PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID 676765750
Organism
Sisymbrium irio
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Sisymbrieae; Sisymbrium
Family B3
Protein Properties Length: 790aa    MW: 89158.5 Da    PI: 8.9702
Description B3 family protein
Gene Model
Gene Model ID Type Source Coding Sequence
676765750genomeVEGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B343.84.5e-1419931797
               E--HHH.HTT---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE CS
         B3 17 vlpkkfaeehggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvf 97
               ++p kf+++++ +   s+ + l+ ++g +W+v l  rk ++++++++GW+eFv+   ++ g  ++F+++g+s f   v +f
  676765750 19 RVPDKFVSKFKDE--LSVAVALTVPDGHVWRVGL--RKADNKIWFQDGWQEFVDRYSIRIGYLLIFRYEGNSAF--SVYIF 93
               589****999755..99*****************..**********************************9999..88777 PP
2B353.25.5e-17242335199
                EEEE-..-HHHHTT-EE--HHH.HTT.---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE-S CS
         B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfrk 99 
                f  vl ps+  + ++++lp  fae++ +g++ + ++++   +  ++W v++    k gr  +++GW eF  +n+L egD++vF+l ++++f l+v++fr 
  676765750 242 FRVVLRPSYLYRGCIMYLPSGFAEKYlSGIS-GFIKVQ---LAEKQWPVRC--LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAFRV 335
                677899********************84442.444555...567*******..666666779************************99*******99985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
CDDcd100178.14E-151194No hitNo description
SMARTSM010194.3E-101296IPR003340B3 DNA binding domain
SuperFamilySSF1019361.47E-171795IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.2E-181995IPR015300DNA-binding pseudobarrel domain
PfamPF023623.5E-111994IPR003340B3 DNA binding domain
PROSITE profilePS5086312.522096IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.102.0E-22234334IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.16E-21235336IPR015300DNA-binding pseudobarrel domain
CDDcd100179.99E-20240334No hitNo description
PROSITE profilePS5086312.619242336IPR003340B3 DNA binding domain
SMARTSM010198.1E-22242336IPR003340B3 DNA binding domain
PfamPF023622.0E-15242335IPR003340B3 DNA binding domain
PROSITE profilePS513757.936464498IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007560.0011469494IPR002885Pentatricopeptide repeat
PfamPF015350.0015469494IPR002885Pentatricopeptide repeat
PfamPF015350.035497510IPR002885Pentatricopeptide repeat
PROSITE profilePS513756.16537571IPR002885Pentatricopeptide repeat
PROSITE profilePS513757.443574604IPR002885Pentatricopeptide repeat
PfamPF130412.0E-7604651IPR002885Pentatricopeptide repeat
PROSITE profilePS513759.723605639IPR002885Pentatricopeptide repeat
PROSITE profilePS513759.262640670IPR002885Pentatricopeptide repeat
TIGRFAMsTIGR007565.0E-4642675IPR002885Pentatricopeptide repeat
PROSITE profilePS513756.27676706IPR002885Pentatricopeptide repeat
PROSITE profilePS513757.443749783IPR002885Pentatricopeptide repeat
PfamPF015350.045753781IPR002885Pentatricopeptide repeat
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0080156Biological Processmitochondrial mRNA modification
GO:0005739Cellular Componentmitochondrion
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 790 aa     Download sequence    Send to blast
MSCGSLYNLF SFRYMLVQRV PDKFVSKFKD ELSVAVALTV PDGHVWRVGL RKADNKIWFQ  60
DGWQEFVDRY SIRIGYLLIF RYEGNSAFSV YIFNLSHSEI NYHSTGLMDS AHNHFKRARL  120
FEDLEDEDAE VVYPSSVYPV PHPETTVSPN KGYPSSAIQS LFTGPVKAEE TTPTPKVPKK  180
RGRKKKNADP EEINSSAPRD DDPENRSKFY ESASARKRTV TAEERERAIN AAKTFEPTNP  240
FFRVVLRPSY LYRGCIMYLP SGFAEKYLSG ISGFIKVQLA EKQWPVRCLY KAGRAKFSQG  300
WYEFTLENNL GEGDVCVFEL LRTRDFVLKV TAFRVNETSK TIVQAKQIHA QLVINGCRDN  360
SLVGKLIGHY CSKQSTESSK LAHLLVFPRF GHTDKFLFNT LLKCSKPEDS IRIFANWASK  420
SSLLYLNERT FVFVLGACAR SATALRVGRI VHGMVIKLGF LYESELIGTT LLHFYAKHGD  480
LRYARKVFDE MPERTSVTWN AMIGGYCSHK DKGNHNARKA MILFRRFSCC GNGVRPTDTT  540
MVCVLSAISQ TGLLEIGSLV HGYIEKLGFT PQVDVFIGTG LVDMYSKCGC LDSAFSVFEV  600
MKVKNVLTWT SVATGLALNG RGNETPNLLN RMAESGIKPN EVTFTSLLSA YRHIGLVQEG  660
LELFQSMRTR FGVTPVIQHY GCIVDLLGKA GRLQEAYEFV SAMPIKPDAI MLRSLCNACS  720
IYGETVMGEE IGKALLEMER EEKELSGSEC EDYVALSNVL ASKGKWVEVE KLRNEMKERR  780
IKTRPGYSFV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4i1k_A1e-8720533712144B3 domain-containing transcription factor VRN1
4i1k_B1e-8720533712144B3 domain-containing transcription factor VRN1
Search in ModeBase
Cis-element ? help Back to Top
SourceLink
PlantRegMap676765750
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2400980.0AC240098.1 Sisymbrium irio clone SIR-19O02, complete sequence.
GenBankAC2401020.0AC240102.1 Sisymbrium irio clone SIR-40E09, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_006406547.10.0pentatricopeptide repeat-containing protein At3g18970
SwissprotQ9LJ690.0PP243_ARATH; Pentatricopeptide repeat-containing protein At3g18970
TrEMBLV4LC700.0V4LC70_EUTSA; Uncharacterized protein
STRINGXP_006406547.10.0(Eutrema salsugineum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM1281033
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18990.10.0B3 family protein
Publications ? help Back to Top
  1. Lurin C, et al.
    Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis.
    Plant Cell, 2004. 16(8): p. 2089-103
    [PMID:15269332]
  2. Takenaka M,Verbitskiy D,Zehrmann A,Brennicke A
    Reverse genetic screening identifies five E-class PPR proteins involved in RNA editing in mitochondria of Arabidopsis thaliana.
    J. Biol. Chem., 2010. 285(35): p. 27122-9
    [PMID:20566637]
  3. Liu JM, et al.
    The E-Subgroup Pentatricopeptide Repeat Protein Family in Arabidopsis thaliana and Confirmation of the Responsiveness PPR96 to Abiotic Stresses.
    Front Plant Sci, 2016. 7: p. 1825
    [PMID:27994613]