Paenibacillus urinalis strain 2022CK-00829 plasmid unnamed1, 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\nCP118109.1.\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: similar to AA sequence:RefSeq:WP_016084834.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016084838.1
COORDINATES: protein motif:HMM:NF024603.2
COORDINATES: similar to AA sequence:RefSeq:WP_000246817.1
COORDINATES: protein motif:HMM:NF016923.2
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0019068 - virion assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF019481.2
COORDINATES: similar to AA sequence:RefSeq:WP_016250908.1
COORDINATES: similar to AA sequence:RefSeq:WP_000248659.1
COORDINATES: protein motif:HMM:NF013630.2
LysM peptidoglycan-binding domain-containing protein
COORDINATES: protein motif:HMM:NF022151.2
COORDINATES: protein motif:HMM:NF012304.2
COORDINATES: similar to AA sequence:RefSeq:WP_016084643.1
COORDINATES: protein motif:HMM:NF025815.2
COORDINATES: similar to AA sequence:RefSeq:WP_001201945.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:NF018437.2
COORDINATES: protein motif:HMM:NF013499.2
OB-fold nucleic acid binding domain-containing protein
COORDINATES: protein motif:HMM:NF012381.2
COORDINATES: protein motif:HMM:NF015146.2
COORDINATES: similar to AA sequence:RefSeq:WP_016084680.1
COORDINATES: protein motif:HMM:NF021568.2
Na-translocating system protein MpsC family protein
COORDINATES: protein motif:HMM:NF024747.2
4Fe-4S cluster-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012234.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018565.2
COORDINATES: protein motif:HMM:NF022657.2
COORDINATES: protein motif:HMM:NF014560.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050797 - thymidylate synthase (FAD) activity [Evidence IEA]
GO:0006231 - dTMP biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: protein motif:HMM:NF024554.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003896 - DNA primase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
CHC2 zinc finger domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009328277.1
COORDINATES: protein motif:HMM:NF039653.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084739.1
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: similar to AA sequence:RefSeq:WP_011067121.1
GO:0071973 - bacterial-type flagellum-dependent cell motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF014638.2
COORDINATES: protein motif:HMM:NF023069.2
DnaA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000583728.1
GO:0004798 - thymidylate kinase activity [Evidence IEA]
GO:0015949 - nucleobase-containing small molecule interconversion [Evidence IEA]
COORDINATES: protein motif:HMM:NF013670.2
GO:0008745 - N-acetylmuramoyl-L-alanine amidase activity [Evidence IEA]
GO:0009253 - peptidoglycan catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00594.1
COORDINATES: similar to AA sequence:RefSeq:WP_013084831.1
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF017663.2
GO:0000287 - magnesium ion binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
RusA family crossover junction endodeoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_000477374.1
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: similar to AA sequence:RefSeq:WP_016718711.1
COORDINATES: similar to AA sequence:RefSeq:WP_013308516.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0009263 - deoxyribonucleotide biosynthetic process [Evidence IEA]
ribonucleotide-diphosphate reductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_005543563.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0004748 - ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor [Evidence IEA]
ribonucleoside-diphosphate reductase subunit alpha
COORDINATES: protein motif:HMM:NF019584.2
GO:0036211 - protein modification process [Evidence IEA]
class Ib ribonucleoside-diphosphate reductase assembly flavoprotein NrdI
COORDINATES: similar to AA sequence:RefSeq:WP_017814450.1
COORDINATES: protein motif:HMM:NF012956.2
COORDINATES: protein motif:HMM:NF015736.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016084795.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084796.1
COORDINATES: similar to AA sequence:RefSeq:WP_003346233.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084800.1
COORDINATES: similar to AA sequence:RefSeq:WP_016084802.1
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: similar to AA sequence:RefSeq:WP_000159992.1
COORDINATES: protein motif:HMM:NF019311.2
low copy number virion structural protein
COORDINATES: protein motif:HMM:NF012632.2
COORDINATES: similar to AA sequence:RefSeq:WP_016084824.1
COORDINATES: similar to AA sequence:RefSeq:WP_000510552.1
COORDINATES: protein motif:HMM:NF013954.2
GO:0004040 - amidase activity [Evidence IEA]
glucosaminidase domain-containing protein