Agrobacterium fabrum strain 1D132 plasmid pTi1D132, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium; Agrobacterium tumefaciens complex.
Complete genome sequence of Agrobacterium fabrum 1D132
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\nCP033026.1.\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 :: agro05.04\nGenome Coverage :: 610x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/29/2023 12:03:09\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) :: 5,210\nCDSs (total) :: 5,139\nGenes (coding) :: 5,068\nCDSs (with protein) :: 5,068\nGenes (RNA) :: 71\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 4\nPseudo Genes (total) :: 71\nCDSs (without protein) :: 71\nPseudo Genes (ambiguous residues) :: 0 of 71\nPseudo Genes (frameshifted) :: 43 of 71\nPseudo Genes (incomplete) :: 45 of 71\nPseudo Genes (internal stop) :: 11 of 71\nPseudo Genes (multiple problems) :: 26 of 71\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008120558.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012654974.1
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_004118299.1
COORDINATES: protein motif:HMM:NF013970.2
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003603269.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004213243.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875209.1
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_010974847.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653088.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653087.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020820450.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653085.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551142.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011062313.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974876.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341926.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974798.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974878.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525124.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_003525126.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654879.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524938.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974883.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524941.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648958.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654884.1
COORDINATES: similar to AA sequence:RefSeq:WP_006698012.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654887.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974888.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524948.1
COORDINATES: similar to AA sequence:RefSeq:WP_003494913.1
COORDINATES: similar to AA sequence:RefSeq:WP_012049774.1
COORDINATES: similar to AA sequence:RefSeq:WP_007880931.1
COORDINATES: protein motif:HMM:NF037472.2
COORDINATES: similar to AA sequence:RefSeq:WP_003501832.1
COORDINATES: similar to AA sequence:RefSeq:WP_018390189.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019590.2
COORDINATES: similar to AA sequence:RefSeq:WP_007687935.1
COORDINATES: similar to AA sequence:RefSeq:WP_003506626.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011199101.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501767.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501379.1
COORDINATES: similar to AA sequence:RefSeq:WP_004676096.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523830.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523831.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982970.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129344.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508813.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_018516734.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_003523837.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010300.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_010974897.1
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_010974790.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523842.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523843.1
COORDINATES: similar to AA sequence:RefSeq:WP_003591521.1
PAS domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523848.1
transcriptional activater for conjugation
COORDINATES: similar to AA sequence:RefSeq:WP_012654946.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523850.1
GO:0004645 - 1,4-alpha-oligoglucan phosphorylase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007789939.1
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
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007819484.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974903.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974904.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974905.1
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_012654927.1
COORDINATES: similar to AA sequence:RefSeq:WP_004432806.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523862.1
COORDINATES: similar to AA sequence:RefSeq:WP_006783221.1
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_007677454.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892482.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974909.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015241702.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010891511.1
COORDINATES: similar to AA sequence:RefSeq:WP_006204705.1
COORDINATES: protein motif:HMM:NF019421.2
COORDINATES: similar to AA sequence:RefSeq:WP_014761245.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003551160.1
COORDINATES: similar to AA sequence:RefSeq:WP_017968945.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974913.1
(dimethylallyl)adenosine tRNA methylthiotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_010974914.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974915.1
type IV secretion system lytic transglycosylase VirB1
COORDINATES: similar to AA sequence:RefSeq:WP_010891502.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891501.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974916.1
type IV secretion/conjugal transfer ATPase VirB4
COORDINATES: similar to AA sequence:RefSeq:WP_010891499.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537089.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891497.1
type IV secretion system lipoprotein VirB7
COORDINATES: similar to AA sequence:RefSeq:WP_019856525.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891495.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_010891494.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974918.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010891492.1
two-component system response regulator VirG
COORDINATES: similar to AA sequence:RefSeq:WP_010891491.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427359.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891489.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974919.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974778.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974920.1
The ATPase VirD4 is a core component of the VirB/VirD4 form of type IV secretion systems (T4SS), also known as type IVa secretion systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010974921.1
COORDINATES: protein motif:HMM:NF018377.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974776.1
type IV secretion system virulence effector VirE3
COORDINATES: similar to AA sequence:RefSeq:WP_010891482.1
type IV secretion system effector chaperone VirE1
COORDINATES: similar to AA sequence:RefSeq:WP_010974922.1
type IV secretion system single-stranded DNA binding effector VirE2
COORDINATES: similar to AA sequence:RefSeq:WP_010974923.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803489.1
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020012117.1
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_010974775.1
GO:0046855 - inositol phosphate dephosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974926.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974815.1
COORDINATES: protein motif:HMM:NF014125.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974818.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974819.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974821.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649066.1
COORDINATES: similar to AA sequence:RefSeq:WP_101244917.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_034521075.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891459.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427380.1
NAD/NADP octopine/nopaline dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523908.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523910.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523912.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003523913.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523914.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523915.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523916.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523917.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523918.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007774259.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039790.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013518716.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003525188.1
COORDINATES: similar to AA sequence:RefSeq:WP_007757122.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524893.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524895.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517331.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524923.1
COORDINATES: protein motif:HMM:NF015905.2
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523583.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_020046772.1
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_010974812.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974838.1