Natranaerobius thermophilus JW/NM-WN-LF plasmid pNTHE02, complete sequence.
type: Entry
definition: Natranaerobius thermophilus JW/NM-WN-LF plasmid pNTHE02, complete sequence.
sequence version: NC_010724.1
sequence date: 2023-02-22
sequence: sequence
division: CON
label: NC_010724.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02598430
keyword: RefSeq
source: Natranaerobius thermophilus JW/NM-WN-LF
organism: Natranaerobius thermophilus JW/NM-WN-LF
taxonomy: Bacteria; Bacillota; Clostridia; Natranaerobiales; Natranaerobiaceae; Natranaerobius.
reference: 1
references: 21642468
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001036.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4044106\nSource DNA and bacteria available from Juergen Wiegel\n(jwiegel@uga.edu)\nContacts: Juergen Wiegel (jwiegel@uga.edu)\n David Bruce (microbes@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 13:41:11\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) :: 3,021\nCDSs (total) :: 2,954\nGenes (coding) :: 2,933\nCDSs (with protein) :: 2,933\nGenes (RNA) :: 67\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 51\nncRNAs :: 4\nPseudo Genes (total) :: 21\nCDSs (without protein) :: 21\nPseudo Genes (ambiguous residues) :: 0 of 21\nPseudo Genes (frameshifted) :: 3 of 21\nPseudo Genes (incomplete) :: 16 of 21\nPseudo Genes (inter…

sequence
subclass of: SO_0000155
sequence length: 8689
topology: circular
so has quality: SO_0000988
location: 1..8689
location: region:1-8689:1
RO_0002162: 457570

NC_010724
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02598430
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of the anaerobic, halophilic alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF
author: Zhao, B.
author: Mesbah, N.M.
author: Dalin, E.
author: Goodwin, L.
author: Nolan, M.
author: Pitluck, S.
author: Chertkov, O.
author: Brettin, T.S.
author: Han, J.
author: Larimer, F.W.
author: Land, M.L.
author: Hauser, L.
author: Kyrpides, N.
author: Wiegel, J.
journal: J Bacteriol
volume: 193
issue: 15
pages: 4023-4024
year: 2011
pubmed: 21642468

21642468
type: PubMed
SIO_000068: pubmed

2
title: Complete sequence of plasmid2 of Natranaerobius thermophilus JW/NM-WN-LF
author: Copeland, A.
author: Lucas, S.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Chertkov, O.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Kuske, C.R.
author: Schmutz, J.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Lykidis, A.
author: Mesbah, N.M.
author: Wiegel, J.
journal: Unpublished

3
title: Direct Submission
author: Copeland, A.
author: Lucas, S.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Chertkov, O.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Kuske, C.R.
author: Schmutz, J.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Lykidis, A.
author: Mesbah, N.M.
author: Wiegel, J.
journal: Submitted (04-APR-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA

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

position:8689:1
position: 8689
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8689:1:source
so part of: sequence
organism: Natranaerobius thermophilus JW/NM-WN-LF
mol type: genomic DNA
strain: JW/NM-WN-LF
type material: type strain of Natranaerobius thermophilus
plasmid: pNTHE02
note: type strain of Natranaerobius thermophilus

457570
type: Taxonomy
SIO_000068: taxonomy

NTHER_RS14910
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14910
old locus tag: Nther_2951
so part of: sequence
location: 126..1094
location: region:126-1094:1
so has part: feature:126-1094:1:exon
subclass of: SO_0000010

position:126:1
position: 126
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1094:1
position: 1094
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:126-1094:1:exon

NTHER_RS14910
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14910
old locus tag: Nther_2951
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: site-specific integrase
translation: MSKKGSLKKQIVSRLEQMKAWDPKTGYSESRHEWKKAYNEKFKANDPRGSKLNIPEKIFSSNSFQAAMQDSMRFHDFLKEKGIKSIDKIKVAHATEYLNRRIKEGKRPTTVSRERNSLAKLLGLKNCAEIPAKIPQNTRDNIYKSRPDEIGNKSTLNPTEGKYKEVVEFARGTGLRRSEVERVKPENFYRDNGQLKMHLRGKPENTKGARPRTVTVRKDYESYVEAKINETRENGYSRIISTLTENGQISGSLDVHGYGRRDFAWNRYITLSRPLNQIPKEDRYWTRGFNNLCFDKKALREVVRDLGHGEGQLGKVVSNYLL
SIO_010081: NTHER_RS14910
subclass of: SO_0000673
so part of: NTHER_RS14910
location: 126..1094
location: region:126-1094:1
so has part: feature:126-1094:1:exon

WP_012451952.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:126-1094:1:exon

NTHER_RS14915
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14915
old locus tag: Nther_2952
so part of: sequence
location: 1110..1700
location: region:1110-1700:1
so has part: feature:1110-1700:1:exon
subclass of: SO_0000010

position:1110:1
position: 1110
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1700:1
position: 1700
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1110-1700:1:exon

NTHER_RS14915
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14915
old locus tag: Nther_2952
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: MEYLAIKKGLGGKKIQETDKSQSDGVFMTWREYQELISNYKEELNKIKNQKDQENKKAKKDAEYRISEIKYKYKIESEKKDQQIRSLQNAVGRWKAKYNGEGNAGQEKNIPKYSIFRVDKNNGEIRITYQIDTLPGDDPISEYQDAVDIGSSIIQDQDFEFTGVSWTESAGWTARFEISEEKYLEKLKCKGICFVP
SIO_010081: NTHER_RS14915
subclass of: SO_0000673
so part of: NTHER_RS14915
location: 1110..1700
location: region:1110-1700:1
so has part: feature:1110-1700:1:exon

WP_012451953.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1110-1700:1:exon

NTHER_RS14920
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14920
old locus tag: Nther_2953
pseudo: true
so part of: sequence
location: <1672..2358
location: region:1672-2358:1
so has part: feature:1672-2358:1:exon
subclass of: SO_0000010

position:1672:1
position: 1672
reference: sequence
type: ForwardStrandPosition
type: FuzzyPosition

position:2358:1
position: 2358
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1672-2358:1:exon

NTHER_RS14920
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14920
old locus tag: Nther_2953
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012451958.1
GO function: GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
note: incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: HNH endonuclease
SIO_010081: NTHER_RS14920
subclass of: SO_0000673
so part of: NTHER_RS14920
location: <1672..2358
location: region:1672-2358:1
so has part: feature:1672-2358:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1672-2358:1:exon

NTHER_RS14925
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14925
old locus tag: Nther_2954
so part of: sequence
location: 2591..3034
location: region:2591-3034:1
so has part: feature:2591-3034:1:exon
subclass of: SO_0000010

position:2591:1
position: 2591
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3034:1
position: 3034
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2591-3034:1:exon

NTHER_RS14925
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14925
old locus tag: Nther_2954
inference: COORDINATES: protein motif:HMM:TIGR01764.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: helix-turn-helix domain-containing protein
translation: MDTGRYEDKEEITVKEAAEALGVSRDTVMRRIRRGEMKAVKREGSYGDQWFIPASELQIYDMQEVVTVQKSMSPEQVQNIMQKAIRENIENMKEELREEVREDMKEEMESLKQTIEDRDQKLVENLRNRLDQPNNKSLIEKIKDMFK
SIO_010081: NTHER_RS14925
subclass of: SO_0000673
so part of: NTHER_RS14925
location: 2591..3034
location: region:2591-3034:1
so has part: feature:2591-3034:1:exon

WP_012451955.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2591-3034:1:exon

NTHER_RS14930
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14930
old locus tag: Nther_2955
so part of: sequence
location: 3199..3762
location: region:3199-3762:1
so has part: feature:3199-3762:1:exon
subclass of: SO_0000010

position:3199:1
position: 3199
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3762:1
position: 3762
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3199-3762:1:exon

NTHER_RS14930
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14930
old locus tag: Nther_2955
inference: COORDINATES: similar to AA sequence:RefSeq:WP_018704813.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: site-specific integrase
translation: MNHVSPIKDLKKIDHIKRILKQKNKRDYCLFVLGINTGLRISDLLELKVSDLVDENGKPKKNLELKEKKTGKNKQMILNEKARSAIREYVQDSKLSLNDSIFKSQKGGPISREHAYRVINEAAKAVGIKERVGTHTLRKTFGYHAYINGVDISLIQNIFNHSAPSVTLRYIGIEQEDIDDVYININL
SIO_010081: NTHER_RS14930
subclass of: SO_0000673
so part of: NTHER_RS14930
location: 3199..3762
location: region:3199-3762:1
so has part: feature:3199-3762:1:exon

WP_012451956.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3199-3762:1:exon

NTHER_RS16020
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS16020
old locus tag: Nther_2956
so part of: sequence
location: 3783..3941
location: region:3783-3941:1
so has part: feature:3783-3941:1:exon
subclass of: SO_0000010

position:3783:1
position: 3783
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3941:1
position: 3941
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3783-3941:1:exon

NTHER_RS16020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS16020
old locus tag: Nther_2956
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: MSNLKEIIEELEEEKAKKVELMNQLEESKTKKFHEGEYNGLAVAIKKLEKSL
SIO_010081: NTHER_RS16020
subclass of: SO_0000673
so part of: NTHER_RS16020
location: 3783..3941
location: region:3783-3941:1
so has part: feature:3783-3941:1:exon

WP_012451957.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3783-3941:1:exon

NTHER_RS14935
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
gene: iscB
locus tag: NTHER_RS14935
old locus tag: Nther_2957
so part of: sequence
location: 4272..5498
location: region:4272-5498:1
so has part: feature:4272-5498:1:exon
subclass of: SO_0000010

position:4272:1
position: 4272
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5498:1
position: 5498
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4272-5498:1:exon

NTHER_RS14935
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
gene: iscB
locus tag: NTHER_RS14935
old locus tag: Nther_2957
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013173732.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: RNA-guided endonuclease IscB
translation: MVYVLAKNGKPLMPTKKHGKVRHLLKDGKAKIVKRTPFTIQLLYESDNYTQPVNLGVDAGTKHVGLSATTGNEVLFEGEAQLRTNIQELLSTRREARRARRNRKTRYRKPRFNNRKKPNGWLAPSIQNKVDTHLKLVDMVCSILPVSNIKVEVAQFDIHKIKNPEIEGEQYQQGEQLGFWNVREYVLYRDNHTCQYCRGKSKDSILNVHHIRSRQSHGDRPGNLVTLCETCHTKLHKESLENYFHPKDKGFKDESQFTILRWFIYNGIKEKYPDVNLTFGYITKNTRIKNNLPKSHAVDARCISGNPLAKPPVNTLYIKQVRKNNRQLHKFNPSKGGIRKANKAPYLVKGFRLFDKVLYNNRKCFIFGRRKSGYFDLRLLDGTKIHASASHKRLDLIESATSMLKEVS
SIO_010081: NTHER_RS14935
subclass of: SO_0000673
so part of: NTHER_RS14935
location: 4272..5498
location: region:4272-5498:1
so has part: feature:4272-5498:1:exon

WP_012451958.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4272-5498:1:exon

NTHER_RS14940
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14940
old locus tag: Nther_2958
so part of: sequence
location: 5833..7119
location: region:5833-7119:1
so has part: feature:5833-7119:1:exon
subclass of: SO_0000010

position:5833:1
position: 5833
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7119:1
position: 7119
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5833-7119:1:exon

NTHER_RS14940
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14940
old locus tag: Nther_2958
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 protein
translation: MSSLSPSRQRQHQKLQSHGQAQNFLNLIHESGEDYFFLATKKQDEWEQQNALQSPSEVHVLDDRDYYYSPNSFFVPKRHQNTVGKFKCLFIDLDTYKLNDYSPEENYCNIHFEIFYEGKLPLPNLRVFSGRGVQLIYLIHESPIQAKNRWNACQDIIYQIFKPFGADPKTLGSQSILRLPGTFNQKNGRLTYYELIHGSKYCMKSFLKQYSPKVKRIGSTKKSKKQKKTNKSKSNKSKFKKLMNIKTLNYGILKDLEKLAKLRNYDLHGYREMILFLYRLHSLKNDRSPEEALEDTLAFNQTFKEPLPERMVIRDTRSAERYTDKYNFTAEWIIKQLEIDEEELKHLEVVIGTEEKNRRKKEVNREKRRDASGLTEKEKAKAKHLERLKKALRLNPAAKKTELAKELGVSREQVHRLLKDLEDDNCVK
SIO_010081: NTHER_RS14940
subclass of: SO_0000673
so part of: NTHER_RS14940
location: 5833..7119
location: region:5833-7119:1
so has part: feature:5833-7119:1:exon

WP_012451959.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5833-7119:1:exon

NTHER_RS14945
type: Gene
subclass of: SO_0000704
RO_0002162: 457570
locus tag: NTHER_RS14945
old locus tag: Nther_2959
so part of: sequence
location: 7109..7669
location: region:7109-7669:1
so has part: feature:7109-7669:1:exon
subclass of: SO_0000010

position:7109:1
position: 7109
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7669:1
position: 7669
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7109-7669:1:exon

NTHER_RS14945
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 457570
locus tag: NTHER_RS14945
old locus tag: Nther_2959
inference: COORDINATES: protein motif:HMM:NF014505.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: type II toxin-antitoxin system PemK/MazF family toxin
translation: MLNKRLRQALDHLGKTIQNYFNAKKRDNLIKWINTWAGYLKIDDENPTRIKYKAGDIITVELGFNVGRELGGRHPAVVIEDNPKSSKTVMVVPLSSLKKEKNISDIHPNNIYLGELKRFNEITGKEPGTESIAVINQMRTISKLRIIKPKSGSDPRVLLEPEELRKIYEKIKEKYTSKGLNRKLDN
SIO_010081: NTHER_RS14945
subclass of: SO_0000673
so part of: NTHER_RS14945
location: 7109..7669
location: region:7109-7669:1
so has part: feature:7109-7669:1:exon

WP_012451960.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7109-7669:1:exon