Rhizobium oryzihabitans strain M15 plasmid p6, 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\nCP048638.1.\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: similar to AA sequence:RefSeq:WP_003501082.1
frameshifted; incomplete; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003603269.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR01726.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015837 - amine transport [Evidence IEA]
The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011579025.1
COORDINATES: similar to AA sequence:RefSeq:WP_012755126.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015873077.1
COORDINATES: protein motif:HMM:NF027994.2
COORDINATES: protein motif:HMM:NF015648.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003527670.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:TIGR01051.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]; GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: protein motif:HMM:NF013700.2
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: protein motif:HMM:NF017277.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF017736.2
COORDINATES: protein motif:HMM:NF025241.2
COORDINATES: similar to AA sequence:RefSeq:WP_011654541.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003501211.1
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_010973504.1
GO:0016772 - transferase activity, transferring phosphorus-containing groups [Evidence IEA]
phosphoethanolamine--lipid A transferase
COORDINATES: similar to AA sequence:RefSeq:WP_007791575.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
GO:0018104 - peptidoglycan-protein cross-linking [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003495445.1
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501205.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004687725.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016221.2
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020809329.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]