Microvirgula aerodenitrificans strain BE2.4 plasmid unnamed2.
type: Entry
definition: Microvirgula aerodenitrificans strain BE2.4 plasmid unnamed2.
sequence version: NZ_CP028518.1
sequence date: 2023-03-26
sequence: sequence
division: CON
label: NZ_CP028518.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN08822391
keyword: RefSeq
source: Microvirgula aerodenitrificans
organism: Microvirgula aerodenitrificans
taxonomy: Bacteria; Pseudomonadota; Betaproteobacteria; Neisseriales; Chromobacteriaceae; Microvirgula.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP028518.1.\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##Genome-Assembly-Data-START##\nAssembly Date :: MAR-2018\nAssembly Method :: HGAP v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 21:31:22\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,898\nCDSs (total) :: 3,813\nGenes (coding) :: 3,742\nCDSs (with protein) :: 3,742\nGenes (RNA) :: 85\nrRNAs :: 7, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 7, 6, 6 (5S, 16S, 23S)\ntRNAs :: 62\nncRNAs :: 4\nPseudo Genes (total) :: 71\nCDSs (without protein) :: 71\nPseudo Genes (ambiguous residues) :: 0 of 71\nPseudo Genes (frameshifted) :: 40 of 71\nPseudo Genes (incomplete) :: 36 of 71\nPseudo Genes (internal stop) :: 3 of 71\nPseudo Genes (multiple problems) :: 7 of 71\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 5968
topology: circular
so has quality: SO_0000988
location: 1..5968
location: region:1-5968:1
RO_0002162: 57480

NZ_CP028518
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN08822391
type: BioSample
SIO_000068: biosample

1
title: Denitrifier Microvirgula
author: Anderson, E.
author: Jang, J.
author: Ishii, S.
journal: Unpublished

2
title: Direct Submission
author: Anderson, E.
author: Jang, J.
author: Ishii, S.
journal: Submitted (04-APR-2018) Soil, Water and Climate, University of Minnesota, 1475 Gortner Ave, St Paul, MN 55108, USA

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

position:5968:1
position: 5968
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-5968:1:source
so part of: sequence
organism: Microvirgula aerodenitrificans
mol type: genomic DNA
strain: BE2.4
isolation source: Woodchip bioreactor
plasmid: unnamed2
country: USA: Minnesota
collection date: 2016

57480
type: Taxonomy
SIO_000068: taxonomy

DAI18_RS00005
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
locus tag: DAI18_RS00005
old locus tag: DAI18_00005
so part of: sequence
location: <1..455
location: region:1-455:1
so has part: feature:1-455:1:exon
subclass of: SO_0000010

position:455:1
position: 455
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-455:1:exon

DAI18_RS00005
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
locus tag: DAI18_RS00005
old locus tag: DAI18_00005
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 3
transl table: 11
product: hypothetical protein
translation: GKALFLCGIGNLQLLAYPVVQNYCHNGFRYGVIFMLPSRLRLAAALLVPAAALLLSSGYWWSQSWRTRNCWTPPRQAAEHRAIQLASAVAQQTDTLLQMVDVTLQTLGNEYVDEEFSPLGVLPVPVFRPWPKCRCRSTMPRDRWCIPRWD
SIO_010081: DAI18_RS00005
subclass of: SO_0000673
so part of: DAI18_RS00005
location: <1..455
location: region:1-455:1
so has part: feature:1-455:1:exon

WP_159075895.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-455:1:exon

DAI18_RS00010
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
locus tag: DAI18_RS00010
old locus tag: DAI18_00010
so part of: sequence
location: 679..1938
location: region:679-1938:1
so has part: feature:679-1938:1:exon
subclass of: SO_0000010

position:679:1
position: 679
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1938:1
position: 1938
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:679-1938:1:exon

DAI18_RS00010
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
locus tag: DAI18_RS00010
old locus tag: DAI18_00010
EC number: 2.7.7.65
inference: COORDINATES: protein motif:HMM:TIGR00254.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: diguanylate cyclase
translation: MVYVIRRDGSYLARSLSLSQAMTEREPDEVPHPGRSGRRQGLLERDSDFDAVHRLIGWQKLGTGDMAAAVGLDLDAVMSPVESYITQSRLRSVAINILLLLICVLITWLIMRLQRHRAMLQAIYDVLPVGVVVTDPQGHIVDCNQMSEQLLGLERKVQLSSDLSRFEGRLYHADGSRMSAAELPGMRALLGGELVHHEEVGFIHPAQKAMCWLSISAIPCSDAGYGVVIAFIDITHSRNHRQAVEHIAFHDALTGLPNRRLLSDRLNQALSRTARQPGRLVVCFLDLDGFKPVNDKHGHDAGDALLMEIAKRLQKVVRTGDTVARLGGDEFVVVLNGLGSAQEMDDVLERIAAAVATPVELGASQTAQVTASIGVAMHPEDGDDADTLLRYADQAMYRAKQSGQCICHFRREGRESVVW
SIO_010081: DAI18_RS00010
subclass of: SO_0000673
so part of: DAI18_RS00010
location: 679..1938
location: region:679-1938:1
so has part: feature:679-1938:1:exon

WP_159075896.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:679-1938:1:exon

DAI18_RS00015
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
gene: dusA
locus tag: DAI18_RS00015
old locus tag: DAI18_00015
pseudo: true
so part of: sequence
location: 2314..3262
location: region:2314-3262:1
so has part: feature:2314-3262:1:exon
subclass of: SO_0000010

position:2314:1
position: 2314
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3262:1
position: 3262
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2314-3262:1:exon

DAI18_RS00015
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
gene: dusA
locus tag: DAI18_RS00015
old locus tag: DAI18_00015
inference: COORDINATES: similar to AA sequence:RefSeq:WP_019718077.1
GO function: GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0017150 - tRNA dihydrouridine synthase activity [Evidence IEA]
GO process: GO:0002943 - tRNA dihydrouridine synthesis [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: tRNA dihydrouridine(20/20a) synthase DusA
SIO_010081: DAI18_RS00015
subclass of: SO_0000673
so part of: DAI18_RS00015
location: 2314..3262
location: region:2314-3262:1
so has part: feature:2314-3262:1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:2314-3262:1:exon

DAI18_RS19870
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
locus tag: DAI18_RS19870
so part of: sequence
location: 3398..3940
location: region:3398-3940:1
so has part: feature:3398-3940:1:exon
subclass of: SO_0000010

position:3398:1
position: 3398
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3940:1
position: 3940
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3398-3940:1:exon

DAI18_RS19870
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
locus tag: DAI18_RS19870
inference: COORDINATES: protein motif:HMM:NF024808.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: extracellular solute-binding protein
translation: MSATALAGTGDVLHLYNWSGSLSQKILDDFQRQCACRVVQDFYGDNEEMLAKLASGARGYDMVFPSSFVIQAMAKQHLLLPLDHGKLPNLRNVAPAYLNQSYDPGNTYTVPTVLSLTSVGYNVEALKKRGVDAGSWAVIFDPAVLAKVKGKVTVLDSSREVFAAALMYLGIDRTRAICRL
SIO_010081: DAI18_RS19870
subclass of: SO_0000673
so part of: DAI18_RS19870
location: 3398..3940
location: region:3398-3940:1
so has part: feature:3398-3940:1:exon

WP_234412926.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3398-3940:1:exon

DAI18_RS19875
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
locus tag: DAI18_RS19875
so part of: sequence
location: 3954..4166
location: region:3954-4166:1
so has part: feature:3954-4166:1:exon
subclass of: SO_0000010

position:3954:1
position: 3954
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4166:1
position: 4166
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3954-4166:1:exon

DAI18_RS19875
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
locus tag: DAI18_RS19875
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: MIRKARPYWATFSNASYLKELAVGNIWVSLGYSTEFFQAQEDARAAKRKFSIAMCRSARAMNLASTPWRS
SIO_010081: DAI18_RS19875
subclass of: SO_0000673
so part of: DAI18_RS19875
location: 3954..4166
location: region:3954-4166:1
so has part: feature:3954-4166:1:exon

WP_234412927.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3954-4166:1:exon

DAI18_RS19880
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
locus tag: DAI18_RS19880
so part of: sequence
location: 4154..4510
location: region:4154-4510:1
so has part: feature:4154-4510:1:exon
subclass of: SO_0000010

position:4154:1
position: 4154
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4510:1
position: 4510
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4154-4510:1:exon

DAI18_RS19880
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
locus tag: DAI18_RS19880
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: MAILKSARRPDLALQFMNFMLEGRNAAQLTNLNGATNPVSTATAFFRPDLKANPVINPAPATVRQWTVLRELEPKERRYLTRLWTRVKWLVKQQNEGGCMQHPPSFLTAAARAGVVDG
SIO_010081: DAI18_RS19880
subclass of: SO_0000673
so part of: DAI18_RS19880
location: 4154..4510
location: region:4154-4510:1
so has part: feature:4154-4510:1:exon

WP_234412928.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4154-4510:1:exon

DAI18_RS00025
type: Gene
subclass of: SO_0000704
RO_0002162: 57480
gene: xseA
locus tag: DAI18_RS00025
old locus tag: DAI18_00025
pseudo: true
so part of: sequence
location: complement(4473..5795)
location: region:4473-5795:-1
so has part: feature:4473-5795:-1:exon
subclass of: SO_0000010

position:4473:-1
position: 4473
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5795:-1
position: 5795
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4473-5795:-1:exon

DAI18_RS00025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 57480
gene: xseA
locus tag: DAI18_RS00025
old locus tag: DAI18_00025
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008954895.1
GO component: GO:0009318 - exodeoxyribonuclease VII complex [Evidence IEA]
GO function: GO:0008855 - exodeoxyribonuclease VII activity [Evidence IEA]
GO process: GO:0006308 - DNA catabolic process [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 11
product: exodeoxyribonuclease VII large subunit
SIO_010081: DAI18_RS00025
subclass of: SO_0000673
so part of: DAI18_RS00025
location: complement(4473..5795)
location: region:4473-5795:-1
so has part: feature:4473-5795:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4473-5795:-1:exon