Cupriavidus malaysiensis strain USMAA1020 isolate pure plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Burkholderiaceae; Cupriavidus.
Complete genome sequences of three Cupriavidus strains isolated from various Malaysian environments
Submitted (20-OCT-2016) Centre for Chemical Biology, Universiti Sains Malaysia, Persiaran Bukit Jambul, Bayan Lepas, Pulau Pinan 11900, Malaysia
REFSEQ INFORMATION: The reference sequence is identical to\nCP017756.1.\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. version 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 190.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 02:30:47\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 7,230\nCDSs (total) :: 7,131\nGenes (coding) :: 7,032\nCDSs (with protein) :: 7,032\nGenes (RNA) :: 99\nrRNAs :: 7, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 7, 7 (5S, 16S, 23S)\ntRNAs :: 74\nncRNAs :: 4\nPseudo Genes (total) :: 99\nCDSs (without protein) :: 99\nPseudo Genes (ambiguous residues) :: 0 of 99\nPseudo Genes (frameshifted) :: 40 of 99\nPseudo Genes (incomplete) :: 85 of 99\nPseudo Genes (internal stop) :: 14 of 99\nPseudo Genes (multiple problems) :: 34 of 99\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Cupriavidus malaysiensis Ramachandran et al. 2018
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF020387.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012773408.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_007585570.1
type II toxin-antitoxin system prevent-host-death family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_004086683.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018871410.1
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:NF040127.1
COORDINATES: protein motif:HMM:NF017411.2
COORDINATES: protein motif:HMM:NF019416.2
COORDINATES: similar to AA sequence:RefSeq:WP_004636613.1
COORDINATES: similar to AA sequence:RefSeq:WP_004538493.1
COORDINATES: similar to AA sequence:RefSeq:WP_004197209.1
COORDINATES: similar to AA sequence:RefSeq:WP_004626000.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013311.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020204271.1
COORDINATES: similar to AA sequence:RefSeq:WP_011269724.1
COORDINATES: similar to AA sequence:RefSeq:WP_011210483.1
COORDINATES: similar to AA sequence:RefSeq:WP_018004058.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008060734.1
COORDINATES: similar to AA sequence:RefSeq:WP_018003802.1
COORDINATES: similar to AA sequence:RefSeq:WP_003799880.1
COORDINATES: similar to AA sequence:RefSeq:WP_003120032.1
COORDINATES: protein motif:HMM:NF015205.2
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF013506.2
COORDINATES: similar to AA sequence:RefSeq:WP_018308658.1
COORDINATES: similar to AA sequence:RefSeq:WP_012435610.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_017183617.1
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: similar to AA sequence:RefSeq:WP_007851344.1
COORDINATES: similar to AA sequence:RefSeq:WP_011519964.1
COORDINATES: similar to AA sequence:RefSeq:WP_020201315.1
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:NF025502.2
COORDINATES: similar to AA sequence:RefSeq:WP_011297789.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020423960.1
COORDINATES: similar to AA sequence:RefSeq:WP_011485888.1
COORDINATES: similar to AA sequence:RefSeq:WP_008652330.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354471.1
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: protein motif:HMM:NF013670.2
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity [Evidence IEA]
GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013995.2
COORDINATES: similar to AA sequence:RefSeq:WP_012701629.1
COORDINATES: similar to AA sequence:RefSeq:WP_020203540.1
COORDINATES: similar to AA sequence:RefSeq:WP_019334714.1
COORDINATES: similar to AA sequence:RefSeq:WP_006029257.1
COORDINATES: similar to AA sequence:RefSeq:WP_011229302.1
COORDINATES: protein motif:HMM:NF040044.1
COORDINATES: similar to AA sequence:RefSeq:WP_004630643.1
COORDINATES: similar to AA sequence:RefSeq:WP_014194243.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354475.1
COORDINATES: similar to AA sequence:RefSeq:WP_020203556.1
GO:0051782 - negative regulation of cell division [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
translesion DNA synthesis-associated protein ImuA
COORDINATES: similar to AA sequence:RefSeq:WP_011001781.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF023802.2
papain-like cysteine protease family protein
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_018311834.1
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018311835.1
COORDINATES: similar to AA sequence:RefSeq:WP_018311836.1
COORDINATES: similar to AA sequence:RefSeq:WP_011299686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013908285.1
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF028103.2
DNA-primase RepB domain-containing protein
COORDINATES: protein motif:HMM:NF012894.2
COORDINATES: protein motif:HMM:NF019843.2
COORDINATES: protein motif:HMM:NF025125.2
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_000735888.1
COORDINATES: protein motif:HMM:NF018536.2
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:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF021981.2
COORDINATES: protein motif:HMM:NF022580.2
COORDINATES: similar to AA sequence:RefSeq:WP_013691895.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: similar to AA sequence:RefSeq:WP_019097145.1
COORDINATES: similar to AA sequence:RefSeq:WP_014248089.1