Rhizobium oryzihabitans strain M15 plasmid p4, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Plant-Promoting Endophytic Bacterium Rhizobium oryzihabitans sp. nov., Isolated from the Root of Rice
Submitted (06-FEB-2020) Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, zhongguancunnandajie, beijing, beijing 100081, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP048636.1.\nBacteria and source DNA available from Key Laboratory of Microbial\nResources Collection and Preservation.\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 Date :: JUN-2018\nAssembly Method :: HGAP4 v. 2018-06; CANU v. 1.6\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 150.0x\nSequencing Technology :: Illumina miseq+Pacbio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 02:03:37\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) :: 5,749\nCDSs (total) :: 5,670\nGenes (coding) :: 5,255\nCDSs (with protein) :: 5,255\nGenes (RNA) :: 79\nrRNAs :: 6, 4, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 4, 6 (5S, 16S, 23S)\ntRNAs :: 59\nncRNAs :: 4\nPseudo Genes (total) :: 415\nCDSs (without protein) :: 415\nPseudo Genes (ambiguous residues) :: 0 of 415\nPseudo Genes (frameshifted) :: 352 of 415\nPseudo Genes (incomplete) :: 76 of 415\nPseudo Genes (internal stop) :: 8 of 415\nPseudo Genes (multiple problems) :: 21 of 415\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type material of Rhizobium oryzihabitans
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0015803 - branched-chain amino acid transport [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
branched-chain amino acid ABC transporter permease
COORDINATES: protein motif:HMM:NF014684.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012190539.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012235.2
ATP-binding cassette domain-containing protein
COORDINATES: protein motif:HMM:NF024850.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010220034.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013845952.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013845951.1
COORDINATES: similar to AA sequence:RefSeq:WP_012457146.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200205.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010969960.1
COORDINATES: protein motif:HMM:NF013676.2
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_012654892.1
COORDINATES: similar to AA sequence:RefSeq:WP_012654893.1
COORDINATES: similar to AA sequence:RefSeq:WP_043765841.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019087712.1
COORDINATES: similar to AA sequence:RefSeq:WP_000008826.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845947.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845945.1
COORDINATES: similar to AA sequence:RefSeq:WP_010399291.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: protein motif:HMM:NF039997.1
COORDINATES: similar to AA sequence:RefSeq:WP_010658170.1
GO:0004157 - dihydropyrimidinase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009825998.1
COORDINATES: protein motif:HMM:NF013539.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013394161.1