Halopiger xanaduensis SH-6 plasmid pHALXA03, complete sequence.
Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Natrialbales; Natrialbaceae; Halopiger.
Complete sequence of plasmid 3 of Halopiger xanaduensis SH-6
Submitted (03-JUN-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002842.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4091189\nSource DNA and organism available from Iain Anderson\n(ijanderson@lbl.gov)\nContacts: Iain Anderson (ijanderson@lbl.gov)\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 :: Halopiger xanaduensis SH-6\ncollection_date :: Missing\nlat_lon :: 43.2 114.016\ndepth :: Missing\nalt_elev :: Missing\ncountry :: China\nenvironment :: Soil, Salinewater\nnum_replicons :: 4\nref_biomaterial :: DSM 18323\nbiotic_relationship :: Free living\ntrophic_level :: Missing\nrel_to_oxygen :: Missing\nisol_growth_condt :: 17625165\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi05995\nType Strain :: Yes\nFunding Program :: DOE-CSP 2010\nIsolation Site :: Sediment of saline Lake Shangmatala in Inner\n Mongolia, China\nCell Shape :: Pleomorphic-shaped\nMotility :: Nonmotile\nTemperature Range :: Mesophile\nTemperature Optimum :: 37C\nSalinity :: Halophile\npH :: 7.5 - 8.0\nGram Staining :: Gram-\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 :: 454/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/02/2023 02:17:40\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) :: 4,320\nCDSs (total) :: 4,258\nGenes (coding) :: 4,198\nCDSs (with protein) :: 4,198\nGenes (RNA) :: 62\nrRNAs :: 4, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 3, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 2\nPseudo Genes (total) :: 60\nCDSs (without protein) :: 60\nPseudo Genes (ambiguous residues) :: 0 of 60\nPseudo Genes (frameshifted) :: 30 of 60\nPseudo Genes (incomplete) :: 36 of 60\nPseudo Genes (internal stop) :: 11 of 60\nPseudo Genes (multiple problems) :: 15 of 60\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_006671477.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF014409.2
COORDINATES: protein motif:HMM:NF017011.2
COORDINATES: similar to AA sequence:RefSeq:WP_004057905.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946232.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_012946231.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430213.1
orc1/cdc6 family replication initiation protein
COORDINATES: similar to AA sequence:RefSeq:WP_013879138.1
COORDINATES: similar to AA sequence:RefSeq:WP_006885453.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012946216.1
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012946215.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430235.1
COORDINATES: similar to AA sequence:RefSeq:WP_008011897.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430241.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_006107531.1
COORDINATES: similar to AA sequence:RefSeq:WP_006665524.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430249.1
COORDINATES: similar to AA sequence:RefSeq:WP_008451546.1
COORDINATES: similar to AA sequence:RefSeq:WP_006665519.1
COORDINATES: similar to AA sequence:RefSeq:WP_007189735.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946194.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187065.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187067.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187068.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946187.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430266.1
COORDINATES: similar to AA sequence:RefSeq:WP_015321117.1
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006673610.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187074.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF024873.2
ribonuclease H-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012946176.1
COORDINATES: similar to AA sequence:RefSeq:WP_006430278.1
COORDINATES: similar to AA sequence:RefSeq:WP_007737620.1
COORDINATES: protein motif:HMM:NF025577.2
COORDINATES: similar to AA sequence:RefSeq:WP_006187093.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187091.1
COORDINATES: similar to AA sequence:RefSeq:WP_008451502.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187087.1
COORDINATES: similar to AA sequence:RefSeq:WP_004048220.1
COORDINATES: similar to AA sequence:RefSeq:WP_007188075.1
COORDINATES: similar to AA sequence:RefSeq:WP_004214276.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006665492.1
COORDINATES: similar to AA sequence:RefSeq:WP_007139939.1
helix-hairpin-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006665491.1
COORDINATES: similar to AA sequence:RefSeq:WP_006665490.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111405.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946163.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111401.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111400.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111399.1
COORDINATES: similar to AA sequence:RefSeq:WP_006665484.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111386.1
COORDINATES: similar to AA sequence:RefSeq:WP_006665482.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946156.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946155.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111378.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946147.1
COORDINATES: similar to AA sequence:RefSeq:WP_012946146.1
COORDINATES: similar to AA sequence:RefSeq:WP_006671474.1
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012946144.1