Caldicellulosiruptor bescii DSM 6725 plasmid pATHE01, complete sequence.
type: Entry
definition: Caldicellulosiruptor bescii DSM 6725 plasmid pATHE01, complete sequence.
sequence version: NC_012036.1
sequence date: 2022-12-29
sequence: sequence
division: CON
label: NC_012036.1
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\nCP001394.1.\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: 8291
topology: circular
so has quality: SO_0000988
location: 1..8291
location: region:1-8291:1
RO_0002162: 521460

NC_012036
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02598462
type: BioSample
SIO_000068: biosample

1
title: Complete sequence of plasmid1 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:8291:1
position: 8291
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8291:1: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: pATHE01
note: type strain of Caldicelulosiruptor becscii DSM 6725

521460
type: Taxonomy
SIO_000068: taxonomy

ATHE_RS14730
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14730
old locus tag: Athe_2769
so part of: sequence
location: complement(206..370)
location: region:206-370:-1
so has part: feature:206-370:-1:exon
subclass of: SO_0000010

43367485
type: Gene
SIO_000068: ncbigene

position:206:-1
position: 206
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:370:-1
position: 370
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:206-370:-1:exon

ATHE_RS14730
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14730
old locus tag: Athe_2769
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: MTQQITIRVPAKELEEWRLKIKELSDRLGMRIALSELVRQGVPKAIEELESRIK
SIO_010081: ATHE_RS14730
subclass of: SO_0000673
so part of: ATHE_RS14730
location: complement(206..370)
location: region:206-370:-1
so has part: feature:206-370:-1:exon

WP_012660743.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:206-370:-1:exon

ATHE_RS14445
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14445
old locus tag: Athe_2770
so part of: sequence
location: complement(446..616)
location: region:446-616:-1
so has part: feature:446-616:-1:exon
subclass of: SO_0000010

31774206
type: Gene
SIO_000068: ncbigene

position:446:-1
position: 446
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:616:-1
position: 616
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:446-616:-1:exon

ATHE_RS14445
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14445
old locus tag: Athe_2770
inference: COORDINATES: similar to AA sequence:RefSeq:WP_014254031.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MDNLPRVEIPKDKEKIKQLIAALEQQLQKDTNEKDKEIHRKALEDLKASLNKKDHL
SIO_010081: ATHE_RS14445
subclass of: SO_0000673
so part of: ATHE_RS14445
location: complement(446..616)
location: region:446-616:-1
so has part: feature:446-616:-1:exon

WP_012660744.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:446-616:-1:exon

ATHE_RS13995
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS13995
old locus tag: Athe_2771
so part of: sequence
location: complement(609..767)
location: region:609-767:-1
so has part: feature:609-767:-1:exon
subclass of: SO_0000010

31774121
type: Gene
SIO_000068: ncbigene

position:609:-1
position: 609
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:767:-1
position: 767
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:609-767:-1:exon

ATHE_RS13995
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS13995
old locus tag: Athe_2771
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013429069.1
GO process: GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ribbon-helix-helix protein, CopG family
translation: MKMRTVNLRLPEDIFNEIGEIAKKKGLTKSSLIRVIVVEYLEKQKKEGGKNG
SIO_010081: ATHE_RS13995
subclass of: SO_0000673
so part of: ATHE_RS13995
location: complement(609..767)
location: region:609-767:-1
so has part: feature:609-767:-1:exon

WP_012660745.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:609-767:-1:exon

ATHE_RS14000
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14000
old locus tag: Athe_2772
so part of: sequence
location: complement(1222..1629)
location: region:1222-1629:-1
so has part: feature:1222-1629:-1:exon
subclass of: SO_0000010

31774122
type: Gene
SIO_000068: ncbigene

position:1222:-1
position: 1222
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1629:-1
position: 1629
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1222-1629:-1:exon

ATHE_RS14000
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14000
old locus tag: Athe_2772
inference: COORDINATES: protein motif:HMM:NF019884.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: HTH domain-containing protein
translation: MKNIQQLCDELGISRTTVYKYIRRLGIEVKKEGNIAFINDDDIEKIKEALSTASTNSLHTDYKLEYIQSLQQQIETLQKQVDFLKEQLRAKDEQIAKLIQTNQNFQVLLKEKEEQIYQLEGQKQKGSFLKKLFGR
SIO_010081: ATHE_RS14000
subclass of: SO_0000673
so part of: ATHE_RS14000
location: complement(1222..1629)
location: region:1222-1629:-1
so has part: feature:1222-1629:-1:exon

WP_012660746.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1222-1629:-1:exon

ATHE_RS14005
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14005
old locus tag: Athe_2773
so part of: sequence
location: complement(3117..4049)
location: region:3117-4049:-1
so has part: feature:3117-4049:-1:exon
subclass of: SO_0000010

31774123
type: Gene
SIO_000068: ncbigene

position:3117:-1
position: 3117
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4049:-1
position: 4049
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3117-4049:-1:exon

ATHE_RS14005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14005
old locus tag: Athe_2773
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012660747.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO process: GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: sigma-70 family RNA polymerase sigma factor
translation: MQQSEKRQFAKVQSQLLIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKGSFSTYACKVIESKIKRSLPKYELSCAISLDSPVSKEPEEDTSTVADIISDGYSVESEVIRKDTVQKLHRYFAILTEEEKERVLYYISTGKNLPASDNVFKKARRKIIAKMRQEQFEADLDDLTVFISCPAVHIASGSNFGYSPVEATVIDREEKRKQLEVLSAIPQLDKLRVLKQQGEQDRMKLLVAKWEVEEFIERNWDNLTIQNARLLQDYFVYCLSHLSMVQKYGSKYREQIKRVVKKLAL
SIO_010081: ATHE_RS14005
subclass of: SO_0000673
so part of: ATHE_RS14005
location: complement(3117..4049)
location: region:3117-4049:-1
so has part: feature:3117-4049:-1:exon

WP_012660747.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3117-4049:-1:exon

ATHE_RS14010
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14010
old locus tag: Athe_2774
so part of: sequence
location: complement(4080..4658)
location: region:4080-4658:-1
so has part: feature:4080-4658:-1:exon
subclass of: SO_0000010

31774124
type: Gene
SIO_000068: ncbigene

position:4080:-1
position: 4080
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4658:-1
position: 4658
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4080-4658:-1:exon

ATHE_RS14010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14010
old locus tag: Athe_2774
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015907534.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MFTFFDLLSSLKSLSIVEKPKVAGFRCPQNVKCGQYDWESLKREFMLGDFKTLKEFAQAKNISYGFLRNKAKGWTQEKRQLSKTKSQLVVEKTLQKQIEKASDYNTLHVEFWDRLLDLVWQALHDEKTIKTKDGRINIYALEKLALVVERVQKGQRLALGLDEKNSNQPQIEDSIRELIKALHEPDEPSVLN
SIO_010081: ATHE_RS14010
subclass of: SO_0000673
so part of: ATHE_RS14010
location: complement(4080..4658)
location: region:4080-4658:-1
so has part: feature:4080-4658:-1:exon

WP_012660748.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4080-4658:-1:exon

ATHE_RS14020
type: Gene
subclass of: SO_0000704
RO_0002162: 521460
locus tag: ATHE_RS14020
old locus tag: Athe_2776
so part of: sequence
location: complement(6118..8274)
location: region:6118-8274:-1
so has part: feature:6118-8274:-1:exon
subclass of: SO_0000010

31774125
type: Gene
SIO_000068: ncbigene

position:6118:-1
position: 6118
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:8274:-1
position: 8274
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6118-8274:-1:exon

ATHE_RS14020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521460
locus tag: ATHE_RS14020
old locus tag: Athe_2776
inference: COORDINATES: protein motif:HMM:NF024872.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: AAA family ATPase
translation: MRKDIRKYLEFYKGIGLRLTALNGKKPFLADWYYKELSDEELLEYWAQGYNIGGKMGEKSCWMVDIDIDHPAANKIVDLYLPIDTLKFGRATKPLSHLLYFSENCKSLKRDFKFSNQTEKTTIVEIRSTGQQTMIPPSIHPDTKEELRFVGELKEPLKIEADLLTAAVNKIAAATLIGLHWYEGQRQDCALALAGGLLRAGWSEEEAEKFIQAVCLVADDEESKKRIKTVIQTAKKQEENKATTGWRRLAQLIGNEVVAKVIEWLGIKQTKAELLSMAELLSLELPPVEFLLEGLLPNEGLTILAGREKIGKSWLCLELALSLAAGTGFLGRQTKRPYKVLYLALEDSKRRLQQRIKQLGTGISQNCFVLFNIESLQELEKIIIDHNFEVVIVDTMQAFKRAVKLFTNTKLNTYEQDYNISLMLNDIAKRLNCTFIIVHHTKKSGELDFVNEVLGRVTAGADTILHLTRGRTEADGFLKVTGRDVEEQELALRFENGHWSLLGTAKEYAISKERREILEVIKQLGGSATPKQIAEALGKTRSNVNKLLLKLAGDGYVKAVNGIYSLATETEKSIHSIHSIHSIHSIHSIHSVDRVNREVNEGTMENFSVHSVEPLSQLNFSGVSEQSERSERTLLKFEKDKFYIRRLNLKKEEWQEAAEQFKCECGQTLAYAEAFHKFGCRSCGTLYALVQEEDEKGLYIRVVKEEEEALLPIGSEDF
SIO_010081: ATHE_RS14020
subclass of: SO_0000673
so part of: ATHE_RS14020
location: complement(6118..8274)
location: region:6118-8274:-1
so has part: feature:6118-8274:-1:exon

WP_012660750.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6118-8274:-1:exon