Caldicellulosiruptor bescii DSM 6725 plasmid pATHE02, complete sequence.
type: Entry
definition: Caldicellulosiruptor bescii DSM 6725 plasmid pATHE02, complete sequence.
sequence version: NC_012037.1
sequence date: 2022-12-29
sequence: sequence
division: CON
label: NC_012037.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02598462
keyword: RefSeq
source: Caldicellulosiruptor bescii DSM 6725
organism: Caldicellulosiruptor bescii DSM 6725
taxonomy: Bacteria; Bacillota; Clostridia; Thermoanaerobacterales; Thermoanaerobacterales Family III. Incertae Sedis; Caldicellulosiruptor.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001395.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4084710\nSource DNA available from Michael Adams (adams@bmb.uga.edu)\nBacteria available from DSMZ: DSM 6725\nContacts: Michael Adams (adams@bmb.uga.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\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)\nMeta information:\n Organism display name: Caldicelulosiruptor becscii Z-1320, DSM\n6725\n Culture Collection IDs: DSM 6725\n GOLD ID: Gi03121 http://genomesonline.org/GOLD_CARDS/Gi03121.html\n Sequencing Platforms: Sanger, 454\n Phenotypes: Thermoacidophile, Cellulose degrader\n Diseases: None\n Habitat: Fresh water, Hot spring\n Oxygen Requirement: Anaerobe\n Temperature Range: Thermophile\n Biotic Relationship: Free living\n Isolation: Hot spring on the Kamchatka peninsula in Russia.\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 :: 12/29/2022 00:48:36\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.…

sequence
subclass of: SO_0000155
sequence length: 3653
topology: circular
so has quality: SO_0000988
location: 1..3653
location: region:1-3653:1
RO_0002162: 521460

NC_012037
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02598462
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid2 of Caldicelulosiruptor becscii DSM 6725
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Sims, D.
author: Meincke, L.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ovchinnikova, G.
author: Kataeva, I.
author: Adams, M.W.W.
journal: Unpublished

2
title: Direct Submission
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Sims, D.
author: Meincke, L.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Kyrpides, N.
author: Ovchinnikova, G.
author: Kataeva, I.
author: Adams, M.W.W.
journal: Submitted (26-JAN-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA

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

position:3653:1
position: 3653
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-3653:1:source
so part of: sequence
organism: Caldicellulosiruptor bescii DSM 6725
mol type: genomic DNA
strain: DSM 6725
type material: type strain of Caldicellulosiruptor bescii
plasmid: pATHE02
note: type strain of Caldicelulosiruptor becscii DSM 6725

521460
type: Taxonomy
SIO_000068: taxonomy

ATHE_RS14025
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14025
so part of: sequence
location: complement(91..282)
location: region:91-282:-1
so has part: feature:91-282:-1:exon
subclass of: SO_0000010

31774126
type: Gene
SIO_000068: ncbigene

position:91:-1
position: 91
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:282:-1
position: 282
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:91-282:-1:exon

ATHE_RS14025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14025
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: MVKSLEKPLEIPVHSLEKGKKSLGISIRFLEIGKWKNLHDFPRTFLGFVVQSGMNNYASGYEY
SIO_010081: ATHE_RS14025
subclass of: SO_0000673
so part of: ATHE_RS14025
location: complement(91..282)
location: region:91-282:-1
so has part: feature:91-282:-1:exon

WP_099716404.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:91-282:-1:exon

ATHE_RS14030
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14030
old locus tag: Athe_2777
so part of: sequence
location: 1125..2117
location: region:1125-2117:1
so has part: feature:1125-2117:1:exon
subclass of: SO_0000010

31774127
type: Gene
SIO_000068: ncbigene

position:1125:1
position: 1125
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2117:1
position: 2117
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1125-2117:1:exon

ATHE_RS14030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14030
old locus tag: Athe_2777
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: MGKPSIIKQVLNEFEKQIRFGESKHEAKREERERCEVTGETWNPARVEGIFSFSTYREYVKEALEFANWARTEKGCKDLEQARAYVSEYLQSHIDKGYSAWTVKKEAAALAKLYHCRTTDFKVELPARHREEIERSRGYKDHDREFSKERNRDIIIFSKATGLRRRELERVSSRDIFRGPDGRLYVHVSNGKGGRERDVHVLQKYEREVERIVREREGRDRLFDRVPIRMDVHSYRREYARERYREVEREISRERKLFDRVEDLVRSRLTRLYPDRFREIGERQLTRELTRADGLYHRSDGREFDRLALWEVSNDLGHNRIDVVARHYLD
SIO_010081: ATHE_RS14030
subclass of: SO_0000673
so part of: ATHE_RS14030
location: 1125..2117
location: region:1125-2117:1
so has part: feature:1125-2117:1:exon

WP_012660751.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1125-2117:1:exon

ATHE_RS14035
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14035
old locus tag: Athe_2778
so part of: sequence
location: complement(2218..2439)
location: region:2218-2439:-1
so has part: feature:2218-2439:-1:exon
subclass of: SO_0000010

31774128
type: Gene
SIO_000068: ncbigene

position:2218:-1
position: 2218
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2439:-1
position: 2439
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2218-2439:-1:exon

ATHE_RS14035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14035
old locus tag: Athe_2778
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: MKKLTIEFTREEAMYLLGYFTARAMEGYRFDEFEQGIIKKLADKCNVEFVFENGKILQARYKGNLFYCTTPQE
SIO_010081: ATHE_RS14035
subclass of: SO_0000673
so part of: ATHE_RS14035
location: complement(2218..2439)
location: region:2218-2439:-1
so has part: feature:2218-2439:-1:exon

WP_012660752.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2218-2439:-1:exon

ATHE_RS14040
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14040
old locus tag: Athe_2779
so part of: sequence
location: complement(2420..2749)
location: region:2420-2749:-1
so has part: feature:2420-2749:-1:exon
subclass of: SO_0000010

31774129
type: Gene
SIO_000068: ncbigene

position:2420:-1
position: 2420
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2749:-1
position: 2749
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2420-2749:-1:exon

ATHE_RS14040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14040
old locus tag: Athe_2779
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: MLTKQELIQRLLEIKQLCFYIEEDEAKQIENIVEDLLSKIRNVKLNQLKRLVHAERKKYPIGTAENLLFHNLYEKLKNVQPDDTERIDRLYKEYLSLVKGVKESEKANN
SIO_010081: ATHE_RS14040
subclass of: SO_0000673
so part of: ATHE_RS14040
location: complement(2420..2749)
location: region:2420-2749:-1
so has part: feature:2420-2749:-1:exon

WP_012660753.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2420-2749:-1:exon

ATHE_RS14045
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14045
old locus tag: Athe_2780
so part of: sequence
location: complement(2743..3192)
location: region:2743-3192:-1
so has part: feature:2743-3192:-1:exon
subclass of: SO_0000010

31774130
type: Gene
SIO_000068: ncbigene

position:2743:-1
position: 2743
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3192:-1
position: 3192
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2743-3192:-1:exon

ATHE_RS14045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14045
old locus tag: Athe_2780
inference: COORDINATES: protein motif:HMM:NF017542.2
GO process: GO:0006260 - DNA replication [Evidence IEA]; GO:0006276 - plasmid maintenance [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication/maintenance protein RepL
translation: MKKIGYKKMVDPETGEVQTFILIGHDFEDTDFVKLPFISIKLIMEDKDLAKSAMRILSYIVQHKISFNNYTFALSYEYDIKGNIDMSKKQYHLAIKKLIEKDLLIKIGRGRFMLNPRRIRYGRADQLRKFESEYDKIKKTEKGKGDKEC
SIO_010081: ATHE_RS14045
subclass of: SO_0000673
so part of: ATHE_RS14045
location: complement(2743..3192)
location: region:2743-3192:-1
so has part: feature:2743-3192:-1:exon

WP_012660754.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2743-3192:-1:exon