Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 plasmid pAACI03, complete sequence.
type: Entry
definition: Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446 plasmid pAACI03, complete sequence.
sequence version: NC_013208.1
sequence date: 2023-05-02
sequence: sequence
division: CON
label: NC_013208.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN00001901
keyword: RefSeq
source: Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
organism: Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
taxonomy: Bacteria; Bacillota; Bacilli; Bacillales; Alicyclobacillaceae; Alicyclobacillus.
reference: 1
references: 21304673
reference: 2
reference: 3
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001730.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4083332\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\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##Metadata-START##\nOrganism Display Name :: Alicyclobacillus acidocaldarius\n acidocaldarius 104-IA, DSM 446\nCulture Collection ID :: DSM 446, ATCC 27009\nGOLD Stamp ID :: Gi02324\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: GeneMark\nIsolation Site :: \"Yellowstone National Park, acid hot\n spring\"\nIsolation Country :: USA\nLatitude :: 44.376262\nLongitude :: -110.690383\nOxygen Requirement :: Aerobe\nCell Shape :: Rod-shaped\nSporulation :: Sporulating\nTemperature Range :: Thermophile\nTemperature Optimum :: 60C\npH :: 3 - 4\nGram Staining :: gram+\nBiotic Relationship :: Free living\nDiseases :: None\nPhenotypes :: Thermoacidophile\nEnergy Source :: Chemoorganotroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 01:38:04\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation M…

sequence
subclass of: SO_0000155
sequence length: 7907
topology: circular
so has quality: SO_0000988
location: 1..7907
location: region:1-7907:1
RO_0002162: 521098

NC_013208
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN00001901
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IA)
author: Mavromatis, K.
author: Sikorski, J.
author: Lapidus, A.
author: Glavina Del Rio, T.
author: Copeland, A.
author: Tice, H.
author: Cheng, J.F.
author: Lucas, S.
author: Chen, F.
author: Nolan, M.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Ivanova, N.
author: Ovchinnikova, G.
author: Pati, A.
author: Chen, A.
author: Palaniappan, K.
author: Land, M.
author: Hauser, L.
author: Chang, Y.J.
author: Jeffries, C.D.
author: Chain, P.
author: Meincke, L.
author: Sims, D.
author: Chertkov, O.
author: Han, C.
author: Brettin, T.
author: Detter, J.C.
author: Wahrenburg, C.
author: Rohde, M.
author: Pukall, R.
author: Goker, M.
author: Bristow, J.
author: Eisen, J.A.
author: Markowitz, V.
author: Hugenholtz, P.
author: Klenk, H.P.
author: Kyrpides, N.C.
journal: Stand Genomic Sci
volume: 2
issue: 1
pages: 9-18
year: 2010
pubmed: 21304673
comments: Publication Status: Online-Only

21304673
type: PubMed
SIO_000068: pubmed

2
title: The complete plasmid3 of Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Kyrpides, N.
author: Mavromatis, K.
author: Ivanova, N.
author: Ovchinnikova, G.
author: Chertkov, O.
author: Sims, D.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Markowitz, V.
author: Cheng, J.-F.
author: Hugenholtz, P.
author: Woyke, T.
author: Wu, D.
author: Pukall, R.
author: Klenk, H.-P.
author: Eisen, J.A.
journal: Unpublished

3
title: Direct Submission
author: Lucas, S.
author: Copeland, A.
author: Lapidus, A.
author: Glavina del Rio, T.
author: Dalin, E.
author: Tice, H.
author: Bruce, D.
author: Goodwin, L.
author: Pitluck, S.
author: Kyrpides, N.
author: Mavromatis, K.
author: Ivanova, N.
author: Ovchinnikova, G.
author: Chertkov, O.
author: Sims, D.
author: Brettin, T.
author: Detter, J.C.
author: Han, C.
author: Larimer, F.
author: Land, M.
author: Hauser, L.
author: Markowitz, V.
author: Cheng, J.-F.
author: Hugenholtz, P.
author: Woyke, T.
author: Wu, D.
author: Pukall, R.
author: Klenk, H.-P.
author: Eisen, J.A.
journal: Submitted (03-SEP-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA

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

position:7907:1
position: 7907
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7907:1:source
so part of: sequence
organism: Alicyclobacillus acidocaldarius subsp. acidocaldarius DSM 446
mol type: genomic DNA
strain: DSM 446
sub species: acidocaldarius
culture collection: DSM:446
type material: type strain of Alicyclobacillus acidocaldarius
plasmid: pAACI03

521098
type: Taxonomy
SIO_000068: taxonomy

AACI_RS16800
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS16800
so part of: sequence
location: complement(269..574)
location: region:269-574:-1
so has part: feature:269-574:-1:exon
subclass of: SO_0000010

position:269:-1
position: 269
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:574:-1
position: 574
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:269-574:-1:exon

AACI_RS16800
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS16800
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: MGCCLRQSFENWQLVSSYEIELSLETKRNGAFVWSQLQPPKIIRELSPAEKFRVVSIGKELEARHKTITMGIEDYLQVNVENSNDATAEETAQGETAGHTA
SIO_010081: AACI_RS16800
subclass of: SO_0000673
so part of: AACI_RS16800
location: complement(269..574)
location: region:269-574:-1
so has part: feature:269-574:-1:exon

WP_041708617.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:269-574:-1:exon

AACI_RS15490
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS15490
old locus tag: Aaci_3149
so part of: sequence
location: complement(626..3811)
location: region:626-3811:-1
so has part: feature:626-3811:-1:exon
subclass of: SO_0000010

position:626:-1
position: 626
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3811:-1
position: 3811
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:626-3811:-1:exon

AACI_RS15490
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS15490
old locus tag: Aaci_3149
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008340986.1
GO function: GO:0003896 - DNA primase activity [Evidence IEA]
GO process: GO:0006260 - DNA replication [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: phage/plasmid primase, P4 family
translation: MDSKCRLCQSKLKEDVVGLWLQGTSYRKLAEWCEQQGEFISHSAIGVHLLKHELKGDPDLSVDFLRWWFDGLCGYVEIRPIANRRNDKDAAVKAARARRSFTTKELDQLRDYLSRGYRDPTMVRCGWYFGVCLRDKPVKKTEDGEWVGGRAEDVVACPGVWADIDDHGDDGDDERIAQAERALIGLGELGFFPSAVVQSGGGRGRHVYYRFKRSADVATVRRIAAKLAVLLGSDASVAEPARIMRLPGSMHTKSGQIVQVAWVERRDEARYEPTAIETAIEEVAKALGIDLDAPEPTSPSNREESMGDWAPVPLDFVKEQLPTICPRFEAYVREPNMVSEPVWYRMGCVLKALNPASSSLFHEWSQAYDAGPGKRYNWSEAEKKFRGAKPVGVRCATFESLDPMEICRRCVHYSKNSSPATFVRKAYAAQLGLPGIYGRPGQDFTEADLPKMDGLPALDNEEEAEEAWKDGLLSDEQVDPNEAFETADATSTYIEGELEEVLRERDERVLATGAVPSDYWRQQGMRFDIAADWMRNSGFRAVEYDEEKEKYKLVHIDFVRALYEDFPSYYFYSGINLYNGKYYDFKKSDAAFIKRFMAHALMTEHKHWVTPTMLNNLFTLYKTWLEADEVRNVEDAKVSSFFDTDPLFPVQNGILDVSSLKRPVMRDFSPDYLVTWQIDAAWLREWEMPRRGHWTLAMEQAEKDVSDLFREFDLSEETTTALFEAIGYSLAKFDVDEQRYFVLLGPGYNGKGTLLRLLESLFGKFVETVTLQELVENRFAASRLARASINIVADASNQTLKDTETIKKLTGNDLLTAEMKYRDAFPFRPRIKLWMASNHLPPTPDGSFGFFRRPLIFPFHRQLPMKPADWERRLRTPEAKSYLLYLAIKHYLNMRAEGRKLTESKEMLRTRMDYWAANDIVQAAIQYGIFEFPDSQNKDRKDYVVPRALATKAIELFAEELGRKKVSTNTLLERLRGNYADIKEVFATCEDGKRRHVWEGVRLGEVAYELKRVRHVPDPRTGEMVVITSYLMDEYEAEVKKGAEAVRKRWDANKYAGRKVQ
SIO_010081: AACI_RS15490
subclass of: SO_0000673
so part of: AACI_RS15490
location: complement(626..3811)
location: region:626-3811:-1
so has part: feature:626-3811:-1:exon

WP_012812252.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:626-3811:-1:exon

AACI_RS15495
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS15495
so part of: sequence
location: complement(4363..4716)
location: region:4363-4716:-1
so has part: feature:4363-4716:-1:exon
subclass of: SO_0000010

position:4363:-1
position: 4363
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4716:-1
position: 4716
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4363-4716:-1:exon

AACI_RS15495
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS15495
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012810457.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPESEAWRAHGWAWDPRPDLQLDHDLWKLLLTEIVTDEELGWVLNGARCAGCRLVWNGRQYRIEPTIDPRLGFNDEEEWSDFREKYLVPSAQQIQKVLKLLTIKVHSNQKLSDVKVV
SIO_010081: AACI_RS15495
subclass of: SO_0000673
so part of: AACI_RS15495
location: complement(4363..4716)
location: region:4363-4716:-1
so has part: feature:4363-4716:-1:exon

WP_041708619.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4363-4716:-1:exon

AACI_RS15500
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS15500
old locus tag: Aaci_3150
so part of: sequence
location: complement(5308..5928)
location: region:5308-5928:-1
so has part: feature:5308-5928:-1:exon
subclass of: SO_0000010

position:5308:-1
position: 5308
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5928:-1
position: 5928
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5308-5928:-1:exon

AACI_RS15500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS15500
old locus tag: Aaci_3150
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008340983.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BRO family protein
translation: MQPVDMDGNQTMMEWMFEGHRIRVVMINDEPWWVAKDVCEALQIANSRDAVSRLDEDEKNTVAITDGNRGNPNTTIINEAGLYQLTFTSRVDTAKRFRRWLAHEVLPSIRKTGEYKTPGRRQECDIAAKQVAVMEMKARTEQAKLLVDAVHRLEHRLSDLLIERILIASTNLMAGYDAIGIPTDGPSFTEPGRTRFPDLKPYWKPF
SIO_010081: AACI_RS15500
subclass of: SO_0000673
so part of: AACI_RS15500
location: complement(5308..5928)
location: region:5308-5928:-1
so has part: feature:5308-5928:-1:exon

WP_012812253.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5308-5928:-1:exon

AACI_RS15505
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS15505
so part of: sequence
location: complement(6028..6261)
location: region:6028-6261:-1
so has part: feature:6028-6261:-1:exon
subclass of: SO_0000010

position:6028:-1
position: 6028
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6261:-1
position: 6261
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6028-6261:-1:exon

AACI_RS15505
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS15505
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: MELQGHLKEALDNTKEVFFSLSIAGLTLLVGYHSQSMLVIVMRDTAAILSLLAALLRGYKAALDWRVYFSSRRALRD
SIO_010081: AACI_RS15505
subclass of: SO_0000673
so part of: AACI_RS15505
location: complement(6028..6261)
location: region:6028-6261:-1
so has part: feature:6028-6261:-1:exon

WP_041708621.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6028-6261:-1:exon

AACI_RS15515
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS15515
old locus tag: Aaci_3152
so part of: sequence
location: complement(6708..7310)
location: region:6708-7310:-1
so has part: feature:6708-7310:-1:exon
subclass of: SO_0000010

position:6708:-1
position: 6708
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7310:-1
position: 7310
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6708-7310:-1:exon

AACI_RS15515
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS15515
old locus tag: Aaci_3152
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008340980.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MKIVNLTPHELTFFTDDGTVVAKIPPSGSVARVASASKKVGEIDGIPVFSTEFGEVVNLPDPAEDTIYVASTLVAQTATKAGRTDVFSPADLVQDSEGNVVGCKGLQMPEGMKKLPTKKSHVCTRELREYVYAQIKATGDEYLASRLQGEWYGVIQTVLHVIKYLMRLPDLNRIREDNLEEAKAVADKVIEFLKSEAKVD
SIO_010081: AACI_RS15515
subclass of: SO_0000673
so part of: AACI_RS15515
location: complement(6708..7310)
location: region:6708-7310:-1
so has part: feature:6708-7310:-1:exon

WP_012812255.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6708-7310:-1:exon

AACI_RS15520
type: Gene
subclass of: SO_0000704
RO_0002162: 521098
locus tag: AACI_RS15520
old locus tag: Aaci_3153
so part of: sequence
location: complement(7374..7712)
location: region:7374-7712:-1
so has part: feature:7374-7712:-1:exon
subclass of: SO_0000010

position:7374:-1
position: 7374
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7712:-1
position: 7712
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7374-7712:-1:exon

AACI_RS15520
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 521098
locus tag: AACI_RS15520
old locus tag: Aaci_3153
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008340979.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MASVIGDAHEEVQKMLQPFLNTPVRITYTNGGTALVFDKVIRTVNDTPNSILMAFNDGAILFEGNIEIKLSGELLTIKQNGGCLSLVRWADLPKEFRPYSKEIAKLVGRESV
SIO_010081: AACI_RS15520
subclass of: SO_0000673
so part of: AACI_RS15520
location: complement(7374..7712)
location: region:7374-7712:-1
so has part: feature:7374-7712:-1:exon

WP_012812256.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7374-7712:-1:exon