Leisingera aquaemixtae strain R2C4 plasmid unnamed9.
type: Entry
definition: Leisingera aquaemixtae strain R2C4 plasmid unnamed9.
sequence version: NZ_CP041160.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP041160.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN12141652
keyword: RefSeq
source: Leisingera aquaemixtae
organism: Leisingera aquaemixtae
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Leisingera.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP041160.1.\nBacteria and source DNA available from Sarah Glaven, 4555 Overlook\nAve SW, Washington, DC, 20375, USA.\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 Method :: HGAP v. HGAP.2\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 70.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 01:39:34\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) :: 4,246\nCDSs (total) :: 4,174\nGenes (coding) :: 4,133\nCDSs (with protein) :: 4,133\nGenes (RNA) :: 72\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 57\nncRNAs :: 3\nPseudo Genes (total) :: 41\nCDSs (without protein) :: 41\nPseudo Genes (ambiguous residues) :: 0 of 41\nPseudo Genes (frameshifted) :: 23 of 41\nPseudo Genes (incomplete) :: 22 of 41\nPseudo Genes (internal stop) :: 4 of 41\nPseudo Genes (multiple problems) :: 8 of 41\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 6320
topology: linear
so has quality: SO_0000987
location: 1..6320
location: region:1-6320:1
RO_0002162: 1396826

NZ_CP041160
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN12141652
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Leisingera sp. R2C4 Isolated from the Self-Regenerating Biocathode Consortium
author: Eddie, B.
author: Malanoski, A.
author: Bird, L.
author: Glaven, S.
journal: Unpublished

2
title: Direct Submission
author: Eddie, B.
author: Malanoski, A.
author: Bird, L.
author: Glaven, S.
journal: Submitted (18-JUN-2019) NCBI, Naval Research Lab DC, 4555 Overlook Ave SW, Washington, DC 20375, USA

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

position:6320:1
position: 6320
reference: sequence
type: ForwardStrandPosition
type: ExactPosition
type: FuzzyPosition

feature:1-6320:1:source
so part of: sequence
organism: Leisingera aquaemixtae
mol type: genomic DNA
strain: R2C4
isolation source: Biocathode MCL, marine biofilm
plasmid: unnamed9
country: USA: Rutgers, NJ
collection date: 2009

1396826
type: Taxonomy
SIO_000068: taxonomy

R2C4_RS20300
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
locus tag: R2C4_RS20300
old locus tag: R2C4_20315
so part of: sequence
location: <1..1056
location: region:1-1056:1
so has part: feature:1-1056:1:exon
subclass of: SO_0000010

position:1056:1
position: 1056
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1-1056:1:exon

R2C4_RS20300
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
locus tag: R2C4_RS20300
old locus tag: R2C4_20315
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008558542.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: TRAP transporter large permease
translation: RLINVVMAYVGHIRGGLAISTAAACTMFGAVSGSTQATVVAIGSPLRPRMLQAGYKDSFVLALIVNASDIAFLIPPSIGMIIYGVVSSTSIAELFIAGIGPGLLILLLFSAYAYIYAVRNNVPAEPKATWGERFQTMRQALWPMGFPVIIIGGIYGGVFSPTEAAAACVLYALILEVLVFRSIALADVYDTAKSTGLVTAIVFILVGAGAAFSWVISFAQVPQQILGAIGIAEMGAIGVLFVISIAFFIGCMFVDPIVVILVLVPVFAPVVKSVGLDPVLVGTIITLQVAIGSATPPFGCDIFTAIAVFKRPYAEVVRGTPPFILMLLGVSVALIFFPQIALFLRDLAFAK
SIO_010081: R2C4_RS20300
subclass of: SO_0000673
so part of: R2C4_RS20300
location: <1..1056
location: region:1-1056:1
so has part: feature:1-1056:1:exon

WP_141892145.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1-1056:1:exon

R2C4_RS20305
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
locus tag: R2C4_RS20305
old locus tag: R2C4_20320
so part of: sequence
location: 1068..1505
location: region:1068-1505:1
so has part: feature:1068-1505:1:exon
subclass of: SO_0000010

position:1068:1
position: 1068
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1505:1
position: 1505
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1068-1505:1:exon

R2C4_RS20305
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
locus tag: R2C4_RS20305
old locus tag: R2C4_20320
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008558616.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: universal stress protein
translation: MFTSVLVPFDGSQGAEAALAKAAELAQLCGAALTLLTVYRHHSLLEASMHMVRPDQPEDLDEIMRSHAKEVAERGKALARAGGIDAPRAFVKAGPVARTITSFAGEHGHDLIVIGSRGLGSLEGVLLGSVSHKVTSLAETPVLVV
SIO_010081: R2C4_RS20305
subclass of: SO_0000673
so part of: R2C4_RS20305
location: 1068..1505
location: region:1068-1505:1
so has part: feature:1068-1505:1:exon

WP_141892146.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1068-1505:1:exon

R2C4_RS20310
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
gene: eutA
locus tag: R2C4_RS20310
old locus tag: R2C4_20325
so part of: sequence
location: 1516..2280
location: region:1516-2280:1
so has part: feature:1516-2280:1:exon
subclass of: SO_0000010

position:1516:1
position: 1516
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2280:1
position: 2280
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1516-2280:1:exon

R2C4_RS20310
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
gene: eutA
locus tag: R2C4_RS20310
old locus tag: R2C4_20325
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008203776.1
GO process: GO:0042400 - ectoine catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ectoine utilization protein EutA
translation: MALDIHATPSRVAARLDARPVPKRIALVTLATDHTSERDFARICDPDRVGVYVNRIEFENPTTRETLLQTGPRLSAAAAQILPGEAVDVVAYGCTAASIVLGNEAVAGYLNAAKPDTPCVTPSSAAFDAFQALEARRVSLLTPYSPEVTDEMAQYFAAHGPEVVSAACFGLTDDRQMARISEDSIIEAGIAACDAGAEALFLSCTALRAAGCVQRIEDRLGKPVVSSNQAMVWRCLRLAGITDAVPGYGRLFEL
SIO_010081: R2C4_RS20310
subclass of: SO_0000673
so part of: R2C4_RS20310
location: 1516..2280
location: region:1516-2280:1
so has part: feature:1516-2280:1:exon

WP_141892147.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1516-2280:1:exon

R2C4_RS20315
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
gene: eutB
locus tag: R2C4_RS20315
old locus tag: R2C4_20330
so part of: sequence
location: 2299..3306
location: region:2299-3306:1
so has part: feature:2299-3306:1:exon
subclass of: SO_0000010

position:2299:1
position: 2299
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:3306:1
position: 3306
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2299-3306:1:exon

R2C4_RS20315
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
gene: eutB
locus tag: R2C4_RS20315
old locus tag: R2C4_20330
EC number: 4.3.1.19
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008558546.1
GO process: GO:0042400 - ectoine catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hydroxyectoine utilization dehydratase EutB
translation: MTEKITLQDSFQARARIAGRVRQTAMVPSPALSARCGGAVSLKLESSQITGSFKLRGATNAVLSLSEEQRAAGVVGVSTGNHGRGLAYAAAQAGVRCIICMSELVPQNKVEGIKSHGAEVRITGRSQDDAQVEVDRLVAEGMTMLPPFDHRDIIAGQSTVALEMLEQAPDLETVLVPLSGGGLISGVAMVMKAVNPAIRVIGVSMARGAAMHASLQAGKPVQVEELPTLADSLGGGIGLDNAYTFAMTQALVEDVVLVSEAEIAAAIRHAYFVERLVIEGSGSVGIAALLAGRVEHPGRCAVLVSGQNIGMDLHKRIIDGEDVDAAAEAGGGANA
SIO_010081: R2C4_RS20315
subclass of: SO_0000673
so part of: R2C4_RS20315
location: 2299..3306
location: region:2299-3306:1
so has part: feature:2299-3306:1:exon

WP_141892148.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2299-3306:1:exon

R2C4_RS20320
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
gene: eutC
locus tag: R2C4_RS20320
old locus tag: R2C4_20335
so part of: sequence
location: 3299..4291
location: region:3299-4291:1
so has part: feature:3299-4291:1:exon
subclass of: SO_0000010

position:3299:1
position: 3299
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4291:1
position: 4291
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3299-4291:1:exon

R2C4_RS20320
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
gene: eutC
locus tag: R2C4_RS20320
old locus tag: R2C4_20335
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008558588.1
GO process: GO:0042400 - ectoine catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ectoine utilization protein EutC
translation: MPDIRILTEAELRGLVPLDGDAVDCVEQGFTTLAGGGVEMPPIMTLLVPDHNGEVCVKTAYVPGVESFAMKMSPGFFDNPKLGLPSTTGLMVVFSSRTGLLEALLLDNGYLTDVRTAAAGAVAARHLAREDARRVCIIGAGVQARMQLKAMTLVRGVDSAVIWARDTAKAEAAAASLRSELGIDVTAATDAAAAVSSADIVVTTTPAPAPVIKAEWLQPGQLVIAMGSDQAHKCELEPACLAKADLYVPDSQAQCAVKGELRSAIAAGLIAKDQSFAELGGITAGKAAGRRSASDLIIADLTGTGVQDTAIATLAGSRADAAGAGATFTS
SIO_010081: R2C4_RS20320
subclass of: SO_0000673
so part of: R2C4_RS20320
location: 3299..4291
location: region:3299-4291:1
so has part: feature:3299-4291:1:exon

WP_141892149.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3299-4291:1:exon

R2C4_RS20325
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
gene: doeA
locus tag: R2C4_RS20325
old locus tag: R2C4_20340
so part of: sequence
location: 4311..5498
location: region:4311-5498:1
so has part: feature:4311-5498:1:exon
subclass of: SO_0000010

position:4311:1
position: 4311
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:5498:1
position: 5498
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4311-5498:1:exon

R2C4_RS20325
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
gene: doeA
locus tag: R2C4_RS20325
old locus tag: R2C4_20340
EC number: 3.5.4.44
inference: COORDINATES: similar to AA sequence:RefSeq:WP_010975302.1
GO process: GO:0042400 - ectoine catabolic process [Evidence IEA]
note: DoeA (degradation of ectoine A) is also called EutD (ectoine utilization D); Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ectoine hydrolase DoeA
translation: MADPKLYFSRAEYQARLDKTRAEMSRRGLDLLIVTDPSNMNWLTGYDGWSFYVHQCVVVGMDGEPVWYGRGQDANGALRTCWMDPANIIGYPDHYVQSTERHPMDCLSAQLKDRGLNGGVIGVEMDNYYFTAAAYASLQKHLPDARFADANALVNWQRAVKSEAELAYMRQAGQIVGRMHQRIFERVEPGMRKCDLVAEIYDAGLRYDAELGFGGDYPAIVPLLPSGSDAAAPHLTWDDLPMKSGEGTFFEIAGVVHRYHCPLSRTVFLGKPTQTFLDAEKAVLEGMEAGLEVAKAGNTCEDIAKAFFKVLKTYGIEKDNRTGYPIGVSYPPDWGERTMSLRPGDTTILEENMTFHFMTGLWMEDWGFEITESIRIGANGPECLSDVPRKMFVKD
SIO_010081: R2C4_RS20325
subclass of: SO_0000673
so part of: R2C4_RS20325
location: 4311..5498
location: region:4311-5498:1
so has part: feature:4311-5498:1:exon

WP_141892150.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4311-5498:1:exon

R2C4_RS20330
type: Gene
subclass of: SO_0000704
RO_0002162: 1396826
gene: doeB
locus tag: R2C4_RS20330
old locus tag: R2C4_20345
so part of: sequence
location: 5498..>6320
location: region:5498-6320:1
so has part: feature:5498-6320:1:exon
subclass of: SO_0000010

urn:…
SIO_000300: 1
SIO_000628: feature:5498-6320:1:exon

R2C4_RS20330
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1396826
gene: doeB
locus tag: R2C4_RS20330
old locus tag: R2C4_20345
EC number: 3.5.1.125
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013713214.1
GO process: GO:0042400 - ectoine catabolic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: N(2)-acetyl-L-2,4-diaminobutanoate deacetylase DoeB
translation: MHEAKSDFPTIPLDRDGVHHGYLKLPYSRDDSAWGSVMIPLTVIKNGDGPTALLTGANHGDEYEGPIALQELAATTRAEDVTGRLIIVPAFNYPAFRAGTRTSPIDRGNLNRAFPGRPDGTVTEKIADYFQRTLLPMADLAVDFHSGGKTLDFVPFAAAHILEDKATQEACFAAMKAFNAPYSVELLEIDSAGMYDTAVEQMGKVLVTTELGGGGSSTARGNAIAKKGLRNVLIHAGILQGQMQMDDTIRLSMPDDDCFLFSEGDGLFEIMTDL
SIO_010081: R2C4_RS20330
subclass of: SO_0000673
so part of: R2C4_RS20330
location: 5498..>6320
location: region:5498-6320:1
so has part: feature:5498-6320:1:exon

WP_141892151.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5498-6320:1:exon