Lelliottia amnigena strain FDAARGOS_1445 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Lelliottia.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (19-JUL-2021) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, White Oak, MD 20903, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP079897.1.\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 :: SMRT v. 9.0.0, HGAP v. 4.0\nGenome Coverage :: 2064.97x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/29/2023 04:22:55\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) :: 4,404\nCDSs (total) :: 4,288\nGenes (coding) :: 4,232\nCDSs (with protein) :: 4,232\nGenes (RNA) :: 116\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 86\nncRNAs :: 8\nPseudo Genes (total) :: 56\nCDSs (without protein) :: 56\nPseudo Genes (ambiguous residues) :: 0 of 56\nPseudo Genes (frameshifted) :: 18 of 56\nPseudo Genes (incomplete) :: 42 of 56\nPseudo Genes (internal stop) :: 14 of 56\nPseudo Genes (multiple problems) :: 14 of 56\nPseudo Genes (short protein) :: 1 of 56\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_000102650.1
GO:0006629 - lipid metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
patatin-like phospholipase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014592933.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00121.1
GO:0004077 - biotin-[acetyl-CoA-carboxylase] ligase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004118534.1
camphor resistance protein CrcB; may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling; 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_015377870.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_014834018.1
GO:0004803 - transposase activity [Evidence IEA]
Tn3-like element ISPa38 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001247892.1
COORDINATES: similar to AA sequence:RefSeq:WP_001293886.1
COORDINATES: similar to AA sequence:RefSeq:WP_003465043.1
COORDINATES: similar to AA sequence:RefSeq:WP_011809177.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100856.1
COORDINATES: similar to AA sequence:RefSeq:WP_003100853.1
COORDINATES: similar to AA sequence:RefSeq:WP_019897068.1
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_014172315.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612015.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [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_076611902.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_008786570.1
GO:0015103 - inorganic anion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001066652.1
GO:0016208 - AMP binding [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000065802.1
GO:0008794 - arsenate reductase (glutaredoxin) activity [Evidence IEA]
glutaredoxin-dependent arsenate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_004152098.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015105 - arsenite transmembrane transporter activity [Evidence IEA]
GO:0046685 - response to arsenic-containing substance [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000941305.1
COORDINATES: similar to AA sequence:RefSeq:WP_000130816.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000125671.1
COORDINATES: similar to AA sequence:RefSeq:NP_462552.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213599.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087098.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322804.1
COORDINATES: similar to AA sequence:RefSeq:WP_007372647.1
COORDINATES: similar to AA sequence:RefSeq:WP_003852412.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611385.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004213565.1
GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_002435849.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0008941 - nitric oxide dioxygenase activity [Evidence IEA]; GO:0019825 - oxygen binding [Evidence IEA]
GO:0051409 - response to nitrosative stress [Evidence IEA]
COORDINATES: protein motif:HMM:NF013014.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_000657897.1
COORDINATES: similar to AA sequence:RefSeq:WP_007725174.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229630.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:YP_005229629.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906492.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_017896146.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_000723069.1
copper resistance system metallochaperone PcoE
COORDINATES: similar to AA sequence:RefSeq:WP_008455299.1
copper resistance membrane spanning protein PcoS
COORDINATES: similar to AA sequence:RefSeq:WP_020239536.1
copper response regulator transcription factor PcoR
COORDINATES: similar to AA sequence:RefSeq:WP_004098940.1
copper resistance inner membrane protein PcoD
COORDINATES: similar to AA sequence:RefSeq:WP_004098941.1
copper resistance system metallochaperone PcoC
COORDINATES: similar to AA sequence:RefSeq:WP_001378118.1
COORDINATES: similar to AA sequence:RefSeq:WP_001480786.1
COORDINATES: similar to AA sequence:RefSeq:WP_004388333.1
COORDINATES: similar to AA sequence:RefSeq:WP_002436617.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000843499.1
COORDINATES: similar to AA sequence:RefSeq:WP_008322814.1
COORDINATES: similar to AA sequence:RefSeq:WP_002436620.1
COORDINATES: similar to AA sequence:RefSeq:WP_011711636.1
Cu(+)/Ag(+) efflux RND transporter permease subunit SilA
COORDINATES: similar to AA sequence:RefSeq:WP_017146627.1
Cu(+)/Ag(+) efflux RND transporter periplasmic adaptor subunit SilB
COORDINATES: similar to AA sequence:RefSeq:WP_009654303.1
COORDINATES: similar to AA sequence:RefSeq:WP_001572989.1
Cu(+)/Ag(+) efflux RND transporter outer membrane channel SilC
COORDINATES: similar to AA sequence:RefSeq:WP_001572351.1
copper/silver response regulator transcription factor SilR
COORDINATES: similar to AA sequence:RefSeq:WP_011711631.1
copper/silver sensor histidine kinase SilS
COORDINATES: similar to AA sequence:RefSeq:WP_000790485.1
COORDINATES: similar to AA sequence:RefSeq:WP_000647571.1
COORDINATES: similar to AA sequence:RefSeq:WP_007849142.1
internal stop; 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_013087127.1
COORDINATES: similar to AA sequence:RefSeq:WP_004197635.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011906524.1
COORDINATES: similar to AA sequence:RefSeq:NP_052640.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906526.1
ParB/RepB/Spo0J family plasmid partition protein
COORDINATES: similar to AA sequence:RefSeq:YP_005229773.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229772.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: similar to AA sequence:RefSeq:YP_005229768.1
COORDINATES: similar to AA sequence:RefSeq:WP_015345000.1
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014063845.1
COORDINATES: similar to AA sequence:RefSeq:WP_002211749.1
COORDINATES: similar to AA sequence:RefSeq:WP_001104903.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087145.1
COORDINATES: similar to AA sequence:RefSeq:WP_008502215.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087149.1
COORDINATES: similar to AA sequence:RefSeq:WP_014063852.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087156.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_015572066.1
COORDINATES: similar to AA sequence:RefSeq:WP_013087158.1
COORDINATES: similar to AA sequence:RefSeq:WP_011906549.1
COORDINATES: protein motif:HMM:NF036604.2
COORDINATES: similar to AA sequence:RefSeq:NP_052660.1
type I toxin-antitoxin system Hok family toxin
COORDINATES: protein motif:HMM:NF018252.2
GO:0098567 - periplasmic side of plasma membrane [Evidence IEA]
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014376.2
AraC family ligand binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002903735.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000544745.1
COORDINATES: similar to AA sequence:RefSeq:WP_000203527.1