Allorhizobium ampelinum S4 plasmid pTiS4, 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\nCP000637.1.\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_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_018516709.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501695.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501693.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003501256.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538502.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018325683.1
COORDINATES: similar to AA sequence:RefSeq:WP_015931502.1
GO:0004803 - transposase activity [Evidence IEA]
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_012650495.1
COORDINATES: similar to AA sequence:RefSeq:WP_004673664.1
COORDINATES: similar to AA sequence:RefSeq:WP_017996623.1
GO:0045027 - DNA end binding [Evidence IEA]
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012648923.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637238.1
COORDINATES: similar to AA sequence:RefSeq:WP_012553005.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012760334.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
TIGR03885 family FMN-dependent LLM class oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_003586266.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611299.1
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_004675975.1
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_003500561.1
PAS domain-containing methyl-accepting chemotaxis protein
COORDINATES: similar to AA sequence:RefSeq:WP_011982965.1
COORDINATES: similar to AA sequence:RefSeq:WP_012708885.1
metalloregulator ArsR/SmtB family transcription factor
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024947.2
SbcC/MukB-like Walker B domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003518564.1
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_010665991.1
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011982795.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611883.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020046837.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_007637593.1
COORDINATES: similar to AA sequence:RefSeq:WP_003523838.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_015918241.1
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_076611865.1
COORDINATES: similar to AA sequence:RefSeq:WP_011541357.1
COORDINATES: similar to AA sequence:RefSeq:WP_019052766.1
COORDINATES: similar to AA sequence:RefSeq:WP_003568320.1
COORDINATES: protein motif:HMM:TIGR00254.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_003544853.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017335227.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654541.1
COORDINATES: protein motif:HMM:NF021596.2
COORDINATES: similar to AA sequence:RefSeq:WP_013637255.1
COORDINATES: similar to AA sequence:RefSeq:WP_010665832.1
type II toxin-antitoxin system RelE/ParE family toxin
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_003525125.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650569.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508776.1
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_006335205.1
isocitrate lyase/phosphoenolpyruvate mutase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003524938.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_010974883.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501402.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718992.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517406.1
COORDINATES: similar to AA sequence:RefSeq:WP_010974888.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006966602.1
COORDINATES: similar to AA sequence:RefSeq:WP_010409169.1
COORDINATES: similar to AA sequence:RefSeq:WP_007792533.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008495648.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010518233.1
COORDINATES: similar to AA sequence:RefSeq:WP_008840746.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518435.1
COORDINATES: similar to AA sequence:RefSeq:WP_006315297.1
COORDINATES: similar to AA sequence:RefSeq:WP_006315298.1
COORDINATES: similar to AA sequence:RefSeq:WP_003518438.1
Ti-type conjugative transfer system protein TraG
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_012654911.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_003523843.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654946.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516949.1
COORDINATES: similar to AA sequence:RefSeq:WP_003562274.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015342513.1
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_007877398.1
COORDINATES: protein motif:HMM:NF024808.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019859480.1
COORDINATES: similar to AA sequence:RefSeq:WP_018719473.1
COORDINATES: similar to AA sequence:RefSeq:WP_008891864.1
COORDINATES: similar to AA sequence:RefSeq:WP_011242129.1
aspartate aminotransferase family protein
COORDINATES: protein motif:HMM:NF012738.2
spermidine/putrescine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006634414.1
COORDINATES: similar to AA sequence:RefSeq:WP_010967426.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_017269015.1
COORDINATES: similar to AA sequence:RefSeq:WP_017269020.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019459224.1
COORDINATES: protein motif:HMM:NF016873.2
COORDINATES: similar to AA sequence:RefSeq:WP_012092304.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019015547.1
COORDINATES: similar to AA sequence:RefSeq:WP_003819907.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003819905.1
hydantoinase/oxoprolinase family protein
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: similar to AA sequence:RefSeq:WP_017269019.1
COORDINATES: similar to AA sequence:RefSeq:WP_012092302.1
COORDINATES: similar to AA sequence:RefSeq:WP_018095973.1
dipeptide ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_012648997.1
COORDINATES: protein motif:HMM:NF024989.2
COORDINATES: protein motif:HMM:NF012398.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611977.1
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_011508891.1
COORDINATES: protein motif:HMM:NF014125.2
COORDINATES: protein motif:HMM:NF014381.2
NAD/NADP-dependent octopine/nopaline dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011427337.1
COORDINATES: similar to AA sequence:RefSeq:WP_007767713.1
COORDINATES: similar to AA sequence:RefSeq:WP_007767716.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424819.1
COORDINATES: protein motif:HMM:NF033580.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558310.1
COORDINATES: protein motif:HMM:NF024954.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974921.1
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_010974919.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891489.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654600.1
COORDINATES: similar to AA sequence:RefSeq:WP_032488279.1
COORDINATES: similar to AA sequence:RefSeq:WP_014528527.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427356.1
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_007538738.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891495.1
P-type conjugative transfer protein VirB9
COORDINATES: similar to AA sequence:RefSeq:WP_003537093.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891497.1
type IV secretion system lipoprotein VirB7
COORDINATES: similar to AA sequence:RefSeq:WP_003537089.1
COORDINATES: similar to AA sequence:RefSeq:WP_019856522.1
COORDINATES: similar to AA sequence:RefSeq:WP_018009783.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_019856520.1
COORDINATES: similar to AA sequence:RefSeq:WP_010891502.1
COORDINATES: similar to AA sequence:RefSeq:WP_013533344.1
type IV secretion system lytic transglycosylase VirB1
COORDINATES: similar to AA sequence:RefSeq:WP_011970739.1
COORDINATES: similar to AA sequence:RefSeq:WP_012655097.1
COORDINATES: protein motif:HMM:NF017528.2
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_076612018.1
COORDINATES: similar to AA sequence:RefSeq:WP_007011060.1
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_011427378.1
COORDINATES: similar to AA sequence:RefSeq:WP_009996985.1
COORDINATES: similar to AA sequence:RefSeq:WP_017183759.1
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_010974923.1
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_010891482.1
type IV secretion system effector chaperone VirE1
COORDINATES: similar to AA sequence:RefSeq:WP_011427346.1
two-component system VirA-like sensor kinase
COORDINATES: similar to AA sequence:RefSeq:WP_010892482.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449381.1
COORDINATES: similar to AA sequence:RefSeq:WP_011746810.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611465.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_011982903.1
reverse transcriptase domain-containing protein
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF024886.2
COORDINATES: similar to AA sequence:RefSeq:WP_016241516.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612098.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_012649057.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611260.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241891.1
COORDINATES: similar to AA sequence:RefSeq:WP_017996667.1
COORDINATES: similar to AA sequence:RefSeq:WP_007812053.1
COORDINATES: similar to AA sequence:RefSeq:WP_006871394.1
COORDINATES: similar to AA sequence:RefSeq:WP_014242209.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611229.1
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_012553437.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611348.1
COORDINATES: protein motif:HMM:NF005688.0
COORDINATES: similar to AA sequence:RefSeq:WP_012649067.1
COORDINATES: similar to AA sequence:RefSeq:WP_032488268.1
COORDINATES: similar to AA sequence:RefSeq:WP_014492358.1
COORDINATES: similar to AA sequence:RefSeq:WP_011581267.1
COORDINATES: similar to AA sequence:RefSeq:WP_014199017.1
COORDINATES: similar to AA sequence:RefSeq:WP_011808014.1
COORDINATES: similar to AA sequence:RefSeq:WP_007614356.1
COORDINATES: similar to AA sequence:RefSeq:WP_014439754.1
COORDINATES: similar to AA sequence:RefSeq:WP_012042070.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_012321501.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517544.1
COORDINATES: similar to AA sequence:RefSeq:WP_008886220.1
COORDINATES: protein motif:HMM:NF012706.2
COORDINATES: similar to AA sequence:RefSeq:WP_011581173.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450123.1
COORDINATES: similar to AA sequence:RefSeq:WP_011581171.1
COORDINATES: similar to AA sequence:RefSeq:WP_011951324.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887748.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887664.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003510256.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_012649093.1
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_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_003523573.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649102.1
COORDINATES: similar to AA sequence:RefSeq:WP_012649103.1