Allorhizobium ampelinum S4 plasmid pAtS4a, 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\nCP000639.1.\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_003571859.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003595755.1
COORDINATES: similar to AA sequence:RefSeq:WP_017270210.1
COORDINATES: similar to AA sequence:RefSeq:WP_018247203.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014330854.1
COORDINATES: similar to AA sequence:RefSeq:WP_008840408.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241629.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_014330857.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011982858.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009469545.1
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_017268591.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210779.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_011982854.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210781.1
COORDINATES: similar to AA sequence:RefSeq:WP_017265131.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469551.1
COORDINATES: similar to AA sequence:RefSeq:WP_014531075.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011971088.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: similar to AA sequence:RefSeq:WP_014531077.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009469555.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845317.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845318.1
COORDINATES: similar to AA sequence:RefSeq:WP_017268587.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982844.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210791.1
COORDINATES: similar to AA sequence:RefSeq:WP_018210792.1
COORDINATES: similar to AA sequence:RefSeq:WP_011971078.1
COORDINATES: similar to AA sequence:RefSeq:WP_010665990.1
COORDINATES: similar to AA sequence:RefSeq:WP_010875060.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012653035.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611960.1
programmed frameshift; 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.
COORDINATES: similar to AA sequence:RefSeq:WP_018327735.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332229.1
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018237990.1
COORDINATES: similar to AA sequence:RefSeq:WP_018325290.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
plastocyanin/azurin family copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006313095.1
COORDINATES: similar to AA sequence:RefSeq:WP_006313094.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010971022.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_010968681.1
COORDINATES: similar to AA sequence:RefSeq:WP_019566581.1
COORDINATES: similar to AA sequence:RefSeq:WP_004435893.1
COORDINATES: similar to AA sequence:RefSeq:WP_018069533.1
COORDINATES: similar to AA sequence:RefSeq:WP_017960478.1
COORDINATES: similar to AA sequence:RefSeq:WP_020049956.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014332218.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241522.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653056.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018328306.1
COORDINATES: similar to AA sequence:RefSeq:WP_018324858.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006312259.1
COORDINATES: similar to AA sequence:RefSeq:WP_007788017.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007788016.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: similar to AA sequence:RefSeq:WP_013850498.1
COORDINATES: similar to AA sequence:RefSeq:WP_017171841.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241489.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241490.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241491.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241492.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241493.1
COORDINATES: similar to AA sequence:RefSeq:WP_003528894.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010970262.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003537746.1
COORDINATES: similar to AA sequence:RefSeq:WP_017958563.1
COORDINATES: similar to AA sequence:RefSeq:WP_018099083.1
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_015241538.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_014330304.1
COORDINATES: similar to AA sequence:RefSeq:WP_013851074.1
COORDINATES: similar to AA sequence:RefSeq:WP_012881324.1
COORDINATES: similar to AA sequence:RefSeq:WP_010657934.1
COORDINATES: similar to AA sequence:RefSeq:WP_017264315.1
COORDINATES: similar to AA sequence:RefSeq:WP_017265753.1
zincin-like metallopeptidase domain-containing protein