Agrobacterium rhizogenes strain A4 plasmid pArA4, complete sequence.
Agrobacterium rhizogenes (Rhizobium rhizogenes)
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
Complete genome sequence of Agrobacterium rhizogenes A4 (EML492)
Submitted (15-APR-2021) Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Taipei 11529, Taiwan
REFSEQ INFORMATION: The reference sequence is identical to\nCP073112.1.\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 :: Velvet v. v1.2.10\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 366.8x\nSequencing Technology :: Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/19/2022 16:08:16\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) :: 6,783\nCDSs (total) :: 6,715\nGenes (coding) :: 6,624\nCDSs (with protein) :: 6,624\nGenes (RNA) :: 68\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 55\nncRNAs :: 4\nPseudo Genes (total) :: 91\nCDSs (without protein) :: 91\nPseudo Genes (ambiguous residues) :: 0 of 91\nPseudo Genes (frameshifted) :: 42 of 91\nPseudo Genes (incomplete) :: 61 of 91\nPseudo Genes (internal stop) :: 19 of 91\nPseudo Genes (multiple problems) :: 26 of 91\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020046783.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011654634.1
COORDINATES: similar to AA sequence:RefSeq:WP_004119862.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF025388.2
COORDINATES: similar to AA sequence:RefSeq:WP_012760230.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326374.1
COORDINATES: similar to AA sequence:RefSeq:WP_020323947.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573747.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003497293.1
COORDINATES: protein motif:HMM:NF021946.2
phage exclusion protein Lit family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000362946.1
COORDINATES: similar to AA sequence:RefSeq:WP_018482005.1
COORDINATES: similar to AA sequence:RefSeq:WP_018482004.1
COORDINATES: similar to AA sequence:RefSeq:WP_008120571.1
COORDINATES: similar to AA sequence:RefSeq:WP_018482002.1
COORDINATES: similar to AA sequence:RefSeq:WP_008120574.1
COORDINATES: protein motif:HMM:NF024098.2
COORDINATES: similar to AA sequence:RefSeq:WP_018481999.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011082894.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020048036.1
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_019863256.1
GO:0004068 - aspartate 1-decarboxylase activity [Evidence IEA]
GO:0006523 - alanine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003522822.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812492.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007812491.1
COORDINATES: similar to AA sequence:RefSeq:WP_017269019.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046857.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046856.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046854.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012881221.1
frameshifted; internal stop; 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_007812490.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013761251.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007812488.1
COORDINATES: similar to AA sequence:RefSeq:WP_018064072.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007812486.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812485.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812484.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812483.1
COORDINATES: protein motif:HMM:NF012742.2
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012651736.1
COORDINATES: similar to AA sequence:RefSeq:WP_006726406.1
GO:0004456 - phosphogluconate dehydratase activity [Evidence IEA]
GO:0009255 - Entner-Doudoroff pathway through 6-phosphogluconate [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: protein motif:HMM:NF019322.2
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: similar to AA sequence:RefSeq:WP_020046849.1
COORDINATES: similar to AA sequence:RefSeq:WP_011242160.1
COORDINATES: similar to AA sequence:RefSeq:WP_009816227.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650556.1
COORDINATES: protein motif:HMM:NF012515.2
COORDINATES: similar to AA sequence:RefSeq:WP_014330966.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014328125.1
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: protein motif:HMM:NF025839.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974775.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046862.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523852.1
COORDINATES: similar to AA sequence:RefSeq:WP_007819485.1
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_020046876.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046875.1
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_015916357.1
COORDINATES: similar to AA sequence:RefSeq:WP_020046871.1
COORDINATES: similar to AA sequence:RefSeq:WP_017966315.1
GO:0008851 - ethanolamine ammonia-lyase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003543387.1
COORDINATES: similar to AA sequence:RefSeq:WP_006310495.1
COORDINATES: similar to AA sequence:RefSeq:WP_017134613.1
COORDINATES: similar to AA sequence:RefSeq:WP_012042770.1
COORDINATES: similar to AA sequence:RefSeq:WP_007689559.1
COORDINATES: similar to AA sequence:RefSeq:WP_003550297.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565882.1
COORDINATES: protein motif:HMM:NF012669.2
COORDINATES: protein motif:HMM:TIGR01879.1
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: similar to AA sequence:RefSeq:WP_011648946.1
choline/ethanolamine kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008835386.1
GO:0004401 - histidinol-phosphatase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014528009.1
COORDINATES: protein motif:HMM:NF024863.2
COORDINATES: similar to AA sequence:RefSeq:WP_018183154.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531270.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013530475.1
COORDINATES: similar to AA sequence:RefSeq:WP_013530476.1
COORDINATES: similar to AA sequence:RefSeq:WP_006938338.1
COORDINATES: similar to AA sequence:RefSeq:WP_009755866.1
GO:0004370 - glycerol kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007812225.1
GO:0009331 - glycerol-3-phosphate dehydrogenase complex [Evidence IEA]
GO:0004368 - glycerol-3-phosphate dehydrogenase (quinone) activity [Evidence IEA]
GO:0006072 - glycerol-3-phosphate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010900271.1
GO:0003987 - acetate-CoA ligase activity [Evidence IEA]
GO:0019427 - acetyl-CoA biosynthetic process from acetate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015317975.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019205 - nucleobase-containing compound kinase activity [Evidence IEA]
GO:0006139 - nucleobase-containing compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007633223.1
HAMP domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_012734912.1
GO:0042132 - fructose 1,6-bisphosphate 1-phosphatase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015497175.1
GO:0004332 - fructose-bisphosphate aldolase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis, and/or gluconeogenesis; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018265266.1
GO:0004807 - triose-phosphate isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018329825.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341926.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516748.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014330959.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240610.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650718.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018328946.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427427.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_014989425.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018240816.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501400.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655060.1
COORDINATES: similar to AA sequence:RefSeq:WP_014989427.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649951.1
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_018328950.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018482051.1
COORDINATES: similar to AA sequence:RefSeq:WP_020187275.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654735.1
COORDINATES: similar to AA sequence:RefSeq:WP_004677266.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013760951.1
COORDINATES: similar to AA sequence:RefSeq:WP_018328954.1
COORDINATES: similar to AA sequence:RefSeq:WP_018240805.1
COORDINATES: similar to AA sequence:RefSeq:WP_013893929.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007635331.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_018482044.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_020397338.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_011654562.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048127.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_016558651.1
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_020048129.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427446.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF018154.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011427388.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875417.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875418.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538580.1
autoinducer binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013984777.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_020048152.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427455.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048155.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_018482027.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02780.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_018098144.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_014858032.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129936.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427463.1
GO:0016740 - transferase activity [Evidence IEA]