Providencia rettgeri strain AR_0082 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae; Providencia.
Whole genome sequencing of Providencia rettgeri AR_0082
Submitted (31-MAY-2018) NIH Intramural Sequencing Center, 5625 Fishers Lane, Rockville, MD 20852, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP029737.1.\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. 2.3\nGenome Coverage :: 178x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/14/2023 09:46:14\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) :: 4,117\nCDSs (total) :: 4,013\nGenes (coding) :: 3,980\nCDSs (with protein) :: 3,980\nGenes (RNA) :: 104\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 78\nncRNAs :: 4\nPseudo Genes (total) :: 33\nCDSs (without protein) :: 33\nPseudo Genes (ambiguous residues) :: 0 of 33\nPseudo Genes (frameshifted) :: 10 of 33\nPseudo Genes (incomplete) :: 28 of 33\nPseudo Genes (internal stop) :: 4 of 33\nPseudo Genes (multiple problems) :: 9 of 33\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_001097010.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
DNA replication terminus site-binding protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221073.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221072.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221071.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221070.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221069.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221068.1
COORDINATES: similar to AA sequence:RefSeq:WP_002210564.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
GO:0004803 - transposase activity [Evidence IEA]
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_076611607.1
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_032492661.1
subclass B1 metallo-beta-lactamase NDM-1
COORDINATES: similar to AA sequence:RefSeq:WP_004201167.1
COORDINATES: similar to AA sequence:RefSeq:WP_004201168.1
GO:0004640 - phosphoribosylanthranilate isomerase activity [Evidence IEA]
GO:0000162 - tryptophan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006399920.1
twin-arginine translocation (TAT) pathway signal sequence domain protein
COORDINATES: protein motif:HMM:NF022853.2
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004201171.1
GO:0010038 - response to metal ion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013534102.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005411226.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000050481.1
IS91-like element ISCR1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000259031.1
sulfonamide-resistant dihydropteroate synthase Sul1
COORDINATES: similar to AA sequence:RefSeq:WP_000679427.1
quaternary ammonium compound efflux SMR transporter QacE delta 1
COORDINATES: similar to AA sequence:RefSeq:WP_001749984.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
AadA family aminoglycoside 3''-O-nucleotidyltransferase
COORDINATES: protein motif:HMM:NF017990.2
COORDINATES: similar to AA sequence:RefSeq:WP_004187529.1
trimethoprim-resistant dihydrofolate reductase DfrA12
COORDINATES: similar to AA sequence:RefSeq:YP_005221021.1
COORDINATES: similar to AA sequence:RefSeq:WP_016236504.1
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_001138064.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229637.1
IS110-like element IS5075 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000714163.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221058.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221057.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221056.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:YP_005221054.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221053.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221052.1
COORDINATES: similar to AA sequence:RefSeq:WP_000184110.1
COORDINATES: similar to AA sequence:RefSeq:WP_000071869.1
GO:0002953 - 5'-deoxynucleotidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000050847.1
COORDINATES: similar to AA sequence:RefSeq:WP_008950963.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: similar to AA sequence:RefSeq:WP_001187970.1
phosphoadenosine phosphosulfate reductase
COORDINATES: similar to AA sequence:RefSeq:WP_000042274.1
COORDINATES: similar to AA sequence:RefSeq:WP_001093867.1
COORDINATES: similar to AA sequence:RefSeq:WP_011899375.1
COORDINATES: similar to AA sequence:RefSeq:WP_000201432.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000994741.1
COORDINATES: similar to AA sequence:RefSeq:WP_000651508.1
COORDINATES: similar to AA sequence:RefSeq:WP_000340223.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141572.1
COORDINATES: similar to AA sequence:RefSeq:WP_001102699.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
class I ribonucleotide reductase maintenance protein YfaE
COORDINATES: similar to AA sequence:RefSeq:WP_000477209.1
COORDINATES: similar to AA sequence:RefSeq:WP_000018871.1
COORDINATES: similar to AA sequence:RefSeq:WP_000039317.1
COORDINATES: similar to AA sequence:RefSeq:WP_000170086.1
COORDINATES: protein motif:HMM:TIGR03033.1
COORDINATES: similar to AA sequence:RefSeq:WP_001282585.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000987165.1
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_000739140.1
COORDINATES: similar to AA sequence:RefSeq:WP_000085161.1
CbbQ/NirQ/NorQ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000547565.1
COORDINATES: similar to AA sequence:RefSeq:WP_000796664.1
COORDINATES: similar to AA sequence:RefSeq:WP_001447718.1
conjugal transfer mating pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_017085236.1
COORDINATES: similar to AA sequence:RefSeq:WP_001337754.1
COORDINATES: similar to AA sequence:RefSeq:WP_001447719.1
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_001010738.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184404.1
COORDINATES: similar to AA sequence:RefSeq:WP_000637387.1
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: similar to AA sequence:RefSeq:WP_000606836.1
COORDINATES: similar to AA sequence:RefSeq:WP_013141547.1
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_010845916.1
type IV conjugative transfer system lipoprotein TraV
COORDINATES: similar to AA sequence:RefSeq:WP_000647304.1
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_001049717.1
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: similar to AA sequence:RefSeq:WP_000433889.1
type IV conjugative transfer system protein TraL
COORDINATES: similar to AA sequence:RefSeq:WP_001052531.1
COORDINATES: similar to AA sequence:RefSeq:WP_001275801.1
COORDINATES: similar to AA sequence:RefSeq:WP_000869261.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184411.1
COORDINATES: similar to AA sequence:RefSeq:WP_000743450.1
COORDINATES: similar to AA sequence:RefSeq:WP_000178858.1
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: protein motif:HMM:NF041494.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184413.1
COORDINATES: similar to AA sequence:RefSeq:WP_010845927.1
COORDINATES: protein motif:HMM:NF005829.0
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_000467110.1
COORDINATES: similar to AA sequence:RefSeq:WP_001326171.1
COORDINATES: similar to AA sequence:RefSeq:WP_001339197.1
IS4-like element ISVsa5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_000268550.1
COORDINATES: protein motif:HMM:NF012372.2
COORDINATES: similar to AA sequence:RefSeq:YP_005221048.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221046.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221044.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221043.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221042.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221041.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221040.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221039.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221037.1
COORDINATES: similar to AA sequence:RefSeq:WP_000098295.1
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001258027.1
COORDINATES: similar to AA sequence:RefSeq:WP_001096362.1
COORDINATES: similar to AA sequence:RefSeq:WP_000268394.1
COORDINATES: similar to AA sequence:RefSeq:WP_000435225.1
COORDINATES: similar to AA sequence:RefSeq:WP_001256128.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220991.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220990.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220989.1
COORDINATES: similar to AA sequence:RefSeq:WP_000225028.1
COORDINATES: similar to AA sequence:RefSeq:WP_000018404.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220983.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220982.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220980.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220979.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220978.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220977.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220976.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220975.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220973.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220972.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:YP_005220971.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220970.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220969.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005220968.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220966.1
COORDINATES: similar to AA sequence:RefSeq:WP_039272517.1
IS21-like element ISAs29 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_039272515.1
IS21-like element ISAs29 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:YP_005220965.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220964.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220963.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220962.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220961.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220960.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220959.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005220958.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220957.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220956.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220955.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220954.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220953.1
COORDINATES: similar to AA sequence:RefSeq:YP_005220951.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_004201092.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221100.1
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:YP_005221099.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221098.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221097.1
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221096.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221095.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221094.1
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:YP_005221093.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221092.1
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221091.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221090.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221089.1
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005221088.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221087.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221086.1
COORDINATES: similar to AA sequence:RefSeq:YP_005221085.1