Hymenobacter swuensis DY53 plasmid pHsw1, complete sequence.
Bacteria; Bacteroidota; Cytophagia; Cytophagales; Hymenobacteraceae; Hymenobacter.
Complete sequence of plasmid1 of ionizing-radiation resistance bacterium Hymenobacter swuensis DY53
Submitted (21-JAN-2014) Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, 29 Geumgu street, Jeongeup 580-185, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP007144.1.\nThe bacteria is available from Prof. Myung Kyum Kim in Seoul\nWomen's University (mkkim@swu.ac.kr).\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 :: gsAssembler v. 2.6\nGenome Coverage :: 8.3x; 814x\nSequencing Technology :: 454; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/05/2022 11:49:08\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,513\nCDSs (total) :: 4,458\nGenes (coding) :: 4,423\nCDSs (with protein) :: 4,423\nGenes (RNA) :: 55\nrRNAs :: 2, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 3, 3 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 3\nPseudo Genes (total) :: 35\nCDSs (without protein) :: 35\nPseudo Genes (ambiguous residues) :: 0 of 35\nPseudo Genes (frameshifted) :: 7 of 35\nPseudo Genes (incomplete) :: 25 of 35\nPseudo Genes (internal stop) :: 11 of 35\nPseudo Genes (multiple problems) :: 6 of 35\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
GO:0015074 - DNA integration [Evidence IEA]
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
integrase core domain-containing protein
COORDINATES: protein motif:HMM:NF024974.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
gliding motility-associated C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013672.2
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009282368.1
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_009282367.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013764180.1
COORDINATES: similar to AA sequence:RefSeq:WP_020498314.1
COORDINATES: similar to AA sequence:RefSeq:WP_019947382.1
heavy metal translocating P-type ATPase metal-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018477914.1
GO:0008535 - respiratory chain complex IV assembly [Evidence IEA]
cbb3-type cytochrome oxidase assembly protein CcoS
COORDINATES: similar to AA sequence:RefSeq:WP_020596266.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
cytochrome-c oxidase, cbb3-type subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_014774186.1
COORDINATES: protein motif:HMM:NF024834.2
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017730938.1
GO:0003674 - molecular_function [Evidence IEA]
cytochrome c oxidase accessory protein CcoG
COORDINATES: protein motif:HMM:NF017559.2
COORDINATES: similar to AA sequence:RefSeq:WP_019947390.1
sulfite exporter TauE/SafE family protein
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_019947392.1
GO:0004109 - coproporphyrinogen oxidase activity [Evidence IEA]
GO:0006779 - porphyrin-containing compound biosynthetic process [Evidence IEA]
oxygen-dependent coproporphyrinogen oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_009284351.1
COORDINATES: similar to AA sequence:RefSeq:WP_009193982.1
GO:0008883 - glutamyl-tRNA reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803333.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013002523.1
COORDINATES: similar to AA sequence:RefSeq:WP_020557770.1
COORDINATES: similar to AA sequence:RefSeq:WP_013665895.1
COORDINATES: similar to AA sequence:RefSeq:WP_015331025.1
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF028235.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019403993.1
COORDINATES: protein motif:HMM:NF015438.2
COORDINATES: similar to AA sequence:RefSeq:WP_018622357.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009282172.1
COORDINATES: protein motif:HMM:NF024989.2
COORDINATES: protein motif:HMM:NF015925.2
COORDINATES: similar to AA sequence:RefSeq:WP_010254896.1
COORDINATES: similar to AA sequence:RefSeq:WP_019848494.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002612162.1
internal stop; 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_017694027.1
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.
COORDINATES: protein motif:HMM:NF024950.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012257.2
COORDINATES: protein motif:HMM:NF024748.2
COORDINATES: similar to AA sequence:RefSeq:WP_010520892.1
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_009282151.1
COORDINATES: similar to AA sequence:RefSeq:WP_020595138.1
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF033788.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_020214541.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_012026274.1
COORDINATES: similar to AA sequence:RefSeq:WP_008508941.1
COORDINATES: similar to AA sequence:RefSeq:WP_009197058.1
COORDINATES: similar to AA sequence:RefSeq:WP_018479342.1
GO:0008977 - prephenate dehydrogenase (NAD+) activity [Evidence IEA]; GO:0004665 - prephenate dehydrogenase (NADP+) activity [Evidence IEA]
GO:0006571 - tyrosine biosynthetic process [Evidence IEA]
prephenate dehydrogenase/arogenate dehydrogenase family protein
COORDINATES: protein motif:HMM:NF017206.2
COORDINATES: similar to AA sequence:RefSeq:WP_018977613.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
This protein belongs to a clade of FMN-dependent monooxygenases, within a broader family of flavin-dependent oxidoreductases, the luciferase-like monooxygenase (LMM) family, some of whose members use coenzyme F420 rather than FMN; Derived by automated computational analysis using gene prediction method: Protein Homology.
NtaA/DmoA family FMN-dependent monooxygenase
COORDINATES: similar to AA sequence:RefSeq:WP_009780919.1
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF018777.2
COORDINATES: protein motif:HMM:NF018305.2
COORDINATES: protein motif:HMM:NF012301.2
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:NF016296.2
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012958.2
COORDINATES: similar to AA sequence:RefSeq:WP_020604703.1
COORDINATES: similar to AA sequence:RefSeq:WP_008585115.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020595757.1
COORDINATES: similar to AA sequence:RefSeq:WP_019947400.1
COORDINATES: protein motif:HMM:NF013592.2
GO:0008237 - metallopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019135.2
COORDINATES: protein motif:HMM:NF039201.1
T9SS type A sorting domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020769164.1
COORDINATES: similar to AA sequence:RefSeq:WP_019946788.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017594767.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR01730.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949149.1
GO:0051139 - metal cation:proton antiporter activity [Evidence IEA]
CusA/CzcA family heavy metal efflux RND transporter
COORDINATES: protein motif:HMM:NF019057.2
COORDINATES: similar to AA sequence:RefSeq:WP_019949538.1
COORDINATES: protein motif:HMM:NF013098.2
COORDINATES: protein motif:HMM:NF014305.2
COORDINATES: similar to AA sequence:RefSeq:WP_019947182.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803115.1
COORDINATES: similar to AA sequence:RefSeq:WP_019600012.1
COORDINATES: protein motif:HMM:NF015444.2
COORDINATES: similar to AA sequence:RefSeq:WP_013764418.1
zinc-binding alcohol dehydrogenase family protein
COORDINATES: protein motif:HMM:NF012334.2
COORDINATES: protein motif:HMM:NF026925.2
COORDINATES: protein motif:HMM:NF026924.2
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: similar to AA sequence:RefSeq:WP_012929058.1
COORDINATES: similar to AA sequence:RefSeq:WP_013060955.1
COORDINATES: protein motif:HMM:NF013319.2
GO:0008452 - RNA ligase activity [Evidence IEA]
GO:0006396 - RNA processing [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_008508269.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012927681.1
COORDINATES: protein motif:HMM:NF024968.2
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: similar to AA sequence:RefSeq:WP_011586249.1
COORDINATES: similar to AA sequence:RefSeq:WP_015333852.1
COORDINATES: protein motif:HMM:NF014732.2
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
Wzz/FepE/Etk N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF016807.2
COORDINATES: protein motif:HMM:NF013676.2
COORDINATES: protein motif:HMM:NF019265.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF016648.2
COORDINATES: protein motif:HMM:TIGR04056.1
COORDINATES: protein motif:HMM:NF019592.2
RagB/SusD family nutrient uptake outer membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_018619143.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015266461.1
COORDINATES: similar to AA sequence:RefSeq:WP_020607271.1
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF040155.1
COORDINATES: protein motif:HMM:NF014581.2
COORDINATES: similar to AA sequence:RefSeq:WP_012929710.1
COORDINATES: similar to AA sequence:RefSeq:WP_012024360.1
PhzF family phenazine biosynthesis isomerase
COORDINATES: protein motif:HMM:NF015531.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020212562.1
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013334681.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011330355.1
COORDINATES: similar to AA sequence:RefSeq:WP_019947094.1
COORDINATES: protein motif:HMM:NF016013.2
COORDINATES: protein motif:HMM:NF018648.2
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007741182.1
COORDINATES: similar to AA sequence:RefSeq:WP_013668004.1
COORDINATES: similar to AA sequence:RefSeq:WP_013668005.1
COORDINATES: similar to AA sequence:RefSeq:WP_012928427.1
COORDINATES: protein motif:HMM:NF027610.2
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024783.2
COORDINATES: protein motif:HMM:NF015736.2
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: protein motif:HMM:NF012492.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013566226.1
COORDINATES: similar to AA sequence:RefSeq:WP_012469470.1
COORDINATES: similar to AA sequence:RefSeq:WP_007509102.1
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:WP_019022977.1
COORDINATES: protein motif:HMM:NF024487.2
COORDINATES: protein motif:HMM:NF020811.2
COORDINATES: protein motif:HMM:NF024703.2
COORDINATES: protein motif:HMM:NF025120.2
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: similar to AA sequence:RefSeq:WP_019949229.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF016232.2
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR02391.1
COORDINATES: protein motif:HMM:NF019313.2
COORDINATES: protein motif:HMM:NF040295.1
COORDINATES: protein motif:HMM:NF016996.2
L-tyrosine/L-tryptophan isonitrile synthase family protein
COORDINATES: protein motif:HMM:NF014698.2
COORDINATES: protein motif:HMM:NF013646.2
COORDINATES: protein motif:HMM:NF024907.2
COORDINATES: protein motif:HMM:NF020904.2
COORDINATES: similar to AA sequence:RefSeq:WP_019949560.1
type II toxin-antitoxin system PemK/MazF family toxin
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF039931.1
COORDINATES: similar to AA sequence:RefSeq:WP_000355838.1
COORDINATES: protein motif:HMM:NF017437.2
COORDINATES: protein motif:HMM:NF012870.2
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_014771174.1
COORDINATES: similar to AA sequence:RefSeq:WP_008237956.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949108.1
COORDINATES: similar to AA sequence:RefSeq:WP_005868266.1
GO:0003824 - catalytic activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019945666.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_014164623.1
GO:0016880 - acid-ammonia (or amide) ligase activity [Evidence IEA]
adenosylcobinamide-phosphate synthase CbiB
COORDINATES: similar to AA sequence:RefSeq:WP_018339268.1
GO:0042242 - cobyrinic acid a,c-diamide synthase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024911.2
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:NF013648.2
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010932102.1
COORDINATES: similar to AA sequence:RefSeq:WP_015812793.1
COORDINATES: protein motif:HMM:NF012801.2
COORDINATES: similar to AA sequence:RefSeq:WP_012792093.1
bifunctional adenosylcobinamide kinase/adenosylcobinamide-phosphate guanylyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_002694792.1
GO:0008817 - cob(I)yrinic acid a,c-diamide adenosyltransferase activity [Evidence IEA]
cob(I)yrinic acid a,c-diamide adenosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_002930815.1
nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
COORDINATES: protein motif:HMM:NF013955.2