Rhizobium daejeonense strain KACC 13094 plasmid unnamed4, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
Genome sequence of Rhizobium daejeonense KACC 13094
Submitted (09-JAN-2020) Agriculture & Life Science, Kyungpook National University, Daehak-ro 80, Daegu 41566, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP048428.1.\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-Assembly-Data-START##\nAssembly Method :: HGAP v. 2020-01-09\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 114.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/06/2023 01:57:08\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) :: 4,885\nCDSs (total) :: 4,813\nGenes (coding) :: 4,745\nCDSs (with protein) :: 4,745\nGenes (RNA) :: 72\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 56\nncRNAs :: 4\nPseudo Genes (total) :: 68\nCDSs (without protein) :: 68\nPseudo Genes (ambiguous residues) :: 0 of 68\nPseudo Genes (frameshifted) :: 34 of 68\nPseudo Genes (incomplete) :: 48 of 68\nPseudo Genes (internal stop) :: 15 of 68\nPseudo Genes (multiple problems) :: 24 of 68\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_008961041.1
GO:0008658 - penicillin binding [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009550114.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_086558208.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012555931.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003568092.1
COORDINATES: similar to AA sequence:RefSeq:WP_003568096.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003568098.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012555935.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003568102.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006206633.1
GO:0006750 - glutathione biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013434.2
GO:0071949 - FAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003568107.1
GO:0004399 - histidinol dehydrogenase activity [Evidence IEA]
GO:0000105 - histidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018011543.1
internal stop; 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_009819735.1
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_076611329.1
COORDINATES: similar to AA sequence:RefSeq:WP_020187230.1
COORDINATES: similar to AA sequence:RefSeq:WP_007600292.1
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: similar to AA sequence:RefSeq:WP_004119862.1
COORDINATES: protein motif:HMM:TIGR03454.1
COORDINATES: similar to AA sequence:RefSeq:WP_003538323.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651064.1
COORDINATES: similar to AA sequence:RefSeq:WP_006952651.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015241538.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012778824.1
COORDINATES: similar to AA sequence:RefSeq:WP_007788514.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982948.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012653070.1
COORDINATES: similar to AA sequence:RefSeq:WP_013054022.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653127.1
COORDINATES: similar to AA sequence:RefSeq:WP_015497709.1
COORDINATES: similar to AA sequence:RefSeq:WP_006332417.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF012651.2
COORDINATES: similar to AA sequence:RefSeq:WP_017958549.1
COORDINATES: similar to AA sequence:RefSeq:WP_013845948.1
COORDINATES: similar to AA sequence:RefSeq:WP_012763498.1
COORDINATES: protein motif:HMM:NF024977.2
COORDINATES: protein motif:HMM:NF012372.2
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007539843.1
COORDINATES: similar to AA sequence:RefSeq:WP_004129252.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007752855.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013761150.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006472564.1
COORDINATES: similar to AA sequence:RefSeq:WP_019565689.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516677.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_006339852.1
VirB4 family type IV secretion/conjugal transfer ATPase
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_009762568.1
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF038091.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982857.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003568746.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017958562.1
COORDINATES: similar to AA sequence:RefSeq:WP_017958563.1
COORDINATES: similar to AA sequence:RefSeq:WP_007767222.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013845583.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011970461.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019404153.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018390382.1
GO:0015099 - nickel cation transmembrane transporter activity [Evidence IEA]
GO:0035444 - nickel cation transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011970463.1
COORDINATES: similar to AA sequence:RefSeq:WP_007010324.1
COORDINATES: similar to AA sequence:RefSeq:WP_006470267.1
COORDINATES: protein motif:HMM:NF013961.2
transglutaminase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008030578.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030579.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030583.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011493126.1
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: similar to AA sequence:RefSeq:WP_003595851.1
COORDINATES: similar to AA sequence:RefSeq:WP_014238990.1
COORDINATES: protein motif:HMM:NF015639.2
COORDINATES: similar to AA sequence:RefSeq:WP_018236828.1
COORDINATES: similar to AA sequence:RefSeq:WP_012484846.1
COORDINATES: similar to AA sequence:RefSeq:WP_008123095.1
COORDINATES: similar to AA sequence:RefSeq:WP_014129839.1
COORDINATES: similar to AA sequence:RefSeq:WP_008125875.1