Legionella lytica strain PCM 2298 plasmid pLlyPCM2298_2, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Legionellales; Legionellaceae; Legionella.
Submitted (09-MAR-2021) Genetics and Microbiology, UMCS, Akademicka, Lublin 20-033, Poland
REFSEQ INFORMATION: The reference sequence is identical to\nCP071529.1.\nBacteria and source DNA available from Department of Genetics and\nMicrobiology, UMCS, Lublin, Poland.\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 Date :: 20-MAY-2020\nAssembly Method :: Unicycler v. 0.4.4\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: Illumina; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/05/2023 03:43:37\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) :: 3,224\nCDSs (total) :: 3,165\nGenes (coding) :: 3,112\nCDSs (with protein) :: 3,112\nGenes (RNA) :: 59\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 43\nncRNAs :: 4\nPseudo Genes (total) :: 53\nCDSs (without protein) :: 53\nPseudo Genes (ambiguous residues) :: 0 of 53\nPseudo Genes (frameshifted) :: 17 of 53\nPseudo Genes (incomplete) :: 35 of 53\nPseudo Genes (internal stop) :: 11 of 53\nPseudo Genes (multiple problems) :: 9 of 53\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_011212458.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011212459.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012219992.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019235601.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014845160.1
COORDINATES: similar to AA sequence:RefSeq:WP_019233018.1
COORDINATES: similar to AA sequence:RefSeq:WP_019218345.1
COORDINATES: similar to AA sequence:RefSeq:WP_011282722.1
GO:0006402 - mRNA catabolic process [Evidence IEA]; GO:0006109 - regulation of carbohydrate metabolic process [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: similar to AA sequence:RefSeq:WP_019233017.1
COORDINATES: similar to AA sequence:RefSeq:WP_010655324.1
COORDINATES: similar to AA sequence:RefSeq:WP_019233016.1
COORDINATES: similar to AA sequence:RefSeq:WP_019233015.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_019233014.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_019233013.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_019233012.1
COORDINATES: similar to AA sequence:RefSeq:WP_010654218.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_019233008.1
type-F conjugative transfer system protein TraW
COORDINATES: similar to AA sequence:RefSeq:WP_010654215.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_010654214.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: similar to AA sequence:RefSeq:WP_010654213.1
COORDINATES: similar to AA sequence:RefSeq:WP_012979156.1
type-F conjugative transfer system pilin assembly protein TraF
COORDINATES: similar to AA sequence:RefSeq:WP_011212617.1
type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB
COORDINATES: similar to AA sequence:RefSeq:WP_012979154.1
COORDINATES: protein motif:HMM:NF010295.2
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_014845135.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_014845134.1
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_014845133.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212815.1
COORDINATES: protein motif:HMM:NF015205.2
COORDINATES: protein motif:HMM:NF027059.2
type II toxin-antitoxin system MqsR family toxin
COORDINATES: protein motif:HMM:TIGR03830.1
type II toxin-antitoxin system MqsA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010655390.1
COORDINATES: similar to AA sequence:RefSeq:WP_006870515.1
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_019350400.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019350401.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011946314.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014841437.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
PhzF family phenazine biosynthesis protein
COORDINATES: similar to AA sequence:RefSeq:WP_014842181.1
COORDINATES: similar to AA sequence:RefSeq:WP_019216104.1
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: protein motif:HMM:NF012382.2
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: protein motif:HMM:NF024818.2
GO:0005515 - protein binding [Evidence IEA]
PAS domain-containing hybrid sensor histidine kinase/response regulator
COORDINATES: protein motif:HMM:NF012958.2
COORDINATES: similar to AA sequence:RefSeq:WP_011797793.1
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_014842359.1
COORDINATES: similar to AA sequence:RefSeq:WP_014842360.1
COORDINATES: similar to AA sequence:RefSeq:WP_014842361.1
GO:0006313 - DNA transposition [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_007812900.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017210200.1
COORDINATES: similar to AA sequence:RefSeq:WP_014913961.1
COORDINATES: protein motif:HMM:NF014814.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF024824.2
COORDINATES: similar to AA sequence:RefSeq:WP_019529671.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018576363.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010654322.1
COORDINATES: similar to AA sequence:RefSeq:WP_006872668.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF033527.1
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: similar to AA sequence:RefSeq:WP_019218442.1
COORDINATES: protein motif:HMM:NF012512.2
COORDINATES: similar to AA sequence:RefSeq:WP_003631844.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212515.1
COORDINATES: similar to AA sequence:RefSeq:WP_014845129.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212514.1
COORDINATES: similar to AA sequence:RefSeq:WP_010655359.1
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010655360.1
COORDINATES: similar to AA sequence:RefSeq:WP_011212518.1
COORDINATES: similar to AA sequence:RefSeq:WP_014845125.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014845124.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019235347.1
COORDINATES: similar to AA sequence:RefSeq:WP_010655442.1
COORDINATES: similar to AA sequence:RefSeq:WP_014286547.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611931.1
COORDINATES: similar to AA sequence:RefSeq:WP_010655032.1
COORDINATES: protein motif:HMM:TIGR03914.1
This protein belongs to the uracil DNA glycosylase superfamily, members of which act in excision repair of DNA. However, it belongs more specifically to UdgX branch, whose founding member was found to bind uracil in DNA (where it does not belong), without cleaving it, appears to promote DNA repair by a pathway involving RecA, rather than base excision.; This protein belongs to the uracil DNA glycosylase superfamily, members of which act in excision repair of DNA. However, it belongs more specifically to UdgX branch, whose founding member was found to bind uracil in DNA (where it does not belong), without cleaving it, appears to promote DNA repair by a pathway involving RecA, rather than base excision; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010653254.1
GO:0045027 - DNA end binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010653214.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012979179.1
COORDINATES: similar to AA sequence:RefSeq:WP_019350420.1
GO:0003684 - damaged DNA binding [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015444683.1
COORDINATES: similar to AA sequence:RefSeq:WP_012979182.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: protein motif:HMM:NF014626.2
GO:0008233 - peptidase activity [Evidence IEA]; GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]; GO:0009432 - SOS response [Evidence IEA]
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - DNA damage response [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006870753.1
COORDINATES: similar to AA sequence:RefSeq:WP_019350424.1
GO:0004518 - nuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015445050.1
COORDINATES: similar to AA sequence:RefSeq:WP_019235285.1