Delftia lacustris strain FDAARGOS_890 plasmid unnamed.
Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; Comamonadaceae; Delftia.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (02-DEC-2020) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP065749.1.\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 :: Canu v. 1.7\nGenome Coverage :: 494.28x\nSequencing Technology :: Pacbio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/29/2022 05:09:44\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) :: 6,756\nCDSs (total) :: 6,659\nGenes (coding) :: 6,595\nCDSs (with protein) :: 6,595\nGenes (RNA) :: 97\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 79\nncRNAs :: 3\nPseudo Genes (total) :: 64\nCDSs (without protein) :: 64\nPseudo Genes (ambiguous residues) :: 0 of 64\nPseudo Genes (frameshifted) :: 29 of 64\nPseudo Genes (incomplete) :: 44 of 64\nPseudo Genes (internal stop) :: 9 of 64\nPseudo Genes (multiple problems) :: 13 of 64\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003064853.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007871594.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013902588.1
indolepyruvate oxidoreductase subunit beta family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007830582.1
indolepyruvate ferredoxin oxidoreductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_007871584.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [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_012732717.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_018904762.1
COORDINATES: similar to AA sequence:RefSeq:WP_011356328.1
COORDINATES: protein motif:HMM:NF016777.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012432.2
COORDINATES: protein motif:HMM:TIGR02423.1
GO:0018578 - protocatechuate 3,4-dioxygenase activity [Evidence IEA]
GO:0046278 - 3,4-dihydroxybenzoate metabolic process [Evidence IEA]
protocatechuate 3,4-dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_011519954.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008972328.1
COORDINATES: similar to AA sequence:RefSeq:WP_011490983.1
COORDINATES: similar to AA sequence:RefSeq:WP_011490984.1
COORDINATES: similar to AA sequence:RefSeq:WP_018633644.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015366.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558120.1
GO:0004803 - transposase activity [Evidence IEA]
Tn3-like element IS1071 family transposase
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_009735076.1
CaiB/BaiF CoA-transferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011519957.1
COORDINATES: similar to AA sequence:RefSeq:WP_004338692.1
COORDINATES: similar to AA sequence:RefSeq:WP_006297521.1
tripartite tricarboxylate transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011800430.1
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_019561790.1
COORDINATES: similar to AA sequence:RefSeq:WP_012495276.1
COORDINATES: similar to AA sequence:RefSeq:WP_011952810.1
COORDINATES: similar to AA sequence:RefSeq:WP_011519962.1
COORDINATES: protein motif:HMM:NF012402.2
COORDINATES: similar to AA sequence:RefSeq:WP_007439268.1
COORDINATES: similar to AA sequence:RefSeq:WP_013958945.1
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003073461.1
COORDINATES: similar to AA sequence:RefSeq:WP_012535885.1
COORDINATES: similar to AA sequence:RefSeq:WP_012745835.1
COORDINATES: similar to AA sequence:RefSeq:WP_008643232.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003804149.1
COORDINATES: similar to AA sequence:RefSeq:WP_019042336.1
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558243.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013516262.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011254870.1
COORDINATES: similar to AA sequence:RefSeq:WP_014237630.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR02504.1
GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
adenosylcobalamin-dependent ribonucleoside-diphosphate reductase
COORDINATES: protein motif:HMM:NF024755.2
primase-helicase zinc-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR00621.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_013292932.1
COORDINATES: protein motif:HMM:TIGR00616.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:NF019153.2
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF024487.2
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: protein motif:HMM:NF019843.2
COORDINATES: similar to AA sequence:RefSeq:WP_004356264.1
COORDINATES: similar to AA sequence:RefSeq:WP_012204583.1
COORDINATES: similar to AA sequence:RefSeq:WP_014192183.1
COORDINATES: similar to AA sequence:RefSeq:WP_014192182.1
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: similar to AA sequence:RefSeq:WP_018207804.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576691.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516250.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576693.1
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576694.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_013516246.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576697.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: similar to AA sequence:RefSeq:WP_019576699.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576700.1
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_019576701.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_019576702.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_019576705.1
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: similar to AA sequence:RefSeq:WP_013516234.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516233.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_013516231.1
COORDINATES: similar to AA sequence:RefSeq:WP_008902885.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516281.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516293.1
COORDINATES: similar to AA sequence:RefSeq:WP_000572551.1
COORDINATES: similar to AA sequence:RefSeq:WP_011988470.1
COORDINATES: similar to AA sequence:RefSeq:WP_011875889.1
COORDINATES: protein motif:HMM:NF015639.2
COORDINATES: similar to AA sequence:RefSeq:WP_015256800.1
COORDINATES: similar to AA sequence:RefSeq:WP_019576718.1
COORDINATES: protein motif:HMM:NF024724.2
COORDINATES: similar to AA sequence:RefSeq:WP_013615911.1
COORDINATES: protein motif:HMM:NF040044.1
COORDINATES: similar to AA sequence:RefSeq:WP_013723328.1
phospholipase D-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011804577.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: similar to AA sequence:RefSeq:WP_017875854.1
COORDINATES: similar to AA sequence:RefSeq:WP_016446553.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008903689.1
COORDINATES: similar to AA sequence:RefSeq:WP_008294947.1
COORDINATES: similar to AA sequence:RefSeq:WP_015476671.1
COORDINATES: similar to AA sequence:RefSeq:WP_015476672.1
GO:0009291 - unidirectional conjugation [Evidence IEA]
P-type conjugative transfer protein TrbG
COORDINATES: similar to AA sequence:RefSeq:WP_003056121.1
COORDINATES: similar to AA sequence:RefSeq:WP_017677042.1
P-type conjugative transfer protein TrbL
COORDINATES: similar to AA sequence:RefSeq:WP_011516110.1
COORDINATES: similar to AA sequence:RefSeq:WP_003103988.1
P-type conjugative transfer protein TrbJ
COORDINATES: similar to AA sequence:RefSeq:WP_003138981.1
COORDINATES: similar to AA sequence:RefSeq:WP_012076306.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_020203109.1
COORDINATES: similar to AA sequence:RefSeq:WP_017677037.1
COORDINATES: similar to AA sequence:RefSeq:WP_008786751.1
COORDINATES: similar to AA sequence:RefSeq:WP_013721753.1
COORDINATES: similar to AA sequence:RefSeq:WP_013721754.1
COORDINATES: similar to AA sequence:RefSeq:WP_005304543.1
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005304546.1
COORDINATES: similar to AA sequence:RefSeq:WP_014338464.1
COORDINATES: similar to AA sequence:RefSeq:WP_011489329.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011806070.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_005304557.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF024212.2
COORDINATES: similar to AA sequence:RefSeq:WP_003056169.1
relaxase/mobilization nuclease and DUF3363 domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003488045.1
COORDINATES: similar to AA sequence:RefSeq:WP_015914726.1
COORDINATES: similar to AA sequence:RefSeq:WP_011241722.1
COORDINATES: similar to AA sequence:RefSeq:WP_009523272.1
COORDINATES: similar to AA sequence:RefSeq:WP_013722445.1
COORDINATES: similar to AA sequence:RefSeq:WP_003107109.1
COORDINATES: similar to AA sequence:RefSeq:WP_011805836.1
COORDINATES: similar to AA sequence:RefSeq:WP_013721773.1
COORDINATES: similar to AA sequence:RefSeq:WP_020750592.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019726278.1
COORDINATES: similar to AA sequence:RefSeq:WP_017407759.1
COORDINATES: similar to AA sequence:RefSeq:WP_011516017.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012638432.1
COORDINATES: similar to AA sequence:RefSeq:WP_003296366.1
COORDINATES: similar to AA sequence:RefSeq:WP_011811426.1
COORDINATES: similar to AA sequence:RefSeq:WP_010104246.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019579765.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: protein motif:HMM:NF017697.2
poly-gamma-glutamate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005413104.1
COORDINATES: similar to AA sequence:RefSeq:WP_011516219.1
Qat anti-phage system associated protein QatB
COORDINATES: similar to AA sequence:RefSeq:WP_016448857.1
Qat anti-phage system QueC-like protein QatC
COORDINATES: similar to AA sequence:RefSeq:WP_011516217.1
Qat anti-phage system TatD family nuclease QatD
COORDINATES: similar to AA sequence:RefSeq:WP_016809404.1
COORDINATES: similar to AA sequence:RefSeq:WP_011052622.1
COORDINATES: similar to AA sequence:RefSeq:WP_009517003.1
COORDINATES: similar to AA sequence:RefSeq:WP_013449705.1
COORDINATES: similar to AA sequence:RefSeq:WP_013516268.1
COORDINATES: similar to AA sequence:RefSeq:WP_013691873.1
COORDINATES: similar to AA sequence:RefSeq:WP_011876255.1
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF022853.2
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010106167.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004630459.1
COORDINATES: similar to AA sequence:RefSeq:WP_010106168.1
COORDINATES: similar to AA sequence:RefSeq:WP_011831539.1
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: similar to AA sequence:RefSeq:WP_016448641.1
COORDINATES: similar to AA sequence:RefSeq:WP_004533706.1
COORDINATES: similar to AA sequence:RefSeq:WP_018981311.1
COORDINATES: protein motif:HMM:NF025388.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF033429.2
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_019702945.1
COORDINATES: similar to AA sequence:RefSeq:WP_011798331.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_021138877.1
COORDINATES: similar to AA sequence:RefSeq:WP_004636773.1
COORDINATES: similar to AA sequence:RefSeq:WP_004631218.1
COORDINATES: similar to AA sequence:RefSeq:WP_011517526.1
COORDINATES: similar to AA sequence:RefSeq:WP_020200937.1
COORDINATES: similar to AA sequence:RefSeq:WP_012492771.1
COORDINATES: similar to AA sequence:RefSeq:WP_008921974.1
COORDINATES: similar to AA sequence:RefSeq:WP_003379522.1
COORDINATES: similar to AA sequence:RefSeq:WP_011288032.1
COORDINATES: similar to AA sequence:RefSeq:WP_013442779.1
COORDINATES: similar to AA sequence:RefSeq:WP_000904941.1
COORDINATES: similar to AA sequence:RefSeq:WP_011517528.1
COORDINATES: similar to AA sequence:RefSeq:WP_003155746.1
COORDINATES: similar to AA sequence:RefSeq:WP_013124600.1
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF021883.2
COORDINATES: protein motif:HMM:NF014564.2
GO:0008410 - CoA-transferase activity [Evidence IEA]
incomplete; too short partial abutting assembly gap; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.