Allorhizobium ampelinum S4 plasmid pAtS4c, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Allorhizobium; Allorhizobium ampelinum.
Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria
Submitted (14-MAR-2007) Virginia Bioinformatics Institute, Virginia Tech, Washington Street, Box 0477, Blacksburg, VA 24061, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000636.1.\nStrain/DNA available from Tom Burr, Cornell University,\ntjb1@cornell.edu. A. vitis S4 was isolated by Dr. Erno Szegedi in\n1981 from aerial gall that developed on a two-year-old woody\ngrapevine cane.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 19:47:51\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) :: 5,800\nCDSs (total) :: 5,729\nGenes (coding) :: 5,554\nCDSs (with protein) :: 5,554\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) :: 175\nCDSs (without protein) :: 175\nPseudo Genes (ambiguous residues) :: 0 of 175\nPseudo Genes (frameshifted) :: 82 of 175\nPseudo Genes (incomplete) :: 122 of 175\nPseudo Genes (internal stop) :: 28 of 175\nPseudo Genes (multiple problems) :: 52 of 175\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_003518552.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654975.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501258.1
COORDINATES: similar to AA sequence:RefSeq:WP_017991112.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012881217.1
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_018517330.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501256.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538502.1
COORDINATES: similar to AA sequence:RefSeq:WP_015918401.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017957260.1
COORDINATES: similar to AA sequence:RefSeq:WP_013761043.1
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011982903.1
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003588921.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
histidine kinase dimerization/phosphoacceptor domain -containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007760130.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018449122.1
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_006958134.1
COORDINATES: similar to AA sequence:RefSeq:WP_007601629.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: similar to AA sequence:RefSeq:WP_015342378.1
COORDINATES: similar to AA sequence:RefSeq:WP_015918138.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650495.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_007751248.1
COORDINATES: similar to AA sequence:RefSeq:WP_014528282.1
COORDINATES: similar to AA sequence:RefSeq:WP_007439021.1
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_018062848.1
COORDINATES: similar to AA sequence:RefSeq:WP_019860464.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020180352.1
COORDINATES: similar to AA sequence:RefSeq:WP_018855502.1
COORDINATES: similar to AA sequence:RefSeq:WP_007537192.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012650505.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650483.1
COORDINATES: similar to AA sequence:RefSeq:WP_003571493.1
COORDINATES: protein motif:HMM:NF024140.2
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: protein motif:HMM:NF025878.2
COORDINATES: similar to AA sequence:RefSeq:WP_008127690.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007605109.1
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_008996246.1
GO:0004673 - protein histidine kinase activity [Evidence IEA]
HWE histidine kinase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008996247.1
COORDINATES: similar to AA sequence:RefSeq:WP_006724009.1
COORDINATES: similar to AA sequence:RefSeq:WP_019052766.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611858.1
COORDINATES: similar to AA sequence:RefSeq:WP_007787912.1
COORDINATES: similar to AA sequence:RefSeq:WP_015914915.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
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: protein motif:HMM:NF013677.2
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_017504305.1
hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003168184.1
COORDINATES: similar to AA sequence:RefSeq:WP_016555538.1
COORDINATES: similar to AA sequence:RefSeq:WP_007880398.1
COORDINATES: similar to AA sequence:RefSeq:WP_015857238.1
COORDINATES: similar to AA sequence:RefSeq:WP_003546035.1
COORDINATES: similar to AA sequence:RefSeq:WP_012286057.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_020087522.1
putative addiction module antidote protein
COORDINATES: protein motif:HMM:NF024758.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611390.1
COORDINATES: protein motif:HMM:NF013094.2
COORDINATES: similar to AA sequence:RefSeq:WP_004119886.1
COORDINATES: similar to AA sequence:RefSeq:WP_007772327.1
GO:0004743 - pyruvate kinase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007772326.1
COORDINATES: similar to AA sequence:RefSeq:WP_032489007.1
GO:0009027 - tartrate dehydrogenase activity [Evidence IEA]
GO:0046395 - carboxylic acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007801369.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551734.1
COORDINATES: similar to AA sequence:RefSeq:WP_007607852.1
COORDINATES: similar to AA sequence:RefSeq:WP_020052952.1
COORDINATES: similar to AA sequence:RefSeq:WP_020810094.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020810093.1
COORDINATES: similar to AA sequence:RefSeq:WP_020810092.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012650544.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020810090.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020810089.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]; GO:0008483 - transaminase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020810088.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018480553.1
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_014763243.1
COORDINATES: similar to AA sequence:RefSeq:WP_052642687.1
COORDINATES: similar to AA sequence:RefSeq:WP_003550967.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611992.1
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: similar to AA sequence:RefSeq:WP_012650551.1
COORDINATES: similar to AA sequence:RefSeq:WP_007766302.1
dipeptide/oligopeptide/nickel ABC transporter permease/ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007438535.1
COORDINATES: similar to AA sequence:RefSeq:WP_007759469.1
COORDINATES: similar to AA sequence:RefSeq:WP_007759467.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650556.1
COORDINATES: similar to AA sequence:RefSeq:WP_012694798.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650558.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801599.1
COORDINATES: similar to AA sequence:RefSeq:WP_007751186.1
GO:0033735 - aspartate dehydrogenase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012650560.1
COORDINATES: similar to AA sequence:RefSeq:WP_013390775.1
pyridoxal phosphate-dependent aminotransferase
COORDINATES: protein motif:HMM:NF014042.2
2-phospho-L-lactate transferase CofD family protein
COORDINATES: protein motif:HMM:NF019322.2
COORDINATES: similar to AA sequence:RefSeq:WP_020011785.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501420.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501418.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650568.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654727.1
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_007199398.1
COORDINATES: similar to AA sequence:RefSeq:WP_003524938.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007636207.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427429.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982958.1
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_003517402.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654900.1
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_012654903.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974893.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974894.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_040132235.1
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_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_003501346.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518459.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650590.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654946.1
COORDINATES: protein motif:HMM:NF014709.2
COORDINATES: similar to AA sequence:RefSeq:WP_008834332.1
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_012068603.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965027.1
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: protein motif:HMM:NF012610.2
COORDINATES: similar to AA sequence:RefSeq:WP_007583640.1
GO:0036361 - racemase activity, acting on amino acids and derivatives [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011607949.1
COORDINATES: similar to AA sequence:RefSeq:WP_004961022.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_004961020.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013435290.1
COORDINATES: protein motif:HMM:NF013698.2
COORDINATES: protein motif:HMM:NF014430.2
COORDINATES: similar to AA sequence:RefSeq:WP_017846121.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_015278884.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
ribosome-associated ATPase/putative transporter RbbA
COORDINATES: similar to AA sequence:RefSeq:WP_017846123.1
COORDINATES: similar to AA sequence:RefSeq:WP_019089030.1
COORDINATES: similar to AA sequence:RefSeq:WP_008995981.1
COORDINATES: similar to AA sequence:RefSeq:WP_008995980.1
NAD(P)(+) transhydrogenase (Re/Si-specific) subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_011086774.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_019939549.1
COORDINATES: similar to AA sequence:RefSeq:WP_018493163.1
COORDINATES: similar to AA sequence:RefSeq:WP_003573266.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015341157.1
COORDINATES: similar to AA sequence:RefSeq:WP_007600959.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008969103.1
COORDINATES: similar to AA sequence:RefSeq:WP_012239631.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: similar to AA sequence:RefSeq:WP_007753864.1
COORDINATES: similar to AA sequence:RefSeq:WP_043766079.1
COORDINATES: similar to AA sequence:RefSeq:WP_004222857.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013959474.1
COORDINATES: similar to AA sequence:RefSeq:WP_009049540.1
COORDINATES: similar to AA sequence:RefSeq:WP_015927615.1
COORDINATES: similar to AA sequence:RefSeq:WP_003522979.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653203.1
COORDINATES: similar to AA sequence:RefSeq:WP_017966359.1
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003551028.1
electron transfer flavoprotein subunit alpha/FixB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018426547.1
GO:0004735 - pyrroline-5-carboxylate reductase activity [Evidence IEA]
GO:0006561 - proline biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012563986.1
GO:0047400 - phosphonoacetate hydrolase activity [Evidence IEA]
GO:0019636 - phosphonoacetate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024376.2
PhnD/SsuA/transferrin family substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013653572.1
COORDINATES: similar to AA sequence:RefSeq:WP_010892438.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_010974833.1
COORDINATES: similar to AA sequence:RefSeq:WP_013650736.1
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_003501273.1
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