Rhizobium favelukesii strain LPU83 plasmid pLPU83a, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Draft genome sequence of the broad-host-range Rhizobium sp. LPU83 strain, a member of the low-genetic diversity Oregon-like Rhizobium sp. group
Submitted (14-NOV-2013) GRIM, CeBiTec, 33615, NRW, GERMANY
REFSEQ INFORMATION: The reference sequence is identical to\nHG916853.1.\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 :: 04/26/2023 09:02:55\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) :: 7,573\nCDSs (total) :: 7,508\nGenes (coding) :: 6,881\nCDSs (with protein) :: 6,881\nGenes (RNA) :: 65\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 52\nncRNAs :: 4\nPseudo Genes (total) :: 627\nCDSs (without protein) :: 627\nPseudo Genes (ambiguous residues) :: 0 of 627\nPseudo Genes (frameshifted) :: 386 of 627\nPseudo Genes (incomplete) :: 406 of 627\nPseudo Genes (internal stop) :: 63 of 627\nPseudo Genes (multiple problems) :: 205 of 627\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_020046783.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011654634.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654635.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012492.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012760230.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015887542.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018391525.1
COORDINATES: similar to AA sequence:RefSeq:WP_015918400.1
COORDINATES: similar to AA sequence:RefSeq:WP_011578661.1
COORDINATES: similar to AA sequence:RefSeq:WP_003566627.1
COORDINATES: protein motif:HMM:NF017985.2
COORDINATES: protein motif:HMM:NF017837.2
COORDINATES: similar to AA sequence:RefSeq:WP_006206024.1
GO:0005507 - copper ion binding [Evidence IEA]
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015886909.1
COORDINATES: similar to AA sequence:RefSeq:WP_014857614.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007788020.1
COORDINATES: similar to AA sequence:RefSeq:WP_004123570.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611156.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012653061.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007788016.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002718024.1
COORDINATES: similar to AA sequence:RefSeq:WP_008877245.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718022.1
COORDINATES: similar to AA sequence:RefSeq:WP_012483840.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012483839.1
COORDINATES: similar to AA sequence:RefSeq:WP_018483758.1
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_010400577.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006470270.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017503729.1
COORDINATES: similar to AA sequence:RefSeq:WP_006559417.1
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_011093713.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015615701.1
COORDINATES: similar to AA sequence:RefSeq:WP_004667023.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611153.1
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_018116989.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611730.1
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_014761247.1
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_014761245.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_015007641.1
COORDINATES: similar to AA sequence:RefSeq:WP_012553005.1
COORDINATES: similar to AA sequence:RefSeq:WP_018264743.1
COORDINATES: similar to AA sequence:RefSeq:WP_006199609.1
COORDINATES: protein motif:HMM:NF015437.2
autoinducer binding domain-containing protein
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_010875285.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477317.1
COORDINATES: similar to AA sequence:RefSeq:WP_019567132.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015241558.1
COORDINATES: similar to AA sequence:RefSeq:WP_006697492.1
COORDINATES: similar to AA sequence:RefSeq:WP_003565244.1
COORDINATES: protein motif:HMM:NF013152.2
COORDINATES: similar to AA sequence:RefSeq:WP_003565248.1
COORDINATES: similar to AA sequence:RefSeq:WP_007793441.1
COORDINATES: similar to AA sequence:RefSeq:WP_007788834.1
COORDINATES: similar to AA sequence:RefSeq:WP_016553100.1
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016553098.1
COORDINATES: similar to AA sequence:RefSeq:WP_013518309.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611884.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654560.1
COORDINATES: similar to AA sequence:RefSeq:WP_004124603.1
GO:0016757 - glycosyltransferase activity [Evidence IEA]
polysaccharide pyruvyl transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012061860.1
COORDINATES: similar to AA sequence:RefSeq:WP_018097023.1
COORDINATES: similar to AA sequence:RefSeq:WP_012061863.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020010040.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018324280.1
COORDINATES: similar to AA sequence:RefSeq:WP_012061866.1
COORDINATES: similar to AA sequence:RefSeq:WP_018237200.1
COORDINATES: similar to AA sequence:RefSeq:WP_018324277.1
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_013850562.1
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
Wzz/FepE/Etk N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012812328.1
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:NF021641.2
COORDINATES: similar to AA sequence:RefSeq:WP_007881800.1
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_003582386.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016736007.1
COORDINATES: similar to AA sequence:RefSeq:WP_020048036.1
COORDINATES: similar to AA sequence:RefSeq:WP_003551129.1
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_017957069.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565689.1
COORDINATES: similar to AA sequence:RefSeq:WP_003517409.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013635765.1
COORDINATES: similar to AA sequence:RefSeq:WP_008068479.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007013263.1
COORDINATES: similar to AA sequence:RefSeq:WP_015341926.1
COORDINATES: similar to AA sequence:RefSeq:WP_014989420.1
DUF3991 and toprim domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011654726.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654727.1
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_003575312.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654728.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982954.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011654729.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654730.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654731.1
COORDINATES: similar to AA sequence:RefSeq:WP_014989427.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516741.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014762706.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477327.1
COORDINATES: similar to AA sequence:RefSeq:WP_007823654.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654737.1
COORDINATES: similar to AA sequence:RefSeq:WP_012650579.1
COORDINATES: similar to AA sequence:RefSeq:WP_014076976.1
COORDINATES: similar to AA sequence:RefSeq:WP_007538757.1
COORDINATES: similar to AA sequence:RefSeq:WP_018326258.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654742.1
Ti-type conjugative transfer system protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_018326256.1
COORDINATES: similar to AA sequence:RefSeq:WP_003508816.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010300.1
Ti-type conjugative transfer relaxase TraA
COORDINATES: similar to AA sequence:RefSeq:WP_018010299.1
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_011654747.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010297.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011654749.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654750.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537746.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010292.1
COORDINATES: similar to AA sequence:RefSeq:WP_018010291.1
COORDINATES: similar to AA sequence:RefSeq:WP_011654754.1
IncP-type conjugal transfer protein TrbI
COORDINATES: similar to AA sequence:RefSeq:WP_011654755.1
COORDINATES: similar to AA sequence:RefSeq:WP_018899390.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_018482029.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516719.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_012477354.1
GO:0009292 - horizontal gene transfer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011654759.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_018899386.1
COORDINATES: similar to AA sequence:RefSeq:WP_013984785.1
COORDINATES: similar to AA sequence:RefSeq:WP_017273081.1
COORDINATES: similar to AA sequence:RefSeq:WP_003501704.1