Rufibacter tibetensis strain 1351 plasmid 2, complete sequence.
type: Entry
definition: Rufibacter tibetensis strain 1351 plasmid 2, complete sequence.
sequence version: NZ_CP012645.1
sequence date: 2022-10-06
sequence: sequence
division: CON
label: NZ_CP012645.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02711851
keyword: RefSeq
source: Rufibacter tibetensis
organism: Rufibacter tibetensis
taxonomy: Bacteria; Bacteroidota; Cytophagia; Cytophagales; Hymenobacteraceae; Rufibacter.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP012645.1.\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##Assembly-Data-START##\nAssembly Method :: SOAPdenovo v. 2.04\nCoverage :: 505\nSequencing Technology :: Illumina\n##Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/05/2022 14:26:44\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,402\nCDSs (total) :: 4,342\nGenes (coding) :: 4,319\nCDSs (with protein) :: 4,319\nGenes (RNA) :: 60\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 3\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 7 of 23\nPseudo Genes (incomplete) :: 14 of 23\nPseudo Genes (internal stop) :: 6 of 23\nPseudo Genes (multiple problems) :: 3 of 23\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 12516
topology: circular
so has quality: SO_0000988
location: 1..12516
location: region:1-12516:1
RO_0002162: 512763

NZ_CP012645
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02711851
type: BioSample
SIO_000068: biosample

1
title: Complete genome sequence of Rufibacter tibetensis strain 1351t, a radiation-resistant bacterium from tibet plateau
author: Dai, J.
journal: Unpublished

2
title: Direct Submission
author: Dai, J.
journal: Submitted (31-AUG-2015) College of Bioengineering, Hubei University of Technology, Nanli Road 28#, Wuhan, Hubei 430068, P.R. China

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

position:12516:1
position: 12516
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-12516:1:source
so part of: sequence
organism: Rufibacter tibetensis
mol type: genomic DNA
strain: 1351
isolation source: soil
type material: type strain of Rufibacter tibetensis
plasmid: 2
country: China:tibet
collection date: 2008-07-08

512763
type: Taxonomy
SIO_000068: taxonomy

DC20_RS22180
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22180
old locus tag: DC20_22180
so part of: sequence
location: complement(358..1491)
location: region:358-1491:-1
so has part: feature:358-1491:-1:exon
subclass of: SO_0000010

position:358:-1
position: 358
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1491:-1
position: 1491
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:358-1491:-1:exon

DC20_RS22180
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 512763
locus tag: DC20_RS22180
old locus tag: DC20_22180
EC number: 2.4.-.-
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008584437.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: glycosyltransferase
translation: MAYIVIVGPAFPFRGGIAASTESLARTWQQMGHRVEIFTFTTQYPSILFPGKSQYVEGPAPQDLVIHQELSSINPFTWVRLGYKIKKKKPDVVLLRYWLPFMSPSLGTVAKIIRGNKQTKLVALTDNIVPHEKRPGDIALTKYFVDACDAFVTMSATVTKELKQFNKSKPVVSSPHPIYDTYGQKMSRGEALQELNLPEGKYLLFFGFVRYYKGLDILLQAMRDPRLQERGIKLIVAGEYYESPEVYKQIIKEGNLQDRVILHTEYIPHDKVKAYFSIADLVVQPYRHASQSGVTQIAYHFEVPMIVTKVGGLVEMIPDTKVGYVVDVSSEAIADAIERYYLEDKSEEMVKFIQEEKKKYTWEALATAITEVAGMKT
SIO_010081: DC20_RS22180
subclass of: SO_0000673
so part of: DC20_RS22180
location: complement(358..1491)
location: region:358-1491:-1
so has part: feature:358-1491:-1:exon

WP_062546239.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:358-1491:-1:exon

DC20_RS22185
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22185
old locus tag: DC20_22185
so part of: sequence
location: complement(1495..2460)
location: region:1495-2460:-1
so has part: feature:1495-2460:-1:exon
subclass of: SO_0000010

position:1495:-1
position: 1495
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2460:-1
position: 2460
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1495-2460:-1:exon

DC20_RS22185
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 512763
locus tag: DC20_RS22185
old locus tag: DC20_22185
inference: COORDINATES: similar to AA sequence:RefSeq:WP_018478341.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: glycosyltransferase family 2 protein
translation: MQNRVDISVVIPLLNEAESLPELTQWINRVMVSHGFLYEVLLIDDGSTDTSWKVIQELSLQDQNIKGIRFNRNYGKSAALNVGFRETLGRVVITMDADLQDSPDEIPDLYRMIVEEGYDLVSGWKKKRYDPLSKTLPTKLFNAATRKISKIKLHDFNCGLKAYDERVVKNIEVYGEMHRYIPVIAKWNGFSKIGEKVVQHRERKYGTTKFGLERFVYGFLDLMSISFVSRFKKRPMHFFGSLGTISFLIGFLITSWLVIEKMYYSFQNQAVRNVTDQPLFFLALVAVIVGVQLFLAGFLAEMVSLVGRRKDEYLIRDNIGF
SIO_010081: DC20_RS22185
subclass of: SO_0000673
so part of: DC20_RS22185
location: complement(1495..2460)
location: region:1495-2460:-1
so has part: feature:1495-2460:-1:exon

WP_062546240.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1495-2460:-1:exon

DC20_RS22190
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22190
old locus tag: DC20_22190
so part of: sequence
location: complement(2469..3008)
location: region:2469-3008:-1
so has part: feature:2469-3008:-1:exon
subclass of: SO_0000010

position:2469:-1
position: 2469
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3008:-1
position: 3008
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2469-3008:-1:exon

DC20_RS22190
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 512763
locus tag: DC20_RS22190
old locus tag: DC20_22190
inference: COORDINATES: protein motif:HMM:NF025227.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF4199 domain-containing protein
translation: MNEQATMHEPTVTPTSVGVRYGFIAGFSLIIVSLIFMLLERSTNSTLAQVLSFLILGGGIVAAYLYFKEHNHSYMSYGQGLGIGAILGSIAGVLGGVFSAIYTTFIDNTILEKAMEMEVQKMEERGLSDEQIEKAVEVAQMFSGPLAMIILSILLYTIGAFFLSLIIAAIMKRNRPEFE
SIO_010081: DC20_RS22190
subclass of: SO_0000673
so part of: DC20_RS22190
location: complement(2469..3008)
location: region:2469-3008:-1
so has part: feature:2469-3008:-1:exon

WP_062546241.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2469-3008:-1:exon

DC20_RS22195
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22195
old locus tag: DC20_22195
so part of: sequence
location: complement(3031..3549)
location: region:3031-3549:-1
so has part: feature:3031-3549:-1:exon
subclass of: SO_0000010

position:3031:-1
position: 3031
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3549:-1
position: 3549
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3031-3549:-1:exon

DC20_RS22195
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 512763
locus tag: DC20_RS22195
old locus tag: DC20_22195
inference: COORDINATES: protein motif:HMM:NF025227.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: DUF4199 domain-containing protein
translation: MFDKAVVNTAIKYGVTGGIVSFAYILILALIGFENPYDNTSEYSSTLVFGSVFIFLAIKYFKKFHDSELGFGKAFKVGFVTVFFLAFTSAMLLCIYSFLAGEELIKEYIILSQKRMELTRQELTQMMGEVNYKNAYQRLNQLNAFTLAQISFVNRMVAGFFISIVLGVFFRK
SIO_010081: DC20_RS22195
subclass of: SO_0000673
so part of: DC20_RS22195
location: complement(3031..3549)
location: region:3031-3549:-1
so has part: feature:3031-3549:-1:exon

WP_062546242.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3031-3549:-1:exon

DC20_RS22200
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22200
old locus tag: DC20_22200
so part of: sequence
location: complement(3565..4845)
location: region:3565-4845:-1
so has part: feature:3565-4845:-1:exon
subclass of: SO_0000010

position:3565:-1
position: 3565
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4845:-1
position: 4845
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3565-4845:-1:exon

DC20_RS22200
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 512763
locus tag: DC20_RS22200
old locus tag: DC20_22200
inference: COORDINATES: similar to AA sequence:RefSeq:WP_007652919.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: dihydroorotase
translation: MDLLFKAVTIVDSSSSLDGQTVDILLKDGRIQQIASGIEDENAQIVSERGLHCSLGWFDLSAFTGEPGFENRETLENFTKAAAFGGFTEVACLPNLEPIIQTRSAIEYFKHKSSYGPVKLHAIAAITHNLDGKDLSEVLDLKAAGAIAFSEGADSLQAEDTVLKALEYLKLFGGVLINRPENKKIANGGHMHEGTTSTRLGLKGIPSLAEEVQVARDLQLLQYTDGRLHLSQLSTAAGVKAVRKAKQHGLNVTCDVAAHQCAFTDQMVQPFDTNYKVSPPFRGEEDRQAILEGLQDGTIDTLVSGHTPWNEEAKELEFDLAEAGIIGLQTAYSVANETLASHLSSKALIEKLTVGSRNIVGLPLPSLTEGAPANLTFFHPTKTWIFDEKLNASAAKNTPFFGRELTGCVFGTYVNGQFTSNPAYQN
SIO_010081: DC20_RS22200
subclass of: SO_0000673
so part of: DC20_RS22200
location: complement(3565..4845)
location: region:3565-4845:-1
so has part: feature:3565-4845:-1:exon

WP_062546243.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3565-4845:-1:exon

DC20_RS22205
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22205
old locus tag: DC20_22205
so part of: sequence
location: complement(4829..6499)
location: region:4829-6499:-1
so has part: feature:4829-6499:-1:exon
subclass of: SO_0000010

position:4829:-1
position: 4829
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6499:-1
position: 6499
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4829-6499:-1:exon

DC20_RS22205
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 512763
locus tag: DC20_RS22205
old locus tag: DC20_22205
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: MQSSSSEKGVSKLEAAMDAASDLSMDNRLASSTNISGLRSDSLNLGSSSNQFLSPQEGISKITNQRRSSQTYIVSDFQRSTFSPEVLTDLPKEQAITLVSLSTTDIPNLYIDSVWLEQPVLLPNSLAGISVRVAGSNLDESNQVKVTASEDGKLLGATQVLLEPGNKAIAHFKIPLASGTAQQITFEVEDPTTSYDNQYFIVLPEPSSVQLKLNRAQGQNDPIAQAYKAEPAFVFSSDVTRPNGLWVVDIPAGASSRLIQQIYDWIGRGGNVLLIPSATASQKGAVDFLAKIGLKGISEESQETGPKPLIQPDLSDAFFRQVFEKEVKNMKMPEAKPVLTWRSSFHNILKFTDNTPFLSTFRIGKGNVHLFASPINNASSFVAHPLFVPVLYQLALSFDVSRTVLAHQANRGTINIPLENEVVSKQPYSLTMGDQSFIPDQRVRQDMLHMTLPNDVSTPGFYTLVREGKAISTIALNIPREESRLEGYTVEELKEILAGHGDNVQVIEPKETVSLQKQLQTEASGASLWKYCLILCFLCLVIEAVILSAKKSGSVI
SIO_010081: DC20_RS22205
subclass of: SO_0000673
so part of: DC20_RS22205
location: complement(4829..6499)
location: region:4829-6499:-1
so has part: feature:4829-6499:-1:exon

WP_062546244.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4829-6499:-1:exon

DC20_RS22210
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
gene: rrf
locus tag: DC20_RS22210
old locus tag: DC20_22210
so part of: sequence
location: complement(6963..7074)
location: region:6963-7074:-1
so has part: feature:6963-7074:-1:exon
subclass of: SO_0000573

position:6963:-1
position: 6963
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7074:-1
position: 7074
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6963-7074:-1:exon

DC20_RS22210
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 512763
gene: rrf
locus tag: DC20_RS22210
old locus tag: DC20_22210
product: 5S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF00001
inference: COORDINATES: profile:INFERNAL:1.1.1
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: DC20_RS22210
subclass of: SO_0000673
so part of: DC20_RS22210
location: complement(6963..7074)
location: region:6963-7074:-1
so has part: feature:6963-7074:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:6963-7074:-1:exon

DC20_RS22215
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22215
old locus tag: DC20_22215
so part of: sequence
location: complement(7180..10026)
location: region:7180-10026:-1
so has part: feature:7180-10026:-1:exon
subclass of: SO_0000573

position:7180:-1
position: 7180
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:10026:-1
position: 10026
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7180-10026:-1:exon

DC20_RS22215
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 512763
locus tag: DC20_RS22215
old locus tag: DC20_22215
product: 23S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF02541
inference: COORDINATES: profile:INFERNAL:1.1.1
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: DC20_RS22215
subclass of: SO_0000673
so part of: DC20_RS22215
location: complement(7180..10026)
location: region:7180-10026:-1
so has part: feature:7180-10026:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:7180-10026:-1:exon

DC20_RS22220
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22220
old locus tag: DC20_22220
so part of: sequence
location: complement(10208..10281)
location: region:10208-10281:-1
so has part: feature:10208-10281:-1:exon
subclass of: SO_0000663

position:10208:-1
position: 10208
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:10281:-1
position: 10281
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10208-10281:-1:exon

DC20_RS22220
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 512763
locus tag: DC20_RS22220
old locus tag: DC20_22220
product: tRNA-Ala
inference: COORDINATES: profile:tRNAscan-SE:2.0.9
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(10245..10247),aa:Ala,seq:tgc)
SIO_010081: DC20_RS22220
subclass of: SO_0000673
so part of: DC20_RS22220
location: complement(10208..10281)
location: region:10208-10281:-1
so has part: feature:10208-10281:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:10208-10281:-1:exon

DC20_RS22225
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22225
old locus tag: DC20_22225
so part of: sequence
location: complement(10289..10365)
location: region:10289-10365:-1
so has part: feature:10289-10365:-1:exon
subclass of: SO_0000663

position:10289:-1
position: 10289
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:10365:-1
position: 10365
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10289-10365:-1:exon

DC20_RS22225
type: Transfer RNA
subclass of: SO_0000253
RO_0002162: 512763
locus tag: DC20_RS22225
old locus tag: DC20_22225
product: tRNA-Ile
inference: COORDINATES: profile:tRNAscan-SE:2.0.9
note: Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
anticodon: (pos:complement(10329..10331),aa:Ile,seq:gat)
SIO_010081: DC20_RS22225
subclass of: SO_0000673
so part of: DC20_RS22225
location: complement(10289..10365)
location: region:10289-10365:-1
so has part: feature:10289-10365:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:10289-10365:-1:exon

DC20_RS22230
type: Gene
subclass of: SO_0000704
RO_0002162: 512763
locus tag: DC20_RS22230
old locus tag: DC20_22230
so part of: sequence
location: complement(10481..11992)
location: region:10481-11992:-1
so has part: feature:10481-11992:-1:exon
subclass of: SO_0000573

position:10481:-1
position: 10481
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:11992:-1
position: 11992
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:10481-11992:-1:exon

DC20_RS22230
type: Ribosomal RNA
subclass of: SO_0000252
RO_0002162: 512763
locus tag: DC20_RS22230
old locus tag: DC20_22230
product: 16S ribosomal RNA
inference: COORDINATES: nucleotide motif:Rfam:14.4:RF00177
inference: COORDINATES: profile:INFERNAL:1.1.1
note: Derived by automated computational analysis using gene prediction method: cmsearch.
SIO_010081: DC20_RS22230
subclass of: SO_0000673
so part of: DC20_RS22230
location: complement(10481..11992)
location: region:10481-11992:-1
so has part: feature:10481-11992:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:10481-11992:-1:exon