQQLAQQLQ  60
VFWENQFKEI EKTTDFKNHS LPLARIKKIM KADEDVRMIS AEAPVVFARA CEMFILELTL  120
RSWNHTEENK RRTLQKNDIA AAVTRTDIFD FLVDIVPRED LRDEVLGSIP RGTVPEAAAA  180
GYPYGYLPAG TAPIGNPGMV MGNPGGAYPP NPYMGQPIVQ RRGDFREENE RTYQKNFKSL  240
CFIHKKLYLV ILYHLCDLNT EATTVMAMSN DYGAFIEKST ISPTASSSFP SLKGLTFAIK  300
DIFDVEGRVT GFGNPDWLRT HSAATSTAPV VSSLLEAGAT SLGITIMDEM AYSINGENAH  360
YGTPVNPVAS DRVPGGSSSG SAVAVGAGLV DFSIGTDTGG SIRVPASYCG IFGFRPSHGV  420
VSTVGVTPMA QSFDTVGWFA RDTGTLKQVG SVLLQQPDLN ATKPSQLIIA DDCFKLCSVP  480
RDLLVQPLVK SVDKSFGGNT VINKMDLGEY IQENVPSLKH FMTSETQQEF CVPPLMALSS  540
SMRLLQRYEF KVNHGEWVSS VKPEFGPGIS ERIEEAIRVS GEKIDLCRLV KTQLLTALST  600
LLGDNGVLMI PTVPGPPPHL QADVVALESF RSRAFSLLSI AGVSGLCQVS IPLGLHENLP  660
ISVSLVAKHG SDGFLLSLVD CLSKFI

3D Structure ? help Back to Top

PDB ID	Evalue	Query Start	Query End	Hit Start	Hit End	Description
5g49_B	6e-60	66	158	3	95	NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT C-3
Search in ModeBase

Nucleic Localization Signal ? help Back to Top

No.	Start	End	Sequence
1	130	136	RRTLQKN

Functional Description ? help Back to Top
Source	Description
UniProt	Amidase involved in auxin biosynthesis. Converts indole-3-acetamide to indole-3-acetate (PubMed:12620340, PubMed:27135507). Converts phenyl-2-acetamide (PAM) to phenyl-2-acetate. Substrate preference is PAM > IAM (PubMed:27135507). Can also use L-asparagine, oleamide and 1-naphtalene-acetamide as substrates, but not indole-3-acetonitrile or indole-3-acetyl-L-aspartic acid (PubMed:12620340). {ECO:0000269\|PubMed:12620340, ECO:0000269\|PubMed:27135507}.

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_018491076.1	0.0	PREDICTED: amidase 1-like
Swissprot	Q9FR37	0.0	AMI1_ARATH; Amidase 1
TrEMBL	A0A3P6GHA1	0.0	A0A3P6GHA1_BRAOL; Uncharacterized protein
STRING	Bo8g112230.1	0.0	(Brassica oleracea)

Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID	E-value	Description
AT1G08970.4	7e-90	nuclear factor Y, subunit C9

Publications ? help Back to Top
Chew O, et al. A plant outer mitochondrial membrane protein with high amino acid sequence identity to a chloroplast protein import receptor. FEBS Lett., 2004. 557(1-3): p. 109-14 [PMID:14741350] Pollmann S, et al. Subcellular localization and tissue specific expression of amidase 1 from Arabidopsis thaliana. Planta, 2006. 224(6): p. 1241-53 [PMID:16738862] Neu D,Lehmann T,Elleuche S,Pollmann S Arabidopsis amidase 1, a member of the amidase signature family. FEBS J., 2007. 274(13): p. 3440-51 [PMID:17555521] Aronsson H, et al. Toc64/OEP64 is not essential for the efficient import of proteins into chloroplasts in Arabidopsis thaliana. Plant J., 2007. 52(1): p. 53-68 [PMID:17655652] Jarvis P Targeting of nucleus-encoded proteins to chloroplasts in plants. New Phytol., 2008. 179(2): p. 257-85 [PMID:19086173] Mano Y, et al. The AMI1 gene family: indole-3-acetamide hydrolase functions in auxin biosynthesis in plants. J. Exp. Bot., 2010. 61(1): p. 25-32 [PMID:19887500] Lehmann T,Hoffmann M,Hentrich M,Pollmann S Indole-3-acetamide-dependent auxin biosynthesis: a widely distributed way of indole-3-acetic acid production? Eur. J. Cell Biol., 2010. 89(12): p. 895-905 [PMID:20701997] Hoffmann M,Lehmann T,Neu D,Hentrich M,Pollmann S Expression of AMIDASE1 (AMI1) is suppressed during the first two days after germination. Plant Signal Behav, 2010. 5(12): p. 1642-4 [PMID:21150258] Sánchez-Parra B, et al. Characterization of Four Bifunctional Plant IAM/PAM-Amidohydrolases Capable of Contributing to Auxin Biosynthesis. Plants (Basel), 2014. 3(3): p. 324-47 [PMID:27135507] Godee C,Mira MM,Wally O,Hill RD,Stasolla C Cellular localization of the Arabidopsis class 2 phytoglobin influences somatic embryogenesis. J. Exp. Bot., 2017. 68(5): p. 1013-1023 [PMID:28199692] Schwenkert S,Dittmer S,Soll J Structural components involved in plastid protein import. Essays Biochem., 2018. 62(1): p. 65-75 [PMID:29487196]