Agrobacterium fabrum strain 1D132 plasmid pAt1D132b, 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\nCP033025.1.\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_018009855.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006312309.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129924.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129910.1
COORDINATES: similar to AA sequence:RefSeq:WP_020810121.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_020046788.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518564.1
COORDINATES: similar to AA sequence:RefSeq:WP_006451195.1
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: similar to AA sequence:RefSeq:WP_003585893.1
COORDINATES: similar to AA sequence:RefSeq:WP_003585891.1
COORDINATES: similar to AA sequence:RefSeq:WP_003585889.1
COORDINATES: similar to AA sequence:RefSeq:WP_014242088.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012650375.1
COORDINATES: protein motif:HMM:NF012437.2
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012650378.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018901820.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018901819.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_011982997.1
GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017992741.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF039312.1
COORDINATES: protein motif:HMM:NF015131.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012708.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012402.2
hybrid-cluster NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_014240038.1
COORDINATES: similar to AA sequence:RefSeq:WP_016558830.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018900792.1
COORDINATES: similar to AA sequence:RefSeq:WP_011655377.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: similar to AA sequence:RefSeq:WP_018009845.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_018009846.1
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_018009849.1
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_020487238.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654614.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF018839.2
COORDINATES: similar to AA sequence:RefSeq:WP_011654600.1
COORDINATES: similar to AA sequence:RefSeq:WP_032488284.1
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: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF018977.2
GO:0004519 - endonuclease activity [Evidence IEA]
DNA mobilization endonuclease VirD1/MobC family subunit
COORDINATES: protein motif:HMM:NF018885.2
COORDINATES: protein motif:HMM:NF018377.2
COORDINATES: similar to AA sequence:RefSeq:WP_011983001.1
COORDINATES: similar to AA sequence:RefSeq:WP_014330531.1
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_076611960.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: similar to AA sequence:RefSeq:WP_005800888.1
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_012382807.1
COORDINATES: protein motif:HMM:NF013677.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749831.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_046205714.1
IS66-like element IS66 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_018093834.1
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: protein motif:HMM:NF021507.2
phosphodiester glycosidase family protein
COORDINATES: protein motif:HMM:NF012692.2
COORDINATES: similar to AA sequence:RefSeq:WP_007816976.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_007761508.1
COORDINATES: similar to AA sequence:RefSeq:WP_007761500.1
GO:0008448 - N-acetylglucosamine-6-phosphate deacetylase activity [Evidence IEA]
GO:0006040 - amino sugar metabolic process [Evidence IEA]
N-acetylglucosamine-6-phosphate deacetylase
COORDINATES: similar to AA sequence:RefSeq:WP_003518490.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654740.1
COORDINATES: similar to AA sequence:RefSeq:WP_003594540.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974894.1
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_003508820.1
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_006315305.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523843.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654946.1
COORDINATES: protein motif:HMM:NF023197.2
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: similar to AA sequence:RefSeq:WP_012222760.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011389707.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003523583.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_006312342.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654963.1
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_006312337.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012649097.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003523577.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_012649099.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892446.1
COORDINATES: similar to AA sequence:RefSeq:WP_003510276.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_003510279.1