Metamycoplasma orale strain NCTC10112 plasmid 4.
type: Entry
definition: Metamycoplasma orale strain NCTC10112 plasmid 4.
sequence version: NZ_LR214943.1
sequence date: 2023-05-01
sequence: sequence
division: CON
label: NZ_LR214943.1
type: RefSeq
SIO_000068: refseq
dblink: PRJNA224116
dblink: SAMEA4384073
keyword: RefSeq
source: Metamycoplasma orale (Mycoplasma orale)
organism: Metamycoplasma orale
taxonomy: Bacteria; Mycoplasmatota; Mycoplasmoidales; Metamycoplasmataceae; Metamycoplasma.
reference: 1
comment: REFSEQ INFORMATION: The reference sequence is identical to\nLR214943.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/01/2023 02:13:08\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 733\nCDSs (total) :: 692\nGenes (coding) :: 672\nCDSs (with protein) :: 672\nGenes (RNA) :: 41\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 35\nncRNAs :: 3\nPseudo Genes (total) :: 20\nCDSs (without protein) :: 20\nPseudo Genes (ambiguous residues) :: 0 of 20\nPseudo Genes (frameshifted) :: 11 of 20\nPseudo Genes (incomplete) :: 11 of 20\nPseudo Genes (internal stop) :: 1 of 20\nPseudo Genes (multiple problems) :: 2 of 20\n##Genome-Annotation-Data-END##

sequence
subclass of: SO_0000155
sequence length: 9771
topology: linear
so has quality: SO_0000987
location: 1..9771
location: region:1-9771:1
RO_0002162: 2121

NZ_LR214943
type: RefSeq
SIO_000068: refseq

PRJNA224116
type: BioProject
SIO_000068: bioproject

SAMEA4384073
type: BioSample
SIO_000068: biosample

1
title: Direct Submission
journal: Submitted (24-JAN-2019) WTSI, Pathogen Informatics, Wellcome Trust Sanger Institute, CB10 1SA, United Kingdom

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

position:9771:1
position: 9771
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

feature:1-9771:1:source
so part of: sequence
organism: Metamycoplasma orale
mol type: genomic DNA
strain: NCTC10112
serovar: not available: to be reported later
isolation source: Oropharynx
host: Homo sapiens
culture collection: NCTC:10112
type material: type strain of Mycoplasma orale
plasmid: 4
country: USA: Washington DC
collection date: 1900/1967

2121
type: Taxonomy
SIO_000068: taxonomy

EXC29_RS07250
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
locus tag: EXC29_RS07250
old locus tag: NCTC10112_00711
so part of: sequence
location: complement(114..1766)
location: region:114-1766:-1
so has part: feature:114-1766:-1:exon
subclass of: SO_0000010

position:114:-1
position: 114
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:1766:-1
position: 1766
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:114-1766:-1:exon

EXC29_RS07250
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
locus tag: EXC29_RS07250
old locus tag: NCTC10112_00711
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MKKTKPLFLTHKTKIILWSVLSVLLFSFFIFILIVRITSPFKVSIYNYESYLSLNVISKIKKEYSYHTFGEINEFTKAINTNKAVAGIGSDHQIAQLIIDNKIQKFDLKKIFGEDKENKFGGDYKKYIYSYYEEILAKHLDNYDKKIIEIIQQKNPNNIKNRAHLIYQNEVDEKNKVNPIAYDANGDGKADYFYEYLVPYFIQDKLIVYNTNKKYKPHLKGSDDIIKADLNNKETWLDIIQTLIKKYNYKRVHWTNSYLDNAMIGEFYATEENKKNYLNNGIVENLTMNNYREIIDYFVEFVQEATGHSIKDANYNKLVTSGLDLVHDIIEPTTTKADIAIMYNGDALDSYYAEDNFASLKDVQINYKRPKNNYMLLDAWIISKTVSKDEVDKLTNFLRDNVLVGTTYTKEDFHKKYFYNVFNKISATNKYTENDLMNYLFNDNDFLKPKDVNELNKDFFKENHEIFQDSFDFCDATENFNAVNYTPALSNLNRFLEKFYFKDENLEDDQVAMDIFKIENSSKVYHQSYQPLDLKLRTAMNDYYFEKTKS
SIO_010081: EXC29_RS07250
subclass of: SO_0000673
so part of: EXC29_RS07250
location: complement(114..1766)
location: region:114-1766:-1
so has part: feature:114-1766:-1:exon

WP_022936274.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:114-1766:-1:exon

EXC29_RS03470
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
gene: era
locus tag: EXC29_RS03470
old locus tag: NCTC10112_00712
pseudo: true
so part of: sequence
location: complement(1766..2652)
location: region:1766-2652:-1
so has part: feature:1766-2652:-1:exon
subclass of: SO_0000010

position:2652:-1
position: 2652
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:1766-2652:-1:exon

EXC29_RS03470
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
gene: era
locus tag: EXC29_RS03470
old locus tag: NCTC10112_00712
inference: COORDINATES: similar to AA sequence:RefSeq:WP_012498373.1
GO function: GO:0005525 - GTP binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
note: frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
pseudo: true
codon start: 1
transl table: 4
product: GTPase Era
SIO_010081: EXC29_RS03470
subclass of: SO_0000673
so part of: EXC29_RS03470
location: complement(1766..2652)
location: region:1766-2652:-1
so has part: feature:1766-2652:-1:exon

urn:…
SIO_000300: 1
SIO_000628: feature:1766-2652:-1:exon

EXC29_RS03475
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
gene: ybeY
locus tag: EXC29_RS03475
old locus tag: NCTC10112_00714
so part of: sequence
location: complement(2655..3113)
location: region:2655-3113:-1
so has part: feature:2655-3113:-1:exon
subclass of: SO_0000010

position:2655:-1
position: 2655
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:3113:-1
position: 3113
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:2655-3113:-1:exon

EXC29_RS03475
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
gene: ybeY
locus tag: EXC29_RS03475
old locus tag: NCTC10112_00714
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002881602.1
GO function: GO:0046872 - metal ion binding [Evidence IEA]; GO:0004540 - ribonuclease activity [Evidence IEA]
GO process: GO:0042254 - ribosome biogenesis [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: rRNA maturation RNase YbeY
translation: METKNVLFENKSFSSFDFIDEFNEILNLSIKEFDLKTKIPLHVDLLFVTRFKMKKLNNLHRQKNYATDVLSFPFLSDDLDFLEYLPIGQIIICPYIIKKHAKEFNHSVKREYCYMFTHGVAHLLGYDHQTEEEAKVMNEHVENIMTKMNIKR
SIO_010081: EXC29_RS03475
subclass of: SO_0000673
so part of: EXC29_RS03475
location: complement(2655..3113)
location: region:2655-3113:-1
so has part: feature:2655-3113:-1:exon

WP_022936272.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:2655-3113:-1:exon

EXC29_RS03480
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
locus tag: EXC29_RS03480
old locus tag: NCTC10112_00715
so part of: sequence
location: complement(3290..5143)
location: region:3290-5143:-1
so has part: feature:3290-5143:-1:exon
subclass of: SO_0000010

position:3290:-1
position: 3290
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:5143:-1
position: 5143
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:3290-5143:-1:exon

EXC29_RS03480
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
locus tag: EXC29_RS03480
old locus tag: NCTC10112_00715
inference: COORDINATES: protein motif:HMM:NF012670.2
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MGCLQQQKFYNLVQNFCPSLDNIKINSLALIKKANLNDYGLALSAAKIMHALFAYNLNYNLQNHKWVNRDRLIIANSSFLPTYYATARLAKLLTKKEEANFENILNTKIDFIDSSLETYQNNLGSAFSNAVGMAIAENILNNKFNEVKHSIYVLCNDFDLLSGEAQEALSLAANLKLKNLIIISNSTEVLRDSLLSTISNENVAAKYKAMKINYQRIANRISKINYAISKAKVSSKPTIIEIKTTIGENMKYENSTLIYENKLTDADINELKEKLTYKKSNNLDVYKECNDFYKTTYKLRLEKTCKAFKMSKKLQTFLFEESKLNLNDIAINSKLSIPALFGTIIENISNKYQNSIFCTANTINITNIKNSNNMYAPNNISGTNLLLGPRTSILGNVANGINLHSNFVAIASDILDNFALFLESFKLARQMNLKTIFLLSNINELNKNDNIQELRALSNNLYMPLSLNEIKTTIENIFNETANKLPSIIVINEAKNQELLSLIDEKHENNSMYYLIKKIPMTYSLISSSLNIEMAYEIALKLKLSLIYATNLKNIDLNYDKNKTISIENTNFEQWTNLAKYNIGNNNLNTFATSKQKPELINFNIEEITKIVEKLIK
SIO_010081: EXC29_RS03480
subclass of: SO_0000673
so part of: EXC29_RS03480
location: complement(3290..5143)
location: region:3290-5143:-1
so has part: feature:3290-5143:-1:exon

WP_129619179.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:3290-5143:-1:exon

EXC29_RS07255
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
locus tag: EXC29_RS07255
old locus tag: NCTC10112_00716
so part of: sequence
location: complement(5107..6381)
location: region:5107-6381:-1
so has part: feature:5107-6381:-1:exon
subclass of: SO_0000010

position:5107:-1
position: 5107
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6381:-1
position: 6381
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:5107-6381:-1:exon

EXC29_RS07255
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
locus tag: EXC29_RS07255
old locus tag: NCTC10112_00716
inference: COORDINATES: similar to AA sequence:RefSeq:WP_013729261.1
GO function: GO:0004803 - transposase activity [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: IS3 family transposase
translation: MGRQLKINEWLQVFDLYENYKNNKISKRAFEYEYLKICGSNKIFNRYVIRWIKIKIKKYNLGMNIESKTGKSPKKGKGSGRPRKKFPLQEIENRKRALKEISKEDLEWIVDEFYYDEILKKYNTDSIEEVIKKIKNKKNLSTTIKNIIDILGIKKSTFYYKLKHLGQLKREKKVTYEEEIREAFKECKGRYGRERLSLLLKKKYKININPRTLGRNMNKLGLFCEVRQRKRKRENKNLNVKFKNLVKRDYDGIYNDVYATDVTYIPSPKDVYENHVYLSVIIQHRTKKVISWNLSKVNDNNLVLDHFKHTIFPTTEKFIIHSDHGIQYSSQEFVSFINSINGVISMSRIGNSLDNREIEYFFSILKTEIFPNFYQTVKTLTFIELKNKIKEFIDWYNNERFLKKFNLKTPQELWDVYNNKNFTI
SIO_010081: EXC29_RS07255
subclass of: SO_0000673
so part of: EXC29_RS07255
location: complement(5107..6381)
location: region:5107-6381:-1
so has part: feature:5107-6381:-1:exon

WP_232017758.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:5107-6381:-1:exon

EXC29_RS03490
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
locus tag: EXC29_RS03490
old locus tag: NCTC10112_00717
so part of: sequence
location: complement(6489..6839)
location: region:6489-6839:-1
so has part: feature:6489-6839:-1:exon
subclass of: SO_0000010

position:6489:-1
position: 6489
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:6839:-1
position: 6839
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6489-6839:-1:exon

EXC29_RS03490
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
locus tag: EXC29_RS03490
old locus tag: NCTC10112_00717
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MLEEHKKDLDLEKTEYININAKMNLVFKIEKNVIYNEINKIFANYSDIILTKDIEIKINDKKNNIEIFINFKMRNFKDFSKLVKQIILAIEQKIIILTNSKPLNINLVFEGLENEN
SIO_010081: EXC29_RS03490
subclass of: SO_0000673
so part of: EXC29_RS03490
location: complement(6489..6839)
location: region:6489-6839:-1
so has part: feature:6489-6839:-1:exon

WP_022936270.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6489-6839:-1:exon

EXC29_RS03495
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
gene: efp
locus tag: EXC29_RS03495
old locus tag: NCTC10112_00718
so part of: sequence
location: complement(6823..7380)
location: region:6823-7380:-1
so has part: feature:6823-7380:-1:exon
subclass of: SO_0000010

position:6823:-1
position: 6823
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:7380:-1
position: 7380
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:6823-7380:-1:exon

EXC29_RS03495
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
gene: efp
locus tag: EXC29_RS03495
old locus tag: NCTC10112_00718
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002880875.1
GO component: GO:0005737 - cytoplasm [Evidence IEA]
GO function: GO:0003746 - translation elongation factor activity [Evidence IEA]
GO process: GO:0006414 - translational elongation [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: elongation factor P
translation: MISVNDLRPGTTFQLDGSIFVCLEFSHSKQGRGQANVKIKSKDLRTGAITVKTFTGGEKVEKAMIDKVTMDFLYNAGDNIVLMDSETFEQIEIPTANVQWEMNFLKEGQKVTVRKFNSEVLDIELPANVSLKVTSSPDAVKGNTAQAAQKKVIVETGFEVETPLFIKEGEIILISTETGKYVGRA
SIO_010081: EXC29_RS03495
subclass of: SO_0000673
so part of: EXC29_RS03495
location: complement(6823..7380)
location: region:6823-7380:-1
so has part: feature:6823-7380:-1:exon

WP_022936269.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:6823-7380:-1:exon

EXC29_RS03500
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
gene: nadE
locus tag: EXC29_RS03500
old locus tag: NCTC10112_00719
so part of: sequence
location: 7512..8273
location: region:7512-8273:1
so has part: feature:7512-8273:1:exon
subclass of: SO_0000010

position:7512:1
position: 7512
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

position:8273:1
position: 8273
reference: sequence
type: ForwardStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:7512-8273:1:exon

EXC29_RS03500
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
gene: nadE
locus tag: EXC29_RS03500
old locus tag: NCTC10112_00719
EC number: 6.3.1.5
inference: COORDINATES: similar to AA sequence:RefSeq:WP_002880873.1
GO component: GO:0005737 - cytoplasm [Evidence IEA]
GO function: GO:0008795 - NAD+ synthase activity [Evidence IEA]
GO process: GO:0009435 - NAD biosynthetic process [Evidence IEA]
note: Derived by automated computational analysis using gene prediction method: Protein Homology.
codon start: 1
transl table: 4
product: NAD(+) synthase
translation: MNYLNIDQNLSTKKQKQYTIFIKKVKNWISQKVASAKASGITLGLSGGIDSSVLAILCDEVFPKNAYFYYFEIKEDKKTKKDLEELAKHLKNEIKIINLKNEYESLAKTLSIKDKLSKANLKSRLYMSSLYALSQEKNTLVIGTDNYDEYFLGYFTKYGDGGCDLLPFANINKTQVYVLANMLDIPECIIKKEPSANLYPNQTDEKELGFNYETFELWKRDCNLVSKEINDKIIKLHKTSEHKRNLIPKGPKL
SIO_010081: EXC29_RS03500
subclass of: SO_0000673
so part of: EXC29_RS03500
location: 7512..8273
location: region:7512-8273:1
so has part: feature:7512-8273:1:exon

WP_022936268.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:7512-8273:1:exon

EXC29_RS07260
type: Gene
subclass of: SO_0000704
RO_0002162: 2121
locus tag: EXC29_RS07260
old locus tag: NCTC10112_00720
so part of: sequence
location: complement(8505..9710)
location: region:8505-9710:-1
so has part: feature:8505-9710:-1:exon
subclass of: SO_0000010

position:8505:-1
position: 8505
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

position:9710:-1
position: 9710
reference: sequence
type: ReverseStrandPosition
type: ExactPosition

urn:…
SIO_000300: 1
SIO_000628: feature:8505-9710:-1:exon

EXC29_RS07260
type: Coding Sequence
subclass of: SO_0000316
RO_0002162: 2121
locus tag: EXC29_RS07260
old locus tag: NCTC10112_00720
inference: COORDINATES: ab initio prediction:GeneMarkS-2+
note: Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
codon start: 1
transl table: 4
product: hypothetical protein
translation: MFLLPPNNFIDSYNYKVSESFNEQKENYKLISQIVNAKMKAYTLIYRTGVGHIYDTPRTEKKVADNSVLNNNPIWLDIVRSKDQNSGSLILKISKDIMKRNLILKINDKKCDISKRSEKENQFVWEISKFENGYLINFEDIKSIDIASYDRHRDSYALSFGFTIYNMSFTNKETSAKSLASSNQNIIFRQIQKISYKINNSSMDTTLLEDRNSQIYSFETKLHFNNFEKNKRLHEFAEICYANREIKSNTIVHLDYEDISHFELESIALKFNDTIKQLNFKKIKIDNEAEDPSKKYIQQYSIFLSDKYKYDNSTKSWIEDAEYGENGCQLPLTFYGNLGVLVKFKNYYNSETHSFNINSTFETPIFDKENGDIKLSIQKKLLNEKWRELEKNQNWKFYNLD
SIO_010081: EXC29_RS07260
subclass of: SO_0000673
so part of: EXC29_RS07260
location: complement(8505..9710)
location: region:8505-9710:-1
so has part: feature:8505-9710:-1:exon

WP_022936267.1
type: Protein
SIO_000068: ncbiprotein

urn:…
SIO_000300: 1
SIO_000628: feature:8505-9710:-1:exon