Paenibacillus urinalis strain 2022CK-00829 plasmid unnamed2, complete sequence.
Bacteria; Bacillota; Bacilli; Bacillales; Paenibacillaceae; Paenibacillus.
Pathogen: clinical or host-associated sample
Submitted (10-FEB-2023) Utah Public Health Laboratory, Utah Public Health Laboratory Infectious Disease submission group, 4431 S 2700 W, Salt Lake City, UT 84129, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP118110.1.\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 :: Unicycler v. 0.5.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 54.0x\nSequencing Technology :: Illumina MiSeq; Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/21/2023 16:58:56\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) :: 5,483\nCDSs (total) :: 5,362\nGenes (coding) :: 5,297\nCDSs (with protein) :: 5,297\nGenes (RNA) :: 121\nrRNAs :: 9, 9, 9 (5S, 16S, 23S)\ncomplete rRNAs :: 9, 9, 9 (5S, 16S, 23S)\ntRNAs :: 90\nncRNAs :: 4\nPseudo Genes (total) :: 66\nCDSs (without protein) :: 65\nPseudo Genes (ambiguous residues) :: 0 of 66\nPseudo Genes (frameshifted) :: 31 of 66\nPseudo Genes (incomplete) :: 31 of 66\nPseudo Genes (internal stop) :: 12 of 66\nPseudo Genes (multiple problems) :: 8 of 66\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012632.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025108.2
COORDINATES: protein motif:HMM:NF017810.2
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: protein motif:HMM:NF018644.2
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_018751634.1
COORDINATES: similar to AA sequence:RefSeq:WP_017691689.1
copper amine oxidase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017692345.1
COORDINATES: similar to AA sequence:RefSeq:WP_017692344.1
COORDINATES: similar to AA sequence:RefSeq:WP_017692341.1
COORDINATES: similar to AA sequence:RefSeq:WP_017692339.1
COORDINATES: similar to AA sequence:RefSeq:WP_018977650.1
COORDINATES: protein motif:HMM:NF024544.2
COORDINATES: similar to AA sequence:RefSeq:WP_015256736.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256735.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256732.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256731.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF024803.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF012320.2
COORDINATES: similar to AA sequence:RefSeq:WP_015256727.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256725.1
COORDINATES: protein motif:HMM:NF024056.2
COORDINATES: similar to AA sequence:RefSeq:WP_015256723.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256722.1
TcpE family conjugal transfer membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_015256721.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256720.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256719.1
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015256713.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256711.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256710.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256706.1
COORDINATES: similar to AA sequence:RefSeq:WP_000769726.1
COORDINATES: similar to AA sequence:RefSeq:WP_000959521.1
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: similar to AA sequence:RefSeq:WP_015256822.1
COORDINATES: similar to AA sequence:RefSeq:WP_004096206.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014281001.1
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_003250361.1
COORDINATES: protein motif:HMM:NF033679.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256689.1
GO:0003824 - catalytic activity [Evidence IEA]
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF037909.2
COORDINATES: similar to AA sequence:RefSeq:WP_013058769.1
aspartyl-phosphate phosphatase Spo0E family protein
polymorphic toxin-type HINT domain-containing protein
COORDINATES: protein motif:HMM:NF025471.2
COORDINATES: similar to AA sequence:RefSeq:WP_007129666.1
COORDINATES: similar to AA sequence:RefSeq:WP_007129667.1
COORDINATES: similar to AA sequence:RefSeq:WP_006212426.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256685.1
DnaA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015256684.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_019716250.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256828.1
COORDINATES: protein motif:HMM:NF025854.2
COORDINATES: protein motif:HMM:NF012301.2
LytTR family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015256816.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256811.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256810.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256809.1
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_015256806.1
COORDINATES: similar to AA sequence:RefSeq:WP_013919215.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015256796.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256794.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256793.1
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_015256788.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256787.1
COORDINATES: similar to AA sequence:RefSeq:WP_016763254.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010191730.1
GO:0016853 - isomerase activity [Evidence IEA]
GO:1901135 - carbohydrate derivative metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019382153.1
GO:0043801 - hexulose-6-phosphate synthase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019382151.1
winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010652226.1
GO:0004345 - glucose-6-phosphate dehydrogenase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010191725.1
GO:0004616 - phosphogluconate dehydrogenase (decarboxylating) activity [Evidence IEA]
decarboxylating 6-phosphogluconate dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_010191724.1
COORDINATES: similar to AA sequence:RefSeq:WP_013401484.1
GO:0004347 - glucose-6-phosphate isomerase activity [Evidence IEA]
GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003322334.1
COORDINATES: similar to AA sequence:RefSeq:WP_000200617.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015256781.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256780.1
COORDINATES: similar to AA sequence:RefSeq:WP_015256779.1
type II toxin-antitoxin system HicB family antitoxin
COORDINATES: protein motif:HMM:NF024252.2
COORDINATES: similar to AA sequence:RefSeq:WP_015735165.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009592899.1
COORDINATES: protein motif:HMM:NF019908.2
COORDINATES: similar to AA sequence:RefSeq:WP_005718914.1
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
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_011066964.1
COORDINATES: protein motif:HMM:NF012630.2
GO:0031012 - extracellular matrix [Evidence IEA]
GO:0004222 - metalloendopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611387.1
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_015571251.1
COORDINATES: protein motif:HMM:NF025643.2
COORDINATES: similar to AA sequence:RefSeq:WP_009226730.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: protein motif:HMM:NF014543.2
COORDINATES: protein motif:HMM:NF017390.2
COORDINATES: similar to AA sequence:RefSeq:WP_020619273.1
GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]
BlaI/MecI/CopY family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010349630.1
COORDINATES: similar to AA sequence:RefSeq:WP_000121211.1
COORDINATES: similar to AA sequence:RefSeq:WP_014599900.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017262.2
COORDINATES: protein motif:HMM:NF016149.2
COORDINATES: similar to AA sequence:RefSeq:WP_018752103.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015842757.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_011230086.1
COORDINATES: similar to AA sequence:RefSeq:WP_004432083.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000730132.1
COORDINATES: protein motif:HMM:NF021214.2
COORDINATES: similar to AA sequence:RefSeq:WP_009374246.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_018758998.1
COORDINATES: similar to AA sequence:RefSeq:WP_019007680.1
COORDINATES: similar to AA sequence:RefSeq:WP_003645578.1
COORDINATES: protein motif:HMM:TIGR04416.1
COORDINATES: similar to AA sequence:RefSeq:WP_018759869.1
COORDINATES: similar to AA sequence:RefSeq:WP_009224864.1
COORDINATES: similar to AA sequence:RefSeq:WP_019007632.1
COORDINATES: similar to AA sequence:RefSeq:WP_005832212.1
GO:0005507 - copper ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019380917.1
COORDINATES: similar to AA sequence:RefSeq:WP_019382954.1
COORDINATES: similar to AA sequence:RefSeq:WP_019425130.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_019382953.1
four-helix bundle copper-binding protein
COORDINATES: nucleotide motif:Rfam:14.4:RF00379
cyclic di-AMP (ydaO/yuaA leader) riboswitch senses the signaling molecule cyclic di-AMP; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_018882973.1
COORDINATES: similar to AA sequence:RefSeq:WP_016362402.1
COORDINATES: similar to AA sequence:RefSeq:WP_016117863.1
GO:0016311 - dephosphorylation [Evidence IEA]
dual specificity protein phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014112792.1
GO:0030612 - arsenate reductase (thioredoxin) activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006210288.1
COORDINATES: similar to AA sequence:RefSeq:WP_019635319.1
COORDINATES: similar to AA sequence:RefSeq:WP_002103330.1
COORDINATES: similar to AA sequence:RefSeq:WP_018888151.1
GO:0004791 - thioredoxin-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015942203.1
arsinothricin resistance N-acetyltransferase ArsN1
COORDINATES: similar to AA sequence:RefSeq:WP_000802654.1
NAD(P)-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007128043.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009374035.1
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005552637.1
COORDINATES: similar to AA sequence:RefSeq:WP_014368826.1