Agrobacterium tumefaciens strain 12D1 plasmid pAt12D1, complete sequence.
Agrobacterium tumefaciens (Rhizobium radiobacter)
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium; Agrobacterium tumefaciens complex.
Complete genome sequence of Agrobacterium tumefaciens 12D1
Submitted (09-OCT-2018) Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Taipei 11529, Taiwan
REFSEQ INFORMATION: The reference sequence is identical to\nCP033033.1.\nBacteria and source DNA available from Erh-Min Lai.\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Genome-Assembly-Data-START##\nAssembly Method :: AllPaths v. 52188\nAssembly Name :: agro10.02\nGenome Coverage :: 383x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/19/2022 14:06:54\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 5,086\nCDSs (total) :: 5,017\nGenes (coding) :: 4,964\nCDSs (with protein) :: 4,964\nGenes (RNA) :: 69\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 4\nPseudo Genes (total) :: 53\nCDSs (without protein) :: 53\nPseudo Genes (ambiguous residues) :: 0 of 53\nPseudo Genes (frameshifted) :: 33 of 53\nPseudo Genes (incomplete) :: 32 of 53\nPseudo Genes (internal stop) :: 9 of 53\nPseudo Genes (multiple problems) :: 18 of 53\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012650473.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012650474.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654975.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650476.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974841.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654978.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974843.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974844.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974845.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654982.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654983.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974848.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_010974849.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018096456.1
PhzF family phenazine biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_012654989.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974851.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654990.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]; GO:0005488 - binding [Evidence IEA]
GO:0042918 - alkanesulfonate transport [Evidence IEA]
aliphatic sulfonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012654996.1
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_012654997.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974854.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974855.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654999.1
GO:0018786 - haloalkane dehalogenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012655000.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974857.1
COORDINATES: similar to AA sequence:RefSeq:WP_018436417.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
This protein belongs to a clade of uncharacterized proteins related to peroxidases such as the alkylhydroperoxidase AhpD; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012655002.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655003.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012655004.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974862.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974863.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655007.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012655008.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655009.1
COORDINATES: similar to AA sequence:RefSeq:WP_010968091.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974804.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974865.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974866.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN; Derived by automated computational analysis using gene prediction method: Protein Homology.
NtaA/DmoA family FMN-dependent monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_012655013.1
COORDINATES: similar to AA sequence:RefSeq:WP_020809962.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011992924.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974867.1
COORDINATES: protein motif:HMM:NF024772.2
COORDINATES: similar to AA sequence:RefSeq:WP_007787902.1
COORDINATES: similar to AA sequence:RefSeq:WP_007787906.1
COORDINATES: similar to AA sequence:RefSeq:WP_018243638.1
COORDINATES: similar to AA sequence:RefSeq:WP_003543067.1
COORDINATES: similar to AA sequence:RefSeq:WP_018072371.1
COORDINATES: similar to AA sequence:RefSeq:WP_013527935.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611567.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012756584.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129850.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013637316.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565689.1
COORDINATES: similar to AA sequence:RefSeq:WP_004680467.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501420.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505288.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974878.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654877.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974881.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505290.1
COORDINATES: similar to AA sequence:RefSeq:WP_010915956.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011578766.1
COORDINATES: similar to AA sequence:RefSeq:WP_006205780.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501400.1
COORDINATES: similar to AA sequence:RefSeq:WP_011993086.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023693.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007425104.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007711087.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_008193703.1
COORDINATES: similar to AA sequence:RefSeq:WP_012652039.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501391.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011578771.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501388.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018431454.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003501379.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654900.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523830.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654902.1
COORDINATES: similar to AA sequence:RefSeq:WP_011505304.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508813.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_020046837.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_003523837.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523838.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_012654909.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0008233 - peptidase activity [Evidence IEA]
conjugative transfer signal peptidase TraF
COORDINATES: similar to AA sequence:RefSeq:WP_006315304.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654911.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012654912.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654913.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008297617.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654915.1
amino acid ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012654916.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654917.1
COORDINATES: similar to AA sequence:RefSeq:WP_003516056.1
glyoxalase/bleomycin resistance/extradiol dioxygenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523843.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654946.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654921.1
GO:0004645 - 1,4-alpha-oligoglucan phosphorylase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523851.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974787.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003523853.1
COORDINATES: similar to AA sequence:RefSeq:WP_007819484.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974903.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974904.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523858.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523859.1
GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
glycerophosphodiester phosphodiesterase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523860.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523861.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523862.1
COORDINATES: protein motif:HMM:NF024811.2
COORDINATES: similar to AA sequence:RefSeq:WP_003523864.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523865.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654940.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523868.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523869.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654943.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523872.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523873.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654947.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523877.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891455.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
NAD/NADP octopine/nopaline dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523881.1
GO:0004053 - arginase activity [Evidence IEA]
GO:0019547 - arginine catabolic process to ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974827.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523884.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891452.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974828.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012654954.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012654955.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523894.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891638.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891637.1
nopaline ABC transporter substrate-binding protein NocT
COORDINATES: similar to AA sequence:RefSeq:WP_010974830.1
nopaline ABC transporter ATP-binding protein NocP
COORDINATES: similar to AA sequence:RefSeq:WP_003523901.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654961.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_012650632.1
COORDINATES: similar to AA sequence:RefSeq:WP_003510267.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_003523580.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974835.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012654966.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010892444.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012654968.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892446.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654970.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974838.1