Pseudomonas mendocina S5.2 plasmid pPME5, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales; Pseudomonadaceae; Pseudomonas.
Submitted (04-NOV-2015) HIR Building, University of Malaya, Level 1, Microbiome Lab, Kuala Lumpur, Kuala Lumpur 50603, Malaysia
REFSEQ INFORMATION: The reference sequence is identical to\nCP013125.1.\nBacteria and source DNA available from Level 1, Microbiome\nLaboratory, HIR Building, University of Malaya, 50603, Kuala\nLumpur, Malaysia.\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 :: Hierarchical Genome Assembly Process v. 2\nGenome Coverage :: 182.75x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/05/2023 21:00:26\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) :: 5,099\nCDSs (total) :: 5,013\nGenes (coding) :: 4,975\nCDSs (with protein) :: 4,975\nGenes (RNA) :: 86\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 4\nPseudo Genes (total) :: 38\nCDSs (without protein) :: 38\nPseudo Genes (ambiguous residues) :: 0 of 38\nPseudo Genes (frameshifted) :: 19 of 38\nPseudo Genes (incomplete) :: 22 of 38\nPseudo Genes (internal stop) :: 1 of 38\nPseudo Genes (multiple problems) :: 4 of 38\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_015026424.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_003191389.1
histone-like nucleoid-structuring protein, MvaT/MvaU family
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF019880.2
COORDINATES: protein motif:HMM:TIGR02464.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: protein motif:HMM:NF015146.2
COORDINATES: protein motif:HMM:NF037897.2
COORDINATES: protein motif:HMM:NF024724.2
COORDINATES: similar to AA sequence:RefSeq:WP_012777691.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_014602576.1
COORDINATES: similar to AA sequence:RefSeq:WP_015474997.1
GO:0019899 - enzyme binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF015648.2
COORDINATES: similar to AA sequence:RefSeq:WP_015278677.1
COORDINATES: similar to AA sequence:RefSeq:WP_019364772.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013141679.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_019437820.1
COORDINATES: similar to AA sequence:RefSeq:WP_005877888.1
COORDINATES: protein motif:HMM:NF015205.2
COORDINATES: similar to AA sequence:RefSeq:WP_015634814.1
COORDINATES: protein motif:HMM:NF012514.2
COORDINATES: similar to AA sequence:RefSeq:WP_008367527.1
COORDINATES: similar to AA sequence:RefSeq:WP_011349311.1
COORDINATES: protein motif:HMM:NF021255.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019334714.1
COORDINATES: protein motif:HMM:NF016362.2
COORDINATES: similar to AA sequence:RefSeq:WP_008366104.1
COORDINATES: protein motif:HMM:NF015639.2
COORDINATES: similar to AA sequence:RefSeq:WP_019407020.1
COORDINATES: protein motif:HMM:NF015402.2
COORDINATES: similar to AA sequence:RefSeq:WP_019437756.1
COORDINATES: protein motif:HMM:NF040431.1
COORDINATES: similar to AA sequence:RefSeq:WP_003187457.1
COORDINATES: similar to AA sequence:RefSeq:WP_019819535.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_020308214.1
COORDINATES: similar to AA sequence:RefSeq:WP_010466314.1
COORDINATES: similar to AA sequence:RefSeq:WP_017519376.1
COORDINATES: protein motif:HMM:NF040398.1
COORDINATES: similar to AA sequence:RefSeq:WP_012683724.1
COORDINATES: similar to AA sequence:RefSeq:WP_019486766.1
COORDINATES: protein motif:HMM:NF025602.2
COORDINATES: similar to AA sequence:RefSeq:WP_016913422.1
GO:0004540 - ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003285520.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: protein motif:HMM:NF016837.2
GO:0034257 - nicotinamide riboside transmembrane transporter activity [Evidence IEA]
GO:0034258 - nicotinamide riboside transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004630406.1
COORDINATES: similar to AA sequence:RefSeq:WP_010792720.1
COORDINATES: similar to AA sequence:RefSeq:WP_004882459.1
COORDINATES: similar to AA sequence:RefSeq:WP_003149039.1
COORDINATES: similar to AA sequence:RefSeq:WP_005267688.1
COORDINATES: similar to AA sequence:RefSeq:WP_008075287.1
COORDINATES: similar to AA sequence:RefSeq:WP_015060232.1
COORDINATES: similar to AA sequence:RefSeq:WP_002742815.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_009397172.1
COORDINATES: similar to AA sequence:RefSeq:WP_016713122.1
COORDINATES: similar to AA sequence:RefSeq:WP_019331432.1
COORDINATES: similar to AA sequence:RefSeq:WP_016502358.1
COORDINATES: similar to AA sequence:RefSeq:WP_015026462.1
COORDINATES: similar to AA sequence:RefSeq:WP_020307627.1
COORDINATES: similar to AA sequence:RefSeq:WP_020190237.1
COORDINATES: similar to AA sequence:RefSeq:WP_011254766.1
COORDINATES: similar to AA sequence:RefSeq:WP_017172450.1
COORDINATES: similar to AA sequence:RefSeq:WP_005741978.1
COORDINATES: similar to AA sequence:RefSeq:WP_005742183.1
COORDINATES: similar to AA sequence:RefSeq:WP_005742048.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516295.1
COORDINATES: similar to AA sequence:RefSeq:WP_020308232.1
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: similar to AA sequence:RefSeq:WP_010466303.1
COORDINATES: protein motif:HMM:NF002955.0
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_008567175.1
COORDINATES: similar to AA sequence:RefSeq:WP_020795287.1
GO:0016152 - mercury (II) reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008567179.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229640.1
GO:0045340 - mercury ion binding [Evidence IEA]
mercury resistance system periplasmic binding protein MerP
COORDINATES: similar to AA sequence:RefSeq:YP_005229639.1
COORDINATES: similar to AA sequence:RefSeq:WP_008567182.1
GO:0001228 - DNA-binding transcription activator activity, RNA polymerase II-specific [Evidence IEA]
Hg(II)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016499937.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008567186.1
COORDINATES: similar to AA sequence:RefSeq:WP_004883301.1
COORDINATES: similar to AA sequence:RefSeq:WP_011979104.1
COORDINATES: similar to AA sequence:RefSeq:WP_010794485.1
COORDINATES: similar to AA sequence:RefSeq:WP_012508123.1
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_011979106.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017739318.1
COORDINATES: similar to AA sequence:RefSeq:WP_019405866.1
COORDINATES: similar to AA sequence:RefSeq:WP_019405863.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007250575.1
COORDINATES: similar to AA sequence:RefSeq:WP_017108798.1
COORDINATES: similar to AA sequence:RefSeq:WP_020795296.1
COORDINATES: similar to AA sequence:RefSeq:WP_015819790.1
GO:0006402 - mRNA catabolic process [Evidence IEA]; GO:0006109 - regulation of carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF014045.2
COORDINATES: protein motif:HMM:NF014691.2
COORDINATES: protein motif:HMM:NF028242.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:TIGR04346.1
COORDINATES: protein motif:HMM:NF037909.2
COORDINATES: protein motif:HMM:NF022835.2
DotI/IcmL family type IV secretion protein
COORDINATES: protein motif:HMM:NF023713.2
DotH/IcmK family type IV secretion protein
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: protein motif:HMM:NF017300.2
GO:0006274 - DNA replication termination [Evidence IEA]
DNA replication terminus site-binding protein
COORDINATES: protein motif:HMM:NF021128.2
COORDINATES: protein motif:HMM:NF014442.2
COORDINATES: protein motif:HMM:NF028126.2
Members of this family include DotD of type IVB secretion systems and TraH of plasmid conjugative plasmid systems, both lipoproteins; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012485.2
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]
secretin N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF019575.2
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein