Agrobacterium larrymoorei strain CFBP5477 plasmid pTiCFBP5477, complete sequence.
Agrobacterium larrymoorei (Rhizobium larrymoorei)
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
Complete genome sequence of Agrobacterium larrymoorei CFBP5477
Submitted (01-MAY-2023) Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Taipei 115201, Taiwan
Submitted (25-APR-2019) Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Taipei 11529, Taiwan
REFSEQ INFORMATION: The reference sequence is identical to\nCP124736.1.\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 :: Unicycler v. v0.4.9b\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 193.4x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/14/2023 07:02:09\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,797\nCDSs (total) :: 4,720\nGenes (coding) :: 4,670\nCDSs (with protein) :: 4,670\nGenes (RNA) :: 77\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 4\nPseudo Genes (total) :: 50\nCDSs (without protein) :: 50\nPseudo Genes (ambiguous residues) :: 0 of 50\nPseudo Genes (frameshifted) :: 21 of 50\nPseudo Genes (incomplete) :: 32 of 50\nPseudo Genes (internal stop) :: 6 of 50\nPseudo Genes (multiple problems) :: 8 of 50\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
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004129902.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523560.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523559.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523557.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020809962.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523551.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: protein motif:HMM:NF024491.2
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_012653444.1
COORDINATES: similar to AA sequence:RefSeq:WP_010660156.1
COORDINATES: similar to AA sequence:RefSeq:WP_010660155.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012227095.1
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012227094.1
COORDINATES: similar to AA sequence:RefSeq:WP_017504351.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012650533.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048036.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003551129.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017957069.1
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_010974876.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341926.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501418.1
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_003525126.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654879.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427427.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974883.1
COORDINATES: similar to AA sequence:RefSeq:WP_012648956.1
COORDINATES: protein motif:HMM:NF015431.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007636902.1
GO:0004020 - adenylylsulfate kinase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF017760.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF013080.2
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012654883.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_003517402.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524956.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003524955.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524954.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524951.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974891.1
GO:0016787 - hydrolase activity [Evidence IEA]
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
GO:0030261 - chromosome condensation [Evidence IEA]
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_003501349.1
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_010974898.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523843.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974789.1
PAS domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_003523848.1
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
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005436 - sodium:phosphate symporter activity [Evidence IEA]
GO:0044341 - sodium-dependent phosphate transport [Evidence IEA]
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
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
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
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010891519.1
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_010974906.1
COORDINATES: similar to AA sequence:RefSeq:WP_004432806.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974785.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654892.1
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
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_010892482.1
COORDINATES: similar to AA sequence:RefSeq:WP_019963851.1
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
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006204705.1
COORDINATES: similar to AA sequence:RefSeq:WP_018855502.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_012649017.1
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_012649040.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803489.1
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_011970376.1
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020012117.1
GO:0016853 - isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974775.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654927.1
GO:0046855 - inositol phosphate dephosphorylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012654928.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974822.1
COORDINATES: protein motif:HMM:NF014125.2
COORDINATES: similar to AA sequence:RefSeq:WP_003477861.1
COORDINATES: protein motif:HMM:NF012334.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_010974816.1
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_010892366.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892367.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974826.1
NAD/NADP-dependent octopine/nopaline dehydrogenase family protein
involved in nopaline catabolism (ornithine cyclodeaminase)
COORDINATES: similar to AA sequence:RefSeq:WP_003523877.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891455.1
NAD/NADP octopine/nopaline dehydrogenase family protein
involved in nopaline catabolism (arginase)
COORDINATES: similar to AA sequence:RefSeq:WP_010891454.1
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
involved in nopaline catabolism (nopaline dehydrogenase)
COORDINATES: similar to AA sequence:RefSeq:WP_010891452.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
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
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012654961.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_018325663.1
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_012650640.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974838.1