Granulicella tundricola MP5ACTX9 plasmid pACIX903, complete sequence.
Bacteria; Acidobacteriota; Terriglobia; Terriglobales; Acidobacteriaceae; Granulicella.
Complete sequence of plasmid3 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\nCP002483.1.\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: similar to AA sequence:RefSeq:WP_013566619.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013566620.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF013753.2
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_002725006.1
GO:0004803 - transposase activity [Evidence IEA]
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020714013.1
COORDINATES: similar to AA sequence:RefSeq:WP_086558229.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013573024.1
COORDINATES: similar to AA sequence:RefSeq:WP_020715800.1
GO:0008237 - metallopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020715801.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013573047.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020713825.1
glutathione-independent formaldehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_009281229.1
COORDINATES: similar to AA sequence:RefSeq:WP_014784157.1
COORDINATES: protein motif:HMM:NF012935.2
COORDINATES: protein motif:HMM:NF025004.2
gluconate 2-dehydrogenase subunit 3 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015898140.1
COORDINATES: protein motif:HMM:NF016115.2
COORDINATES: similar to AA sequence:RefSeq:WP_019143284.1
COORDINATES: similar to AA sequence:RefSeq:WP_013568605.1
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF014385.2
COORDINATES: protein motif:HMM:NF027890.2
COORDINATES: similar to AA sequence:RefSeq:WP_011522280.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013573007.1
COORDINATES: protein motif:HMM:NF016154.2
COORDINATES: similar to AA sequence:RefSeq:WP_013573009.1
COORDINATES: similar to AA sequence:RefSeq:WP_013582180.1
COORDINATES: similar to AA sequence:RefSeq:WP_013582181.1
COORDINATES: similar to AA sequence:RefSeq:WP_013582182.1
COORDINATES: protein motif:HMM:NF016557.2
COORDINATES: similar to AA sequence:RefSeq:WP_012335393.1
COORDINATES: protein motif:HMM:NF012301.2
COORDINATES: similar to AA sequence:RefSeq:WP_020714181.1
COORDINATES: similar to AA sequence:RefSeq:WP_014266100.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013581534.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573038.1
COORDINATES: protein motif:HMM:NF014567.2
PAS domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_013572994.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573078.1
COORDINATES: similar to AA sequence:RefSeq:WP_005995515.1
COORDINATES: similar to AA sequence:RefSeq:WP_013580154.1
COORDINATES: similar to AA sequence:RefSeq:WP_014266101.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_013569479.1
COORDINATES: similar to AA sequence:RefSeq:WP_014266905.1
COORDINATES: similar to AA sequence:RefSeq:WP_012680884.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013573021.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573022.1
COORDINATES: similar to AA sequence:RefSeq:WP_008829243.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573303.1
COORDINATES: similar to AA sequence:RefSeq:WP_008367728.1
COORDINATES: similar to AA sequence:RefSeq:WP_014611549.1
COORDINATES: similar to AA sequence:RefSeq:WP_010613289.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007633164.1
COORDINATES: protein motif:HMM:NF020037.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF017183.2
COORDINATES: protein motif:HMM:NF024895.2
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF013015.2
COORDINATES: similar to AA sequence:RefSeq:WP_013573264.1
COORDINATES: similar to AA sequence:RefSeq:WP_005879711.1
UMUC domain-containing protein DNA-repair protein
COORDINATES: similar to AA sequence:RefSeq:WP_013573299.1
COORDINATES: protein motif:HMM:NF019938.2
COORDINATES: similar to AA sequence:RefSeq:WP_013570682.1
COORDINATES: similar to AA sequence:RefSeq:WP_020710027.1
COORDINATES: similar to AA sequence:RefSeq:WP_014786981.1
COORDINATES: similar to AA sequence:RefSeq:WP_020716065.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014266345.1
COORDINATES: similar to AA sequence:RefSeq:WP_016983991.1
COORDINATES: similar to AA sequence:RefSeq:WP_014784520.1
COORDINATES: protein motif:HMM:NF014626.2
COORDINATES: similar to AA sequence:RefSeq:WP_014265999.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_014266000.1
COORDINATES: similar to AA sequence:RefSeq:WP_013580866.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014265982.1
GO:0005384 - manganese ion transmembrane transporter activity [Evidence IEA]
GO:0030026 - cellular manganese ion homeostasis [Evidence IEA]
COORDINATES: protein motif:HMM:NF004785.0
COORDINATES: similar to AA sequence:RefSeq:WP_014783947.1
COORDINATES: similar to AA sequence:RefSeq:WP_014265984.1
COORDINATES: similar to AA sequence:RefSeq:WP_013567768.1
COORDINATES: protein motif:HMM:NF018604.2
COORDINATES: similar to AA sequence:RefSeq:WP_017287357.1
COORDINATES: similar to AA sequence:RefSeq:WP_007417048.1
COORDINATES: similar to AA sequence:RefSeq:WP_014265987.1
COORDINATES: similar to AA sequence:RefSeq:WP_013580885.1
GO:0004133 - glycogen debranching enzyme activity [Evidence IEA]
GO:0005980 - glycogen catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014265989.1
COORDINATES: similar to AA sequence:RefSeq:WP_014265990.1
COORDINATES: similar to AA sequence:RefSeq:WP_014265991.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0050151 - oleate hydratase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01494.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012905.2
COORDINATES: similar to AA sequence:RefSeq:WP_014265994.1
GO:0016209 - antioxidant activity [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014265995.1
COORDINATES: similar to AA sequence:RefSeq:WP_013580886.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012069674.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: protein motif:HMM:NF023390.2
COORDINATES: protein motif:HMM:NF012607.2
COORDINATES: protein motif:HMM:NF019268.2
COORDINATES: similar to AA sequence:RefSeq:WP_014501188.1
COORDINATES: similar to AA sequence:RefSeq:WP_000122735.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014786539.1
COORDINATES: similar to AA sequence:RefSeq:WP_013568890.1
COORDINATES: protein motif:HMM:NF028103.2
COORDINATES: protein motif:HMM:TIGR00621.2
COORDINATES: similar to AA sequence:RefSeq:WP_020481801.1
PDDEXK nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF018691.2
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014266944.1
COORDINATES: similar to AA sequence:RefSeq:WP_013581513.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013568917.1
VirB4 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_013573282.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_015898294.1
COORDINATES: similar to AA sequence:RefSeq:WP_013581508.1
COORDINATES: similar to AA sequence:RefSeq:WP_013570247.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573278.1
COORDINATES: similar to AA sequence:RefSeq:WP_015898289.1
COORDINATES: similar to AA sequence:RefSeq:WP_013569438.1
COORDINATES: similar to AA sequence:RefSeq:WP_017638716.1
COORDINATES: similar to AA sequence:RefSeq:WP_013581500.1
COORDINATES: similar to AA sequence:RefSeq:WP_013569433.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013570237.1
COORDINATES: similar to AA sequence:RefSeq:WP_020228721.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573042.1
COORDINATES: similar to AA sequence:RefSeq:WP_013573317.1
COORDINATES: similar to AA sequence:RefSeq:WP_012354731.1
COORDINATES: similar to AA sequence:RefSeq:WP_014255278.1
COORDINATES: protein motif:HMM:NF020279.2
cytochrome c oxidase assembly factor Coa1 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009961778.1
COORDINATES: similar to AA sequence:RefSeq:WP_020712886.1
COORDINATES: similar to AA sequence:RefSeq:WP_007252462.1
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF018305.2
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017464.2
COORDINATES: similar to AA sequence:RefSeq:WP_013569277.1
COORDINATES: similar to AA sequence:RefSeq:WP_013569276.1
COORDINATES: similar to AA sequence:RefSeq:WP_010183900.1
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020662571.1
COORDINATES: similar to AA sequence:RefSeq:WP_020712161.1
COORDINATES: similar to AA sequence:RefSeq:WP_013579815.1
COORDINATES: similar to AA sequence:RefSeq:WP_010219335.1
COORDINATES: similar to AA sequence:RefSeq:WP_020801639.1
internal stop; 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.