LOCUS NC_010724 8689 bp DNA circular CON 22-FEB-2023
DEFINITION Natranaerobius thermophilus JW/NM-WN-LF plasmid pNTHE02, complete
sequence.
ACCESSION NC_010724 NZ_ABKR01000000 NZ_ABKR01000001-NZ_ABKR01000048
VERSION NC_010724.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN02598430
Assembly: GCF_000020005.1
KEYWORDS RefSeq.
SOURCE Natranaerobius thermophilus JW/NM-WN-LF
ORGANISM Natranaerobius thermophilus JW/NM-WN-LF
Bacteria; Bacillota; Clostridia; Natranaerobiales;
Natranaerobiaceae; Natranaerobius.
REFERENCE 1 (bases 1 to 8689)
AUTHORS Zhao,B., Mesbah,N.M., Dalin,E., Goodwin,L., Nolan,M., Pitluck,S.,
Chertkov,O., Brettin,T.S., Han,J., Larimer,F.W., Land,M.L.,
Hauser,L., Kyrpides,N. and Wiegel,J.
TITLE Complete genome sequence of the anaerobic, halophilic
alkalithermophile Natranaerobius thermophilus JW/NM-WN-LF
JOURNAL J Bacteriol 193 (15), 4023-4024 (2011)
PUBMED 21642468
REFERENCE 2 (bases 1 to 8689)
AUTHORS Copeland,A., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E.,
Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Chertkov,O., Brettin,T.,
Detter,J.C., Han,C., Kuske,C.R., Schmutz,J., Larimer,F., Land,M.,
Hauser,L., Kyrpides,N., Lykidis,A., Mesbah,N.M. and Wiegel,J.
CONSRTM US DOE Joint Genome Institute
TITLE Complete sequence of plasmid2 of Natranaerobius thermophilus
JW/NM-WN-LF
JOURNAL Unpublished
REFERENCE 3 (bases 1 to 8689)
AUTHORS Copeland,A., Lucas,S., Lapidus,A., Glavina del Rio,T., Dalin,E.,
Tice,H., Bruce,D., Goodwin,L., Pitluck,S., Chertkov,O., Brettin,T.,
Detter,J.C., Han,C., Kuske,C.R., Schmutz,J., Larimer,F., Land,M.,
Hauser,L., Kyrpides,N., Lykidis,A., Mesbah,N.M. and Wiegel,J.
CONSRTM US DOE Joint Genome Institute
TITLE Direct Submission
JOURNAL Submitted (04-APR-2008) US DOE Joint Genome Institute, 2800
Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
CP001036.1.
URL -- http://www.jgi.doe.gov
JGI Project ID: 4044106
Source DNA and bacteria available from Juergen Wiegel
(jwiegel@uga.edu)
Contacts: Juergen Wiegel (jwiegel@uga.edu)
David Bruce (microbes@cuba.jgi-psf.org)
Quality assurance done by JGI-Stanford
Annotation done by JGI-ORNL and JGI-PGF
Finishing done by JGI-LANL
Finished microbial genomes have been curated to close all gaps with
greater than 98% coverage of at least two independent clones. Each
base pair has a minimum q (quality) value of 30 and the total error
rate is less than one per 50000.
The JGI and collaborators endorse the principles for the
distribution and use of large scale sequencing data adopted by the
larger genome sequencing community and urge users of this data to
follow them. it is our intention to publish the work of this
project in a timely fashion and we welcome collaborative
interaction on the project and analysis.
(http://www.genome.gov/page.cfm?pageID=10506376).
The annotation was added by the NCBI Prokaryotic Genome Annotation
Pipeline (PGAP). Information about PGAP can be found here:
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Date :: 02/22/2023 13:41:11
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.4
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 3,021
CDSs (total) :: 2,954
Genes (coding) :: 2,933
CDSs (with protein) :: 2,933
Genes (RNA) :: 67
rRNAs :: 4, 4, 4 (5S, 16S, 23S)
complete rRNAs :: 4, 4, 4 (5S, 16S, 23S)
tRNAs :: 51
ncRNAs :: 4
Pseudo Genes (total) :: 21
CDSs (without protein) :: 21
Pseudo Genes (ambiguous residues) :: 0 of 21
Pseudo Genes (frameshifted) :: 3 of 21
Pseudo Genes (incomplete) :: 16 of 21
Pseudo Genes (internal stop) :: 4 of 21
Pseudo Genes (multiple problems) :: 2 of 21
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..8689
/organism="Natranaerobius thermophilus JW/NM-WN-LF"
/mol_type="genomic DNA"
/strain="JW/NM-WN-LF"
/type_material="type strain of Natranaerobius
thermophilus"
/db_xref="taxon:457570"
/plasmid="pNTHE02"
/note="type strain of Natranaerobius thermophilus"
gene 126..1094
/locus_tag="NTHER_RS14910"
/old_locus_tag="Nther_2951"
CDS 126..1094
/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"
/protein_id="WP_012451952.1"
/translation="MSKKGSLKKQIVSRLEQMKAWDPKTGYSESRHEWKKAYNEKFKA
NDPRGSKLNIPEKIFSSNSFQAAMQDSMRFHDFLKEKGIKSIDKIKVAHATEYLNRRI
KEGKRPTTVSRERNSLAKLLGLKNCAEIPAKIPQNTRDNIYKSRPDEIGNKSTLNPTE
GKYKEVVEFARGTGLRRSEVERVKPENFYRDNGQLKMHLRGKPENTKGARPRTVTVRK
DYESYVEAKINETRENGYSRIISTLTENGQISGSLDVHGYGRRDFAWNRYITLSRPLN
QIPKEDRYWTRGFNNLCFDKKALREVVRDLGHGEGQLGKVVSNYLL"
gene 1110..1700
/locus_tag="NTHER_RS14915"
/old_locus_tag="Nther_2952"
CDS 1110..1700
/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"
/protein_id="WP_012451953.1"
/translation="MEYLAIKKGLGGKKIQETDKSQSDGVFMTWREYQELISNYKEEL
NKIKNQKDQENKKAKKDAEYRISEIKYKYKIESEKKDQQIRSLQNAVGRWKAKYNGEG
NAGQEKNIPKYSIFRVDKNNGEIRITYQIDTLPGDDPISEYQDAVDIGSSIIQDQDFE
FTGVSWTESAGWTARFEISEEKYLEKLKCKGICFVP"
gene <1672..2358
/locus_tag="NTHER_RS14920"
/old_locus_tag="Nther_2953"
/pseudo
CDS <1672..2358
/locus_tag="NTHER_RS14920"
/old_locus_tag="Nther_2953"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012451958.1"
/GO_function="GO:0003676 - nucleic acid binding [Evidence
IEA]"
/GO_function="GO:0004519 - endonuclease activity [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
/codon_start=1
/transl_table=11
/product="HNH endonuclease"
gene 2591..3034
/locus_tag="NTHER_RS14925"
/old_locus_tag="Nther_2954"
CDS 2591..3034
/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"
/protein_id="WP_012451955.1"
/translation="MDTGRYEDKEEITVKEAAEALGVSRDTVMRRIRRGEMKAVKREG
SYGDQWFIPASELQIYDMQEVVTVQKSMSPEQVQNIMQKAIRENIENMKEELREEVRE
DMKEEMESLKQTIEDRDQKLVENLRNRLDQPNNKSLIEKIKDMFK"
gene 3199..3762
/locus_tag="NTHER_RS14930"
/old_locus_tag="Nther_2955"
CDS 3199..3762
/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"
/protein_id="WP_012451956.1"
/translation="MNHVSPIKDLKKIDHIKRILKQKNKRDYCLFVLGINTGLRISDL
LELKVSDLVDENGKPKKNLELKEKKTGKNKQMILNEKARSAIREYVQDSKLSLNDSIF
KSQKGGPISREHAYRVINEAAKAVGIKERVGTHTLRKTFGYHAYINGVDISLIQNIFN
HSAPSVTLRYIGIEQEDIDDVYININL"
gene 3783..3941
/locus_tag="NTHER_RS16020"
/old_locus_tag="Nther_2956"
CDS 3783..3941
/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"
/protein_id="WP_012451957.1"
/translation="MSNLKEIIEELEEEKAKKVELMNQLEESKTKKFHEGEYNGLAVA
IKKLEKSL"
gene 4272..5498
/gene="iscB"
/locus_tag="NTHER_RS14935"
/old_locus_tag="Nther_2957"
CDS 4272..5498
/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"
/protein_id="WP_012451958.1"
/translation="MVYVLAKNGKPLMPTKKHGKVRHLLKDGKAKIVKRTPFTIQLLY
ESDNYTQPVNLGVDAGTKHVGLSATTGNEVLFEGEAQLRTNIQELLSTRREARRARRN
RKTRYRKPRFNNRKKPNGWLAPSIQNKVDTHLKLVDMVCSILPVSNIKVEVAQFDIHK
IKNPEIEGEQYQQGEQLGFWNVREYVLYRDNHTCQYCRGKSKDSILNVHHIRSRQSHG
DRPGNLVTLCETCHTKLHKESLENYFHPKDKGFKDESQFTILRWFIYNGIKEKYPDVN
LTFGYITKNTRIKNNLPKSHAVDARCISGNPLAKPPVNTLYIKQVRKNNRQLHKFNPS
KGGIRKANKAPYLVKGFRLFDKVLYNNRKCFIFGRRKSGYFDLRLLDGTKIHASASHK
RLDLIESATSMLKEVS"
gene 5833..7119
/locus_tag="NTHER_RS14940"
/old_locus_tag="Nther_2958"
CDS 5833..7119
/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"
/protein_id="WP_012451959.1"
/translation="MSSLSPSRQRQHQKLQSHGQAQNFLNLIHESGEDYFFLATKKQD
EWEQQNALQSPSEVHVLDDRDYYYSPNSFFVPKRHQNTVGKFKCLFIDLDTYKLNDYS
PEENYCNIHFEIFYEGKLPLPNLRVFSGRGVQLIYLIHESPIQAKNRWNACQDIIYQI
FKPFGADPKTLGSQSILRLPGTFNQKNGRLTYYELIHGSKYCMKSFLKQYSPKVKRIG
STKKSKKQKKTNKSKSNKSKFKKLMNIKTLNYGILKDLEKLAKLRNYDLHGYREMILF
LYRLHSLKNDRSPEEALEDTLAFNQTFKEPLPERMVIRDTRSAERYTDKYNFTAEWII
KQLEIDEEELKHLEVVIGTEEKNRRKKEVNREKRRDASGLTEKEKAKAKHLERLKKAL
RLNPAAKKTELAKELGVSREQVHRLLKDLEDDNCVK"
gene 7109..7669
/locus_tag="NTHER_RS14945"
/old_locus_tag="Nther_2959"
CDS 7109..7669
/locus_tag="NTHER_RS14945"
/old_locus_tag="Nther_2959"
/EC_number="3.1.-.-"
/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"
/protein_id="WP_012451960.1"
/translation="MLNKRLRQALDHLGKTIQNYFNAKKRDNLIKWINTWAGYLKIDD
ENPTRIKYKAGDIITVELGFNVGRELGGRHPAVVIEDNPKSSKTVMVVPLSSLKKEKN
ISDIHPNNIYLGELKRFNEITGKEPGTESIAVINQMRTISKLRIIKPKSGSDPRVLLE
PEELRKIYEKIKEKYTSKGLNRKLDN"
CONTIG join(CP001036.1:1..8689)
//
