Agrobacterium vaccinii strain B7.6 plasmid pB7.6, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
Agrobacterium spp. associated with crown gall tumors on blueberry
Submitted (27-MAY-2020) AG Smalla, Julius Kuehn-Institut, Federal Research Centre for Cultivated Plants (JKI), EP, Messeweg 11-12, Braunschweig 38104, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP054152.1.\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 :: Hybrid assembly using SPAdes, Flye, Canu\n and Unicycler v. Spades, Galaxy Version\n 3.12.0+galaxy1; Flye, Galaxy Version 2.6;\n Canu, Galaxy Version 1.8; Unicycler,\n Galaxy Version 0.4.8.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 97x\nSequencing Technology :: Oxford Nanopore MiniION and Illumina\n MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/06/2023 04:20:48\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) :: 4,635\nCDSs (total) :: 4,561\nGenes (coding) :: 4,521\nCDSs (with protein) :: 4,521\nGenes (RNA) :: 74\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 4\nPseudo Genes (total) :: 40\nCDSs (without protein) :: 40\nPseudo Genes (ambiguous residues) :: 0 of 40\nPseudo Genes (frameshifted) :: 17 of 40\nPseudo Genes (incomplete) :: 29 of 40\nPseudo Genes (internal stop) :: 12 of 40\nPseudo Genes (multiple problems) :: 12 of 40\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_003571859.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012653006.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518553.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518555.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003518556.1
type II toxin-antitoxin system MqsA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007872692.1
COORDINATES: similar to AA sequence:RefSeq:WP_006698803.1
COORDINATES: similar to AA sequence:RefSeq:WP_018858689.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018858688.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006724079.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017642439.1
COORDINATES: similar to AA sequence:RefSeq:WP_003492241.1
COORDINATES: similar to AA sequence:RefSeq:WP_006698757.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006698759.1
COORDINATES: similar to AA sequence:RefSeq:WP_004434329.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427422.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011654719.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013593.2
COORDINATES: similar to AA sequence:RefSeq:WP_015918474.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013637466.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017958833.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012724228.1
COORDINATES: similar to AA sequence:RefSeq:WP_010171031.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974415.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517275.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015222925.1
COORDINATES: similar to AA sequence:RefSeq:WP_007694630.1
COORDINATES: similar to AA sequence:RefSeq:WP_009777787.1
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003517409.1
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_019565689.1
COORDINATES: similar to AA sequence:RefSeq:WP_015916063.1
COORDINATES: similar to AA sequence:RefSeq:WP_018860096.1
COORDINATES: similar to AA sequence:RefSeq:WP_010160656.1
COORDINATES: similar to AA sequence:RefSeq:WP_007758512.1
COORDINATES: similar to AA sequence:RefSeq:WP_011004407.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018067613.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014763132.1
COORDINATES: similar to AA sequence:RefSeq:WP_003498884.1
COORDINATES: similar to AA sequence:RefSeq:WP_015917295.1
COORDINATES: similar to AA sequence:RefSeq:WP_006727346.1
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006315784.1
COORDINATES: similar to AA sequence:RefSeq:WP_017270994.1
GO:0015087 - cobalt ion transmembrane transporter activity [Evidence IEA]; GO:0015095 - magnesium ion transmembrane transporter activity [Evidence IEA]
GO:0006824 - cobalt ion transport [Evidence IEA]; GO:0015693 - magnesium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003517714.1
COORDINATES: similar to AA sequence:RefSeq:WP_012556104.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
prolyl oligopeptidase family serine peptidase
COORDINATES: similar to AA sequence:RefSeq:WP_017277969.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_018094973.1
COORDINATES: similar to AA sequence:RefSeq:WP_018099081.1
GO:0008853 - exodeoxyribonuclease III activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006728693.1
COORDINATES: protein motif:HMM:NF025013.2
COORDINATES: similar to AA sequence:RefSeq:WP_007255052.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005663536.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
YbhB/YbcL family Raf kinase inhibitor-like protein
COORDINATES: similar to AA sequence:RefSeq:WP_003547960.1
COORDINATES: similar to AA sequence:RefSeq:WP_012763224.1
COORDINATES: similar to AA sequence:RefSeq:WP_013761150.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003551728.1
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]
COORDINATES: similar to AA sequence:RefSeq:WP_003551726.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003551722.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637213.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517422.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517423.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003510189.1
COORDINATES: similar to AA sequence:RefSeq:WP_020812789.1
GO:0005971 - ribonucleoside-diphosphate reductase complex [Evidence IEA]
GO:0030145 - manganese ion binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
class 1b ribonucleoside-diphosphate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_007700571.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
class 1b ribonucleoside-diphosphate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_011426927.1
GO:0009263 - deoxyribonucleotide biosynthetic process [Evidence IEA]
class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI
COORDINATES: similar to AA sequence:RefSeq:WP_004692439.1
GO:0097573 - glutathione oxidoreductase activity [Evidence IEA]
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_010973353.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005227444.1
catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate; 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:NF037968.1
COORDINATES: similar to AA sequence:RefSeq:WP_003576998.1
bifunctional diguanylate cyclase/phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_013637154.1
GO:0004332 - fructose-bisphosphate aldolase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013637153.1
COORDINATES: similar to AA sequence:RefSeq:WP_003526851.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003590942.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018449580.1
COORDINATES: similar to AA sequence:RefSeq:WP_007609695.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637148.1
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_007801418.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006316203.1
COORDINATES: similar to AA sequence:RefSeq:WP_012385706.1
COORDINATES: similar to AA sequence:RefSeq:WP_004674765.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015887880.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637143.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331523.1
GO:0008381 - mechanosensitive monoatomic ion channel activity [Evidence IEA]
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011652729.1
COORDINATES: similar to AA sequence:RefSeq:WP_011088246.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_003518366.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518364.1
GO:0016020 - membrane [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019566827.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967202.1
COORDINATES: similar to AA sequence:RefSeq:WP_018517692.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003519470.1
COORDINATES: similar to AA sequence:RefSeq:WP_011969704.1
COORDINATES: similar to AA sequence:RefSeq:WP_007879052.1
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: similar to AA sequence:RefSeq:WP_010967199.1
COORDINATES: similar to AA sequence:RefSeq:WP_014989519.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518654.1
GO:0003839 - gamma-glutamylcyclotransferase activity [Evidence IEA]
GO:0006751 - glutathione catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006316106.1
COORDINATES: similar to AA sequence:RefSeq:WP_013762167.1
COORDINATES: similar to AA sequence:RefSeq:WP_010660357.1
Fe(3+)-hydroxamate ABC transporter permease FhuB
COORDINATES: similar to AA sequence:RefSeq:WP_010660358.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003498276.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007877165.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012556039.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016646 - oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: similar to AA sequence:RefSeq:WP_017486248.1
COORDINATES: similar to AA sequence:RefSeq:WP_013341159.1
COORDINATES: similar to AA sequence:RefSeq:WP_016552959.1
frameshifted; 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_003545887.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003515217.1
COORDINATES: similar to AA sequence:RefSeq:WP_020009010.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523942.1
COORDINATES: similar to AA sequence:RefSeq:WP_019337721.1
COORDINATES: similar to AA sequence:RefSeq:WP_003510192.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974521.1
tannase/feruloyl esterase family alpha/beta hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_010974520.1
COORDINATES: protein motif:HMM:NF012354.2
COORDINATES: similar to AA sequence:RefSeq:WP_016987911.1
COORDINATES: similar to AA sequence:RefSeq:WP_005766116.1
COORDINATES: similar to AA sequence:RefSeq:WP_014088996.1
COORDINATES: similar to AA sequence:RefSeq:WP_019567210.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330541.1
COORDINATES: similar to AA sequence:RefSeq:WP_006313207.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006313206.1
COORDINATES: similar to AA sequence:RefSeq:WP_010972803.1
DctP family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007757166.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015933209.1
GO:0004497 - monooxygenase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007757169.1
COORDINATES: similar to AA sequence:RefSeq:WP_006699177.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_006023692.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: protein motif:HMM:NF022172.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974636.1
COORDINATES: similar to AA sequence:RefSeq:WP_018901388.1
COORDINATES: similar to AA sequence:RefSeq:WP_011146587.1
COORDINATES: protein motif:HMM:NF028169.2
TetR-like C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007788931.1
COORDINATES: similar to AA sequence:RefSeq:WP_007626714.1
COORDINATES: similar to AA sequence:RefSeq:WP_004670321.1
COORDINATES: similar to AA sequence:RefSeq:WP_014105414.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016558376.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010968043.1
COORDINATES: similar to AA sequence:RefSeq:WP_007598189.1
COORDINATES: similar to AA sequence:RefSeq:WP_007598187.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565657.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637274.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637275.1
COORDINATES: similar to AA sequence:RefSeq:WP_003577078.1
ankyrin repeat domain-containing protein
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005525 - GTP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013637225.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_003577065.1
GO:0004673 - protein histidine kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012760468.1
GO:0030554 - adenyl nucleotide binding [Evidence IEA]; GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013637216.1
COORDINATES: similar to AA sequence:RefSeq:WP_006466775.1
COORDINATES: similar to AA sequence:RefSeq:WP_003575056.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006312289.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016733346.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020050408.1
COORDINATES: similar to AA sequence:RefSeq:WP_019173525.1
GO:0015293 - symporter activity [Evidence IEA]
bile acid:sodium symporter family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003170527.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF025637.2
COORDINATES: similar to AA sequence:RefSeq:WP_014764657.1
COORDINATES: similar to AA sequence:RefSeq:WP_020808223.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724017.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018210407.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_020046788.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003553728.1
COORDINATES: protein motif:HMM:NF025298.2
COORDINATES: similar to AA sequence:RefSeq:WP_012648915.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.