Candidatus Riesia pediculicola USDA plasmid pPAN, complete sequence.
type: Entry
definition: Candidatus Riesia pediculicola USDA plasmid pPAN, complete sequence.
sequence version: NC_013962.1
sequence date: 2022-12-21
sequence: sequence
division: CON
label: NC_013962.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMN02603451
keyword: RefSeq
source: Candidatus Riesia pediculicola USDA
organism: Candidatus Riesia pediculicola USDA
taxonomy: Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Candidatus Riesia.
reference: 1
reference: 2
comment: REFSEQ INFORMATION: The reference sequence is identical to\nCP001086.1.\nSource of DNA used for sequencing: First instar of Pediculus\nhumanus corporis strain USDA, from lab of John Clark, University of\nMassachusetts, Amherst, MA 01003.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/21/2022 00:45:06\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) :: 519\nCDSs (total) :: 478\nGenes (coding) :: 468\nCDSs (with protein) :: 468\nGenes (RNA) :: 41\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 33\nncRNAs :: 2\nPseudo Genes (total) :: 10\nCDSs (without protein) :: 10\nPseudo Genes (ambiguous residues) :: 0 of 10\nPseudo Genes (frameshifted) :: 1 of 10\nPseudo Genes (incomplete) :: 9 of 10\nPseudo Genes (internal stop) :: 1 of 10\nPseudo Genes (multiple problems) :: 1 of 10\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.

sequence
subclass of: SO_0000155
sequence length: 7737
topology: circular
so has quality: SO_0000988
location: 1..7737
location: region:1-7737:1
RO_0002162: 515618

NC_013962
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMN02603451
type: BioSample
SIO_000068: biosample

1
title: Genome sequence of Riesia pediculicola USDA
author: Kirkness, E.F.
journal: Unpublished

2
title: Direct Submission
author: Kirkness, E.F.
journal: Submitted (19-MAY-2008) The J. Craig Venter Institute, Rockville, MD 20850, USA

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

position:7737:1
position: 7737
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-7737:1:source
so part of: sequence
organism: Candidatus Riesia pediculicola USDA
mol type: genomic DNA
strain: USDA
host: Pediculus humanus corporis
plasmid: pPAN

515618
type: Taxonomy
SIO_000068: taxonomy

RIEPE_RS02595
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
gene: panB
locus tag: RIEPE_RS02595
old locus tag: RIEPE_A0001
so part of: sequence
location: 117..974
location: region:117-974:1
so has part: feature:117-974:1:exon
subclass of: SO_0000010

position:117:1
position: 117
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:974:1
position: 974
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:117-974:1:exon

RIEPE_RS02595
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
gene: panB
locus tag: RIEPE_RS02595
old locus tag: RIEPE_A0001
EC number: 2.1.2.11
inference: COORDINATES: similar to AA sequence:RefSeq:WP_005181535.1
GO function: GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity [Evidence IEA]
GO process: GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: 3-methyl-2-oxobutanoate hydroxymethyltransferase
translation: MKKNPKLNTTIEDIRIWKKNSSKFAALTAYDAAFSRMFWKEGIEVMLIGDSLGMTVQGKSSTVSVTTKEIAYHTKMVRRGAPMAWLISDLPFMSFFNLDQACRNASVLIRAGANMVKLEGGSWLCPTVERLSERSVSVCGHVGLTPQSINIIGSHRVQGMDSSSYRRILSDAKSLESSGIQILVLECIPNELTYEISQSLSIPTIGIGAGPSTDGQILVMHDIFGIDTGLSVRPRFVRNFLSESGGDFRKAISLFKESVRSGDFPRSDHCFRIGSGKVRDFKGNF
SIO_010081: RIEPE_RS02595
subclass of: SO_0000673
so part of: RIEPE_RS02595
location: 117..974
location: region:117-974:1
so has part: feature:117-974:1:exon

WP_013034927.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:117-974:1:exon

RIEPE_RS02600
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
gene: panC
locus tag: RIEPE_RS02600
old locus tag: RIEPE_A0002
so part of: sequence
location: 976..1836
location: region:976-1836:1
so has part: feature:976-1836:1:exon
subclass of: SO_0000010

position:976:1
position: 976
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:1836:1
position: 1836
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:976-1836:1:exon

RIEPE_RS02600
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
gene: panC
locus tag: RIEPE_RS02600
old locus tag: RIEPE_A0002
inference: COORDINATES: protein motif:HMM:TIGR00018.1
GO function: GO:0004592 - pantoate-beta-alanine ligase activity [Evidence IEA]
GO process: GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: pantoate--beta-alanine ligase
translation: MFLEKSIISCRKKLNSVSCPIIFVPTMGNLHEGHLRMISFAKKRRSSDFLVVSIFVNPIQFEREEDYISYPRTIDSDLRLLDALGVVDLVFFPEESQMYPNGTSRITLVNHPISEELEGFFRPGHFSGVGTILVKFFNIIRPSYLYLGEKDYQQLLMVRKLVIDLDYPLKVVGFPIVRDKEGLAYSSRNSLLSKEERLVAFRLNSTLNEVVEQFTSKNLLSEKDLSRHFQRRISRFGFVVESFLVRDSLSLLPISSDSRKVIFLASVWLGSVRLIDNKCVSMNSHT
SIO_010081: RIEPE_RS02600
subclass of: SO_0000673
so part of: RIEPE_RS02600
location: 976..1836
location: region:976-1836:1
so has part: feature:976-1836:1:exon

WP_013034929.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:976-1836:1:exon

RIEPE_RS02605
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02605
old locus tag: RIEPE_A0004
so part of: sequence
location: 1948..2406
location: region:1948-2406:1
so has part: feature:1948-2406:1:exon
subclass of: SO_0000010

position:1948:1
position: 1948
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:2406:1
position: 2406
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1948-2406:1:exon

RIEPE_RS02605
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02605
old locus tag: RIEPE_A0004
inference: COORDINATES: similar to AA sequence:RefSeq:WP_011520248.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: Hsp20 family protein
translation: MVYRPFSLMPILGEDLLSDRFTQMDKLFSRITGAKPLSEFPSYDLKQKGKDRFELIVSVPGYRKEELDISLLQDKLMIKGTVISSTSSEEEKKHSFKWLHRGIERKNFSISFDLDHKVQINQSVLKDGLLKLDFSYEIPEKEKPKKISIDQS
SIO_010081: RIEPE_RS02605
subclass of: SO_0000673
so part of: RIEPE_RS02605
location: 1948..2406
location: region:1948-2406:1
so has part: feature:1948-2406:1:exon

WP_041855293.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:1948-2406:1:exon

RIEPE_RS02760
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02760
so part of: sequence
location: complement(2341..2544)
location: region:2341-2544:-1
so has part: feature:2341-2544:-1:exon
subclass of: SO_0000010

position:2341:-1
position: 2341
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:2544:-1
position: 2544
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2341-2544:-1:exon

RIEPE_RS02760
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02760
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013034923.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: hypothetical protein
translation: MLEGYENLGTSSEGLGGRRRVGQGGWMQGRDFLLRHPSDKKSKVSRSTLIDRNLLRFFFFWNLVTEI
SIO_010081: RIEPE_RS02760
subclass of: SO_0000673
so part of: RIEPE_RS02760
location: complement(2341..2544)
location: region:2341-2544:-1
so has part: feature:2341-2544:-1:exon

WP_081440605.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2341-2544:-1:exon

RIEPE_RS02610
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02610
old locus tag: RIEPE_A0005
so part of: sequence
location: complement(2684..3523)
location: region:2684-3523:-1
so has part: feature:2684-3523:-1:exon
subclass of: SO_0000010

position:2684:-1
position: 2684
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3523:-1
position: 3523
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2684-3523:-1:exon

RIEPE_RS02610
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02610
old locus tag: RIEPE_A0005
inference: COORDINATES: protein motif:HMM:NF021637.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiator protein A
translation: MNFRDEIFTMEHPIFSLRGGDKKMRKYINFRNKSTIEIVPSRWGSATIFDKDMWIYITSKLVRDLDENKKIRRTISFVPHDFFRSTNRDSGGRSYVELKRTLSRLSGTRIEICQIGTNGKMNIVEFGLIDQWKIISKMDRKKGNFHSSKTISITIPEWLYERIIQHRVLQINKRYFSIRKAMERRLYEIARKHCGLQKKFTISLKRLHEKIGSHSCLNAFKHKIYSSSIQQKEERTLPDYVISIEKSTNQVTFRREGAKNELLFSQIKKLEKKSEQSSR
SIO_010081: RIEPE_RS02610
subclass of: SO_0000673
so part of: RIEPE_RS02610
location: complement(2684..3523)
location: region:2684-3523:-1
so has part: feature:2684-3523:-1:exon

WP_013034920.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2684-3523:-1:exon

RIEPE_RS02615
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02615
old locus tag: RIEPE_A0006
so part of: sequence
location: complement(3543..3722)
location: region:3543-3722:-1
so has part: feature:3543-3722:-1:exon
subclass of: SO_0000010

position:3543:-1
position: 3543
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3722:-1
position: 3722
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3543-3722:-1:exon

RIEPE_RS02615
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02615
old locus tag: RIEPE_A0006
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: MLEGYENLGTSSEGLGGRRRVGQGGWMQGRDFLLRHPSDKKSKVSRSTLIDRNLLRFNR
SIO_010081: RIEPE_RS02615
subclass of: SO_0000673
so part of: RIEPE_RS02615
location: complement(3543..3722)
location: region:3543-3722:-1
so has part: feature:3543-3722:-1:exon

WP_013034923.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3543-3722:-1:exon

RIEPE_RS02620
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02620
old locus tag: RIEPE_A0007
so part of: sequence
location: complement(3862..4701)
location: region:3862-4701:-1
so has part: feature:3862-4701:-1:exon
subclass of: SO_0000010

position:3862:-1
position: 3862
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4701:-1
position: 4701
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3862-4701:-1:exon

RIEPE_RS02620
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02620
old locus tag: RIEPE_A0007
inference: COORDINATES: protein motif:HMM:NF021637.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: replication initiator protein A
translation: MNFRDEIFTMEHPIFSLRGGDKKMRKYINFRNKSTIEIVPSRWGSATIFDKDMWIYITSKLVRDLDENKKIRRTISFVPHDFFRSTNRDSGGRSYVELKRTLSRLSGTRIEICQIGTNGKMNIVEFGLIDQWKIISKMDRKKGNFHSSKTISITIPEWLYERIIQHRVLQINKRYFSIRKAMERRLYEIARKHCGLQKKFTISLKRLHEKIGSHSCLNAFKHKIYSSSIQQKEERTLPDYVISIEKSTNQVTFRREGAKNELLFSQIKKLEKKSEQSSR
SIO_010081: RIEPE_RS02620
subclass of: SO_0000673
so part of: RIEPE_RS02620
location: complement(3862..4701)
location: region:3862-4701:-1
so has part: feature:3862-4701:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:3862-4701:-1:exon

RIEPE_RS02625
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02625
old locus tag: RIEPE_A0008
so part of: sequence
location: complement(4721..4900)
location: region:4721-4900:-1
so has part: feature:4721-4900:-1:exon
subclass of: SO_0000010

position:4721:-1
position: 4721
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:4900:-1
position: 4900
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:4721-4900:-1:exon

RIEPE_RS02625
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02625
old locus tag: RIEPE_A0008
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: MLEGYENLGTSSEGLGGRRRVGQGGWMQGRDFLLRHPSDKKSKVSRSTLIDRNLLRFNR
SIO_010081: RIEPE_RS02625
subclass of: SO_0000673
so part of: RIEPE_RS02625
location: complement(4721..4900)
location: region:4721-4900:-1
so has part: feature:4721-4900:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:4721-4900:-1:exon

RIEPE_RS02630
type: Gene
subclass of: SO_0000704
RO_0002162: 515618
locus tag: RIEPE_RS02630
old locus tag: RIEPE_A0009
so part of: sequence
location: complement(5040..5969)
location: region:5040-5969:-1
so has part: feature:5040-5969:-1:exon
subclass of: SO_0000010

position:5040:-1
position: 5040
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5969:-1
position: 5969
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5040-5969:-1:exon

RIEPE_RS02630
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 515618
locus tag: RIEPE_RS02630
old locus tag: RIEPE_A0009
EC number: 1.1.1.169
inference: COORDINATES: protein motif:HMM:TIGR00745.1
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 11
product: 2-dehydropantoate 2-reductase
translation: MKDLRNDPIKITVLGCGCIGKLWLSSLASTKHFVQGWTKEKIHKTLKFKIKSIDGRKHHISVPINNRRKLRESHLLIVTLKAWQVSKEISKVICDLNDHCILLLIHNGMGVLEELPKKIKQPIIEGNTTHASHYQNDYVKHVAWGETCIGPANRKAKKFPMIASTLNQIFPKVIWCKNIRFFNWKKLAINCSINPLSSIYRCQNGKLLKLATHQINRICQEVSSIMKREGFSEIDARSLFRSTIDVIDSTSKNFSSMYQDLLNRKKSEIDYINGYVIKRAKHFQIKVPENELLFSQIKKLEKKSEQSSR
SIO_010081: RIEPE_RS02630
subclass of: SO_0000673
so part of: RIEPE_RS02630
location: complement(5040..5969)
location: region:5040-5969:-1
so has part: feature:5040-5969:-1:exon

WP_013034926.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5040-5969:-1:exon