Rhizobium oryzihabitans strain M15 plasmid p1, 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\nCP048633.1.\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_011652406.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020012504.1
GO:0008490 - arsenite secondary active transmembrane transporter activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017960886.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
This arsenate reductase requires both glutathione and glutaredoxin to convert arsenate to arsenite, after which the efflux transporter formed by ArsA and ArsB can extrude the arsenite from the cell, providing resistance.; frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020050408.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013761981.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020810055.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_008535171.1
COORDINATES: similar to AA sequence:RefSeq:WP_010165166.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012798.2
incomplete; partial in the middle of a contig; missing C-terminus; 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_015341926.1
COORDINATES: protein motif:HMM:NF024098.2
COORDINATES: similar to AA sequence:RefSeq:WP_018494858.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019565689.1
COORDINATES: similar to AA sequence:RefSeq:WP_013637316.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048036.1
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006312951.1
COORDINATES: similar to AA sequence:RefSeq:WP_006697489.1
COORDINATES: similar to AA sequence:RefSeq:WP_006315784.1
COORDINATES: similar to AA sequence:RefSeq:WP_016736649.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010974318.1
COORDINATES: similar to AA sequence:RefSeq:WP_006699353.1
COORDINATES: similar to AA sequence:RefSeq:WP_007758851.1
COORDINATES: similar to AA sequence:RefSeq:WP_007758852.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003910 - DNA ligase (ATP) activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014531966.1
GO:0045027 - DNA end binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003526114.1
COORDINATES: similar to AA sequence:RefSeq:WP_003528032.1
COORDINATES: similar to AA sequence:RefSeq:WP_018099081.1
GO:0008853 - exodeoxyribonuclease III activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020809023.1
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_003504687.1
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_020811055.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020811056.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020809046.1
GO:0030552 - cAMP binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010970566.1
COORDINATES: similar to AA sequence:RefSeq:WP_018068460.1
COORDINATES: similar to AA sequence:RefSeq:WP_020808140.1
COORDINATES: similar to AA sequence:RefSeq:WP_010187967.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: protein motif:HMM:NF024975.2
COORDINATES: similar to AA sequence:RefSeq:WP_018496607.1
COORDINATES: similar to AA sequence:RefSeq:WP_018116074.1
COORDINATES: similar to AA sequence:RefSeq:WP_007637101.1
GO:0004673 - protein histidine kinase activity [Evidence IEA]
HWE histidine kinase domain-containing protein
COORDINATES: protein motif:HMM:NF024431.2
COORDINATES: similar to AA sequence:RefSeq:WP_012650494.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611865.1
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_018480553.1
COORDINATES: similar to AA sequence:RefSeq:WP_003504364.1
COORDINATES: similar to AA sequence:RefSeq:WP_003499838.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_003504368.1
COORDINATES: similar to AA sequence:RefSeq:WP_013761405.1
COORDINATES: similar to AA sequence:RefSeq:WP_003522672.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003504374.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033580.1
COORDINATES: similar to AA sequence:RefSeq:WP_007880398.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016555538.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982986.1
COORDINATES: similar to AA sequence:RefSeq:WP_020473591.1
COORDINATES: similar to AA sequence:RefSeq:WP_020808303.1
COORDINATES: similar to AA sequence:RefSeq:WP_010164822.1
COORDINATES: similar to AA sequence:RefSeq:WP_012557531.1
COORDINATES: similar to AA sequence:RefSeq:WP_011428362.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019566738.1
COORDINATES: similar to AA sequence:RefSeq:WP_003580386.1
COORDINATES: similar to AA sequence:RefSeq:WP_012483516.1
COORDINATES: similar to AA sequence:RefSeq:WP_007601864.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330183.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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: protein motif:HMM:NF014430.2
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_017967626.1
DNA polymerase ligase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007121525.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007256790.1
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF015445.2
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_011970324.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501631.1
GO:0097367 - carbohydrate derivative binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003526921.1
COORDINATES: similar to AA sequence:RefSeq:WP_007256785.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501640.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0000976 - transcription cis-regulatory region binding [Evidence IEA]
GO:0006351 - DNA-templated transcription [Evidence IEA]; GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014989547.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006865 - amino acid transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003526923.1
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]
amino acid ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF013434.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014989553.1
GO:0003824 - catalytic activity [Evidence IEA]
sugar phosphate isomerase/epimerase family protein
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_006313255.1
COORDINATES: similar to AA sequence:RefSeq:WP_018860470.1
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_012218152.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016646 - oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009357484.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611992.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501156.1
COORDINATES: protein motif:HMM:NF022995.2
COORDINATES: similar to AA sequence:RefSeq:WP_006315298.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650525.1
COORDINATES: similar to AA sequence:RefSeq:WP_018260113.1
COORDINATES: similar to AA sequence:RefSeq:WP_020572902.1
COORDINATES: similar to AA sequence:RefSeq:WP_018327317.1
COORDINATES: similar to AA sequence:RefSeq:WP_010972061.1
COORDINATES: protein motif:HMM:NF021616.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011407605.1
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_016921625.1
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_003501254.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501255.1
COORDINATES: similar to AA sequence:RefSeq:WP_019200234.1
COORDINATES: similar to AA sequence:RefSeq:WP_012755578.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007801540.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_012760230.1