Granulicella tundricola MP5ACTX9 plasmid pACIX904, complete sequence.
Bacteria; Acidobacteriota; Terriglobia; Terriglobales; Acidobacteriaceae; Granulicella.
Complete sequence of plasmid4 of Granulicella sp. MP5ACTX9
Submitted (24-JAN-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002484.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4088693\nSource DNA and organism available from Max M. Haggblom\n(haggblom@aesop.rutgers.edu)\nContacts: Max M. Haggblom (haggblom@aesop.rutgers.edu)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Granulicella sp. MP5ACTX9\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Acid mine\nnum_replicons :: 6\nref_biomaterial :: Missing\nbiotic_relationship :: Missing\ntrophic_level :: Chemoorganotroph\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi06612\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: Glimmer\nGram Staining :: Gram-\nPhenotypes :: Acidophile\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: WGS\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/29/2022 02:35:13\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) :: 4,705\nCDSs (total) :: 4,652\nGenes (coding) :: 4,604\nCDSs (with protein) :: 4,604\nGenes (RNA) :: 53\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 4\nPseudo Genes (total) :: 48\nCDSs (without protein) :: 48\nPseudo Genes (ambiguous residues) :: 0 of 48\nPseudo Genes (frameshifted) :: 17 of 48\nPseudo Genes (incomplete) :: 33 of 48\nPseudo Genes (internal stop) :: 14 of 48\nPseudo Genes (multiple problems) :: 16 of 48\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF033594.2
GO:0004803 - transposase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF026041.2
COORDINATES: protein motif:HMM:NF033550.5
COORDINATES: similar to AA sequence:RefSeq:WP_014263497.1
toxin-antitoxin system subunit antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018935906.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013581713.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013581714.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573047.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013581171.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
phosphoglucomutase/phosphomannomutase family protein
COORDINATES: protein motif:HMM:NF014724.2
COORDINATES: protein motif:HMM:NF013652.2
COORDINATES: similar to AA sequence:RefSeq:WP_013566929.1
GO:0016765 - transferase activity, transferring alkyl or aryl (other than methyl) groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF014686.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF025114.2
NAD(P)-binding domain-containing protein
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF019421.2
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014266336.1
COORDINATES: protein motif:HMM:NF016670.2
COORDINATES: similar to AA sequence:RefSeq:WP_013573267.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_086558189.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014784027.1
COORDINATES: similar to AA sequence:RefSeq:WP_018914791.1
putative addiction module antidote protein
COORDINATES: similar to AA sequence:RefSeq:WP_015744737.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015472933.1
COORDINATES: similar to AA sequence:RefSeq:WP_006458453.1
COORDINATES: similar to AA sequence:RefSeq:WP_013651357.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013578890.1
COORDINATES: similar to AA sequence:RefSeq:WP_013579180.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016876069.1
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: protein motif:HMM:NF012859.2
COORDINATES: similar to AA sequence:RefSeq:WP_013573187.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558108.1
COORDINATES: similar to AA sequence:RefSeq:WP_013568494.1
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_014265810.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013578680.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_013578679.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014265809.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: similar to AA sequence:RefSeq:WP_006099699.1
glycoside hydrolase family 99-like domain-containing protein
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF021616.2
COORDINATES: similar to AA sequence:RefSeq:WP_013568504.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF021134.2
COORDINATES: protein motif:HMM:NF014606.2
polysaccharide biosynthesis/export family protein
COORDINATES: protein motif:HMM:NF014732.2
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
Wzz/FepE/Etk N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013227.2
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: protein motif:HMM:TIGR03025.1
COORDINATES: protein motif:HMM:NF024831.2
COORDINATES: protein motif:HMM:NF039499.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573241.1