Rhodopseudomonas palustris strain RCB100 plasmid unnamed1, complete sequence.
type: Entry
definition: Rhodopseudomonas palustris strain RCB100 plasmid unnamed1, complete sequence.
sequence version: NZ_CP066700.1
sequence date: 2023-03-25
sequence: sequence
division: CON
label: NZ_CP066700.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN17028957
keyword: RefSeq
source: Rhodopseudomonas palustris (Rhodopseudomonas rutila)
organism: Rhodopseudomonas palustris
taxonomy: Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales; Nitrobacteraceae; Rhodopseudomonas.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP066700.1.\nBacteria and source DNA available from Dr. Kathryn R. Fixen Lab.\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 :: Unicycler v. v0.4.8\nGenome Coverage :: 243.0226\nSequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 03:55:49\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) :: 5,027\nCDSs (total) :: 4,968\nGenes (coding) :: 4,921\nCDSs (with protein) :: 4,921\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 47\nCDSs (without protein) :: 47\nPseudo Genes (ambiguous residues) :: 0 of 47\nPseudo Genes (frameshifted) :: 23 of 47\nPseudo Genes (incomplete) :: 30 of 47\nPseudo Genes (internal stop) :: 3 of 47\nPseudo Genes (multiple problems) :: 8 of 47\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 8427
topology: circular
so has quality: SO_0000988
location: 1..8427
location: region:1-8427:1
RO_0002162: 1076

NZ_CP066700
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN17028957
type: BioSample
SIO_000068: biosample

1
title: Complete Genome Sequence of Rhodopseudomonas palustris RCB100, an Anoxygenic Phototroph That Degrades 3-Chlorobenzoate
author: Haq, I.U.
author: Fixen, K.R.
journal: Microbiol Resour Announc 10 (15) (2021)
comments: DOI: 10.1128/MRA.00043-21

2
title: Direct Submission
author: Haq, I.U.
author: Fixen, K.R.
journal: Submitted (15-DEC-2020) Department of Plant and Microbial Biology, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN 55108, USA

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

position:8427:1
position: 8427
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-8427:1:source
so part of: sequence
organism: Rhodopseudomonas palustris
mol type: genomic DNA
strain: RCB100
isolation source: soil
plasmid: unnamed1
country: USA: New York, Ithaca
collection date: 2000-03

1076
type: Taxonomy
SIO_000068: taxonomy

I8G32_RS25020
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25020
old locus tag: I8G32_05002
so part of: sequence
location: join(8401..8427,1..1197)
location: region:1-8427:1
so has part: feature:8401-8427:1:exon
so has part: feature:1-1197:1:exon
subclass of: SO_0000010

66895999
type: Gene
SIO_000068: ncbigene

urn:…
SIO_000300: 1
SIO_000628: feature:8401-8427:1:exon

position:8401:1
position: 8401
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 2
SIO_000628: feature:1-1197:1:exon

position:1197:1
position: 1197
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

I8G32_RS25020
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25020
old locus tag: I8G32_05002
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012340185.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiator protein A
translation: MANPSNLNFMPREQFAALSLHEKNDYLQGLAERFAASTGREHEPLDKDALSRLRRYYSRRKFADLELEGKPDTGLNASLRRLSNAIRNADLNQDIEAVLMQEMPQRVLREPPTDDAQLMFFVPTIYDAPIKDDVNLMDVAPFTLGKNVRQGVITYEMKDCLITIEGGAEVGLATVFDYDIFLNMVSYLAEEVRRYRIDDAKGLRPSLPPKMYRPTAAHLLKFSRRASGGRQYQEIEAALRRLSKTSITITNLAGGKRRQVDTRPLIGEHTIISSTNTGKVDQIEIRIPDWVYSSVVRSDKALPLLTLHPDYFLITSGLGRFIYRLARKAAGKDEARYSVAELHKRSGSSREPRKFLFDLKEFVTRTQTFPMPDFDLALEQGKGGPILLMKRRPAMPTTPEVIQLAAN
SIO_010081: I8G32_RS25020
subclass of: SO_0000673
so part of: I8G32_RS25020
location: join(8401..8427,1..1197)
location: region:1-8427:1
so has part: feature:8401-8427:1:exon
so has part: feature:1-1197:1:exon

WP_042441897.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8401-8427:1:exon

urn:…
SIO_000300: 2
SIO_000628: feature:1-1197:1:exon

I8G32_RS25025
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25025
old locus tag: I8G32_05003
so part of: sequence
location: complement(1737..2288)
location: region:1737-2288:-1
so has part: feature:1737-2288:-1:exon
subclass of: SO_0000010

66896000
type: Gene
SIO_000068: ncbigene

position:1737:-1
position: 1737
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2288:-1
position: 2288
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1737-2288:-1:exon

I8G32_RS25025
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25025
old locus tag: I8G32_05003
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: MLPAATVLPPLSGLFQPLLVPLKTQKVTATFSGRKHIGERLALLVRANYVARARSLAARPGVHWLTPKAATHFHPVFGEEWARAASGKGFTDNLHMPQRLLDYAMGRQKGSAATRMMFVFGSAAMLERAMTTLPDRDARVWRAVFFKSLPDLVEDFGGTWLQATGERRNPFERVEPAQATGAP
SIO_010081: I8G32_RS25025
subclass of: SO_0000673
so part of: I8G32_RS25025
location: complement(1737..2288)
location: region:1737-2288:-1
so has part: feature:1737-2288:-1:exon

WP_162470452.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1737-2288:-1:exon

I8G32_RS25030
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25030
so part of: sequence
location: 2272..2712
location: region:2272-2712:1
so has part: feature:2272-2712:1:exon
subclass of: SO_0000010

66896001
type: Gene
SIO_000068: ncbigene

position:2272:1
position: 2272
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2712:1
position: 2712
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2272-2712:1:exon

I8G32_RS25030
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25030
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: MAAGSTGYIQYNTGNSFDANSGLTWTNASSRLTATNISATALTVNGVAITGSNSGDRIVSTSANVVAGNGGTISFTTGGVSGTTYFGTTGVLVGPGISTTGMISTASIYAAGSVQIGGNGSEGCNAALDSGKMRRNPTTGHMQVCR
SIO_010081: I8G32_RS25030
subclass of: SO_0000673
so part of: I8G32_RS25030
location: 2272..2712
location: region:2272-2712:1
so has part: feature:2272-2712:1:exon

WP_174270131.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2272-2712:1:exon

I8G32_RS25035
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25035
old locus tag: I8G32_05005
so part of: sequence
location: complement(2716..3342)
location: region:2716-3342:-1
so has part: feature:2716-3342:-1:exon
subclass of: SO_0000010

66896002
type: Gene
SIO_000068: ncbigene

position:2716:-1
position: 2716
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3342:-1
position: 3342
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2716-3342:-1:exon

I8G32_RS25035
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25035
old locus tag: I8G32_05005
inference: COORDINATES: similar to AA sequence:RefSeq:WP_015042075.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MPKILRETAHISRKLTQNIFRAFDYARAGGFPLNLYVVINIRETDACAAASAFERIRHKYRDWLAHHSRKLGVRIPPMYVFTFEAPGHPHVNWALRVPPRLVDEFQRKLPGWVEKVQGPLGPFDINVQPIAPDGAYKALANYIVKGCDPEYVAHFHLAALAEQHGPQGAFWGRRAGVSPSLNKAERDAAGFNPKRREVRSRSHERDAA
SIO_010081: I8G32_RS25035
subclass of: SO_0000673
so part of: I8G32_RS25035
location: complement(2716..3342)
location: region:2716-3342:-1
so has part: feature:2716-3342:-1:exon

WP_011160374.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2716-3342:-1:exon

I8G32_RS25040
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25040
old locus tag: I8G32_05006
so part of: sequence
location: 3542..4099
location: region:3542-4099:1
so has part: feature:3542-4099:1:exon
subclass of: SO_0000010

66896003
type: Gene
SIO_000068: ncbigene

position:3542:1
position: 3542
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:4099:1
position: 4099
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3542-4099:1:exon

I8G32_RS25040
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25040
old locus tag: I8G32_05006
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017501690.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: recombinase family protein
translation: MIYGYARVSTSDQDTAAQVEQLTAAGAAKVFRENISGASAERPQLKKALAALDAGDVLLVTRIDRLARSTRDLLNIVHDVKEAGATFKSIAEPWADTSTELAEFMLTVLGAAAKLERATILARTSEGRARAKAKGKSLGRPYKLTPAQQDEARAMLAAGRGVREIAPIFNVSPPTISRLKTNAAS
SIO_010081: I8G32_RS25040
subclass of: SO_0000673
so part of: I8G32_RS25040
location: 3542..4099
location: region:3542-4099:1
so has part: feature:3542-4099:1:exon

WP_011160373.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3542-4099:1:exon

I8G32_RS25045
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25045
old locus tag: I8G32_05007
so part of: sequence
location: 4240..6069
location: region:4240-6069:1
so has part: feature:4240-6069:1:exon
subclass of: SO_0000010

66896004
type: Gene
SIO_000068: ncbigene

position:4240:1
position: 4240
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:6069:1
position: 6069
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4240-6069:1:exon

I8G32_RS25045
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25045
old locus tag: I8G32_05007
inference: COORDINATES: similar to AA sequence:RefSeq:WP_003501107.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO process: GO:0006306 - DNA methylation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: N-6 DNA methylase
translation: MTATTRKSPTSFPRGRRLGPLVPDAPVSLQAGRVMAEAWSAQLPEQRRQHAAWSFVTEAVRSYAQAAGETLGCSLNISPVTVALTYNLNTSAAELARTLGRAACSLPIDDACYQLSACYTAMLPPALRSSQGAYYTPPALTERLLQLAEEAGVDWRTARVLDPACGGGAFLVPVAARMRRALGAIEPGRILDHFAKSLQGFEIDPFAAWLTQAWLEIAFAPELRATKRRFPAVVQVCDSLDQVLGNDRQAFDLVIGNPPYGRLKLPPAQRLRYRRSLYGHANLYGVFTDLALRWTKVGGVIAYVTPTSFFAGEYFKALRALLAREAPPLSIDFITARKGVFEGVLQEAMLATYRRGGDAAAATVHYLTLNQNGSATPDHAGIFHLPTEAAEPWLAPRTPAQQALVTRLAAMPDRLADWGYKVSTGPLVWNRFKPQLRNRPSRDVLPLIWAEAVTSDGRFIFRAQKKNHQPYFKPGPADDWLKVSTACVLVQRTTAKEQARRLIAAELPAAFIKEHGSVIVENHLNMVKPLSGKPRISPATLAAVLNSEIADQVFRCISGSVAVSAFELQALPLPNVESMAPIENLVKRKAPAAAIHEALRRLYFGDPQT
SIO_010081: I8G32_RS25045
subclass of: SO_0000673
so part of: I8G32_RS25045
location: 4240..6069
location: region:4240-6069:1
so has part: feature:4240-6069:1:exon

WP_011160372.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:4240-6069:1:exon

I8G32_RS25050
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25050
old locus tag: I8G32_05008
so part of: sequence
location: 6066..7136
location: region:6066-7136:1
so has part: feature:6066-7136:1:exon
subclass of: SO_0000010

66896005
type: Gene
SIO_000068: ncbigene

position:6066:1
position: 6066
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7136:1
position: 7136
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6066-7136:1:exon

I8G32_RS25050
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25050
old locus tag: I8G32_05008
inference: COORDINATES: similar to AA sequence:RefSeq:WP_017116034.1
GO function: GO:0003677 - DNA binding [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO process: GO:0009307 - DNA restriction-modification system [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: BsuBI/PstI family type II restriction endonuclease
translation: MTLPPLLPWPQVHERLQLIFPEGAPHRANSVWEIAARSVFVMLYVGAVEGNDIWIRPDQVTRMTDDQALRTSDAERIAWTKLSKKPSKEAAPGRWYAGNTRESIRDDTIRNSLVPNNAVIERSGLATTSSHGRYALDAAFAALFDPALSGPPFEAAAAAWQASHLSVGARMRIAVVRKGASSGTDRLLVTFPNGETRLMAPGPSSDLSRHVIEVFAPTFLGNPAVIFLSESRDKVVARDDELAKRIGLNILADKNLPDIILADLAPAHPLLVFIEVVASDGPVSEARKSALLALTDAASYPREHIAFVTVYRDRSAAQFKKTVDSLAWGSFAWFASEPAHLVELIDGGNNPRKLKS
SIO_010081: I8G32_RS25050
subclass of: SO_0000673
so part of: I8G32_RS25050
location: 6066..7136
location: region:6066-7136:1
so has part: feature:6066-7136:1:exon

WP_011160371.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6066-7136:1:exon

I8G32_RS25055
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25055
old locus tag: I8G32_05009
so part of: sequence
location: 7289..7942
location: region:7289-7942:1
so has part: feature:7289-7942:1:exon
subclass of: SO_0000010

66896006
type: Gene
SIO_000068: ncbigene

position:7289:1
position: 7289
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:7942:1
position: 7942
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7289-7942:1:exon

I8G32_RS25055
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25055
old locus tag: I8G32_05009
inference: COORDINATES: similar to AA sequence:RefSeq:WP_008960256.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: ParA family protein
translation: MKTIALVTQKGGAGKTTLAAAIAVAAMEAGESVIALDLDPQGSLAAWGDQRAKAERQSPAVDSIPADKVPHLPQILKALAGKGYTLAILDCPGVSSTATGLAMQAADLSLVPARPTRLDIQATRPTIQALLKLQRPFLFVLNQCPPVTRSGRASEAAVGLSSMGSLAEPLMVSRADYQDAIAAGQGVTEYAPSGKAAEEARELWRSIQHKLKTKAAA
SIO_010081: I8G32_RS25055
subclass of: SO_0000673
so part of: I8G32_RS25055
location: 7289..7942
location: region:7289-7942:1
so has part: feature:7289-7942:1:exon

WP_011160370.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7289-7942:1:exon

I8G32_RS25060
type: Gene
subclass of: SO_0000704
RO_0002162: 1076
locus tag: I8G32_RS25060
old locus tag: I8G32_05010
so part of: sequence
location: 7939..8250
location: region:7939-8250:1
so has part: feature:7939-8250:1:exon
subclass of: SO_0000010

66896007
type: Gene
SIO_000068: ncbigene

position:7939:1
position: 7939
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8250:1
position: 8250
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7939-8250:1:exon

I8G32_RS25060
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 1076
locus tag: I8G32_RS25060
old locus tag: I8G32_05010
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: MSQKRPSIIDTLDIAPEAEAEPATPAKPKVVKMRAPKAAPEAAPEGIEVHRTSIYVPLPAHERLREIAFVERKKVHDLIMEGIDAVIAKRGHSETAKRKPKAS
SIO_010081: I8G32_RS25060
subclass of: SO_0000673
so part of: I8G32_RS25060
location: 7939..8250
location: region:7939-8250:1
so has part: feature:7939-8250:1:exon

WP_042441899.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7939-8250:1:exon