Massilia putida strain 6NM-7 plasmid unnamed1, complete sequence.
Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales; Oxalobacteraceae; Massilia group; Massilia.
The complete genome of Massilia putida, a heavy metal resistant bacterium from wolfram mine tailing
Submitted (03-JAN-2017) State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Jiangnan University Guangdong Institute of Microbiology, No 100 Xialiezhong Road, Guangzhou, Guangdong 510070, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP019036.1.\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. 2.3.0\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 160.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/07/2022 05:00:46\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 6,712\nCDSs (total) :: 6,600\nGenes (coding) :: 6,437\nCDSs (with protein) :: 6,437\nGenes (RNA) :: 112\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 87\nncRNAs :: 4\nPseudo Genes (total) :: 163\nCDSs (without protein) :: 163\nPseudo Genes (ambiguous residues) :: 0 of 163\nPseudo Genes (frameshifted) :: 55 of 163\nPseudo Genes (incomplete) :: 118 of 163\nPseudo Genes (internal stop) :: 14 of 163\nPseudo Genes (multiple problems) :: 22 of 163\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017524.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
plasmid mobilization relaxosome protein MobC
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_007247378.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005888920.1
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: similar to AA sequence:RefSeq:WP_011578684.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798465.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611121.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004632818.1
GO:0008324 - cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
CDF family Co(II)/Ni(II) efflux transporter DmeF
COORDINATES: similar to AA sequence:RefSeq:WP_012217754.1
COORDINATES: similar to AA sequence:RefSeq:WP_003546569.1
metal/formaldehyde-sensitive transcriptional repressor
COORDINATES: similar to AA sequence:RefSeq:WP_013691200.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00080
yybP-ykoY riboswitch is a manganese riboswitch that directly binds Mn; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013209736.1
ankyrin repeat domain-containing protein
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014726321.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: similar to AA sequence:RefSeq:WP_014726316.1
COORDINATES: similar to AA sequence:RefSeq:WP_017333730.1
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_007731408.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008249050.1
GO:0043828 - tRNA 2-selenouridine synthase activity [Evidence IEA]
GO:0002098 - tRNA wobble uridine modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011486310.1
GO:0006629 - lipid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011486311.1
autoinducer binding domain-containing protein
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF027824.2
COORDINATES: protein motif:HMM:NF013677.2
COORDINATES: similar to AA sequence:RefSeq:WP_009498392.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: protein motif:HMM:NF024116.2
COORDINATES: similar to AA sequence:RefSeq:WP_012002855.1
COORDINATES: protein motif:HMM:NF022853.2
protein-disulfide reductase DsbD N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020706513.1
COORDINATES: similar to AA sequence:RefSeq:WP_002718011.1
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_001262004.1
COORDINATES: similar to AA sequence:RefSeq:WP_007883246.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558168.1
programmed frameshift; 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_019142700.1
COORDINATES: protein motif:HMM:NF020893.2
bifunctional DedA family/phosphatase PAP2 family protein
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_012536922.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014385.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009896725.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
COORDINATES: similar to AA sequence:RefSeq:WP_019882021.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008932165.1
COORDINATES: similar to AA sequence:RefSeq:WP_001247892.1
COORDINATES: similar to AA sequence:RefSeq:WP_001138014.1
COORDINATES: similar to AA sequence:RefSeq:WP_017173692.1
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_005662877.1
GO:0051782 - negative regulation of cell division [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
translesion DNA synthesis-associated protein ImuA
COORDINATES: protein motif:HMM:NF036631.2
COORDINATES: similar to AA sequence:RefSeq:WP_008918740.1
COORDINATES: similar to AA sequence:RefSeq:WP_017877540.1
COORDINATES: similar to AA sequence:RefSeq:WP_019923820.1