Hymenobacter swuensis DY53 plasmid pHsw3, complete sequence.
type: Entry
definition: Hymenobacter swuensis DY53 plasmid pHsw3, complete sequence.
sequence version: NZ_CP007146.1
sequence date: 2022-10-06
sequence: sequence
division: CON
label: NZ_CP007146.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN03081528
keyword: RefSeq
source: Hymenobacter swuensis DY53
organism: Hymenobacter swuensis DY53
taxonomy: Bacteria; Bacteroidota; Cytophagia; Cytophagales; Hymenobacteraceae; Hymenobacter.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP007146.1.\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.

sequence
subclass of: SO_0000155
sequence length: 6969
topology: circular
so has quality: SO_0000988
location: 1..6969
location: region:1-6969:1
RO_0002162: 1227739

NZ_CP007146
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN03081528
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid3 of ionizing-radiation resistance bacterium Hymenobacter swuensis DY53
author: Jung, J.-H.
author: Jeong, S.-W.
author: Joe, M.-H.
author: Cho, y.-j.
author: Kim, M.-K.
author: Lim, S.-Y.
journal: Unpublished

2
title: Direct Submission
author: Jung, J.-H.
author: Jeong, S.-W.
author: Joe, M.-H.
author: Cho, y.-j.
author: Kim, M.-K.
author: Lim, S.-Y.
journal: Submitted (21-JAN-2014) Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, 29 Geumgu street, Jeongeup 580-185, South Korea

position:1:1
position: 1
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6969:1
position: 6969
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-6969:1:source
so part of: sequence
organism: Hymenobacter swuensis DY53
mol type: genomic DNA
strain: DY53
type material: type strain of Hymenobacter swuensis
plasmid: pHsw3

1227739
type: Taxonomy
SIO_000068: taxonomy

HSW_RS22235
type: Gene
subclass of: SO_0000704
RO_0002162: 1227739
locus tag: HSW_RS22235
old locus tag: Hsw_PC0001
so part of: sequence
location: join(6732..6969,1..752)
location: region:1-6969:1
so has part: feature:6732-6969:1:exon
so has part: feature:1-752:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:6732-6969:1:exon

position:6732:1
position: 6732
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-752:1:exon

position:752:1
position: 752
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

HSW_RS22235
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1227739
locus tag: HSW_RS22235
old locus tag: Hsw_PC0001
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: replication initiation protein
translation: MGEVEARIFVEALRGINHGQYGDTALPPIDIPVAAILRNDDSAKAYAVVRAACKALFEKDLNLLQANSRRPNDFHKTHIVSDLELNTGTGRIRGNWAPKMRPYLIQLSEAGNFTSANIATLLTMTPNAQRLYWILKSYAGIGTKDAVLYQESIENVKLLLLEDAGLYPLWADFNRYVLEPIKQEFASADVAFPVSWEPLKTGRKVTAIEFTIPREERRTRKALAAAAAAPVAGAPAAAPDRFAEWLAGQAPNLQKAYAGLISTSNRSQNSNHLSPAVARKIVEYVAGQSELEATLYTTRHRIATTTEPVKDKAGYSYAQLVKALGREFR
SIO_010081: HSW_RS22235
subclass of: SO_0000673
so part of: HSW_RS22235
location: join(6732..6969,1..752)
location: region:1-6969:1
so has part: feature:6732-6969:1:exon
so has part: feature:1-752:1:exon

WP_155833132.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6732-6969:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-752:1:exon

HSW_RS22240
type: Gene
subclass of: SO_0000704
RO_0002162: 1227739
locus tag: HSW_RS22240
so part of: sequence
location: 1056..1958
location: region:1056-1958:1
so has part: feature:1056-1958:1:exon
subclass of: SO_0000010

position:1056:1
position: 1056
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1958:1
position: 1958
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1056-1958:1:exon

HSW_RS22240
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1227739
locus tag: HSW_RS22240
EC number: 2.1.1.72
inference: COORDINATES: protein motif:HMM:TIGR00571.1
GO function: GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO process: GO:0006306 - DNA methylation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Dam family site-specific DNA-(adenine-N6)-methyltransferase
translation: MKLPHPIPYQGSKRNLASQILRYFPANCDRLIEPFAGSAAITVAAAHYFKANRFLINDINTPLTRLWENIINAPASVVKHYHDIWHGQIGKEEPYYYEIRNRFNDTQNPEYLLFLLAKCVKAAVRYNAQGQFNQSPDKRRLGKNPKTMREDILRVSQLLTGRTQVMSTDYQAVLALAAADDLVYMDPPYQGTGKNGGFNYAGNIEFDNFVVSLFDLNNRDIPYILSYDGRTGEKTYGSALPDELNLVKIEINAGRSSQATLLSRDEITFEAVFLSPALVAKIDLGAINTALVGQTELFIE
SIO_010081: HSW_RS22240
subclass of: SO_0000673
so part of: HSW_RS22240
location: 1056..1958
location: region:1056-1958:1
so has part: feature:1056-1958:1:exon

WP_052346878.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1056-1958:1:exon

HSW_RS22245
type: Gene
subclass of: SO_0000704
RO_0002162: 1227739
locus tag: HSW_RS22245
so part of: sequence
location: 1958..2683
location: region:1958-2683:1
so has part: feature:1958-2683:1:exon
subclass of: SO_0000010

position:2683:1
position: 2683
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1958-2683:1:exon

HSW_RS22245
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1227739
locus tag: HSW_RS22245
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002708497.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HNH endonuclease signature motif containing protein
translation: MAENLPTYPKEFLEQVQGITNKRARFVIDFILAHGRVTTEDLADAGYEHAPRAAMDVKDAGIPLMMTRIKSERTGKQVAAYSFGDLSKVQTERVAGRTTFSKKFRSELYQLCGGRCQVCNGKFEERYLQIDHRVPYEVVGELSDRSPEHFMMLCGSCNRAKSWSCEHCKNWLGLKKPELCMTCYWGSPANYNHIALEQVRRLDLQWNGDEVQYYDALKVIADQHGIEVPEFVKQIIASRPT
SIO_010081: HSW_RS22245
subclass of: SO_0000673
so part of: HSW_RS22245
location: 1958..2683
location: region:1958-2683:1
so has part: feature:1958-2683:1:exon

WP_044005579.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1958-2683:1:exon

HSW_RS22250
type: Gene
subclass of: SO_0000704
RO_0002162: 1227739
locus tag: HSW_RS22250
old locus tag: Hsw_PC0004
so part of: sequence
location: complement(2680..3276)
location: region:2680-3276:-1
so has part: feature:2680-3276:-1:exon
subclass of: SO_0000010

position:2680:-1
position: 2680
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3276:-1
position: 3276
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2680-3276:-1:exon

HSW_RS22250
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1227739
locus tag: HSW_RS22250
old locus tag: Hsw_PC0004
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPRRPNFPTTTDETQRLELAFLLRSGLLQPDCSRSTTLTWSSRGEVTGRIGLEAHNHENGRYLRLHYTVNGATSYDYRVELESVPSNLPGNGGQRLYMVCPVSGRRATVLYLRAGTGTFAHRLAYGPDRLYYDSQLEPKRLRGMGKYFAVDREWEKEYRKGRKTHYRGRPTRWYARLLGLEAQADAVAPQLLQLLQRC
SIO_010081: HSW_RS22250
subclass of: SO_0000673
so part of: HSW_RS22250
location: complement(2680..3276)
location: region:2680-3276:-1
so has part: feature:2680-3276:-1:exon

WP_044005573.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2680-3276:-1:exon

HSW_RS22255
type: Gene
subclass of: SO_0000704
RO_0002162: 1227739
locus tag: HSW_RS22255
old locus tag: Hsw_PC0005
so part of: sequence
location: complement(4172..5527)
location: region:4172-5527:-1
so has part: feature:4172-5527:-1:exon
subclass of: SO_0000010

position:4172:-1
position: 4172
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5527:-1
position: 5527
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4172-5527:-1:exon

HSW_RS22255
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1227739
locus tag: HSW_RS22255
old locus tag: Hsw_PC0005
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MATVLASPALASSDGVADKFQRLKVYGQRGQTVILNLSNSSLIVKGSLPTFLQGHNNELLTFTQIGQVVRELAEWVGLAPERLETRRLELSADARLASDVRAFLESLRHHKGSNFSIVLPTKGAARPLEYVSTHVDMWVKFYDQSKYAAQEGYPVTVPNKVRYEVVARRARAVSKLLGKGKAAVTLADLATPATYAAAAAALLRVFGEVERERPLDFNGLTPKEMALLQSGGSREWWKEVQKNVHPNTFKQHRREYDRLRAAHDERTKTDVYGDTIRAAVGASLATSQGGGECTFFHTLSQLETGTHPHTPTTLLLPAAAGEGWEDGRQDGWEARPLAVVQSDDDEGASERAEGSMQARTPSAGGPVDGGSQHAPAPMEVRPAQPGQRYCHTCGLPINTGNPNAKFCSPKERGAQHAKQCKNADSNARLADRRKVEAREARIGGTLPLFAA
SIO_010081: HSW_RS22255
subclass of: SO_0000673
so part of: HSW_RS22255
location: complement(4172..5527)
location: region:4172-5527:-1
so has part: feature:4172-5527:-1:exon

WP_155833131.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4172-5527:-1:exon