Halopiger xanaduensis SH-6 plasmid pHALXA02, complete sequence.
Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Natrialbales; Natrialbaceae; Halopiger.
Complete sequence of plasmid 2 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\nCP002841.1.\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_007143083.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014053094.1
COORDINATES: similar to AA sequence:RefSeq:WP_014053095.1
COORDINATES: similar to AA sequence:RefSeq:WP_006184775.1
COORDINATES: similar to AA sequence:RefSeq:WP_008457989.1
COORDINATES: similar to AA sequence:RefSeq:WP_008444896.1
COORDINATES: similar to AA sequence:RefSeq:WP_010904033.1
COORDINATES: similar to AA sequence:RefSeq:WP_009762230.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006093032.1
COORDINATES: similar to AA sequence:RefSeq:WP_004968227.1
COORDINATES: similar to AA sequence:RefSeq:WP_007143091.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010904232.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013881810.1
COORDINATES: similar to AA sequence:RefSeq:WP_004971372.1
COORDINATES: similar to AA sequence:RefSeq:WP_004977669.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012289744.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007273776.1
COORDINATES: similar to AA sequence:RefSeq:WP_011222291.1
COORDINATES: similar to AA sequence:RefSeq:WP_007107559.1
COORDINATES: similar to AA sequence:RefSeq:WP_007142746.1
COORDINATES: similar to AA sequence:RefSeq:WP_006651702.1
COORDINATES: similar to AA sequence:RefSeq:WP_006884211.1
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_007143100.1
COORDINATES: similar to AA sequence:RefSeq:WP_009488220.1
COORDINATES: similar to AA sequence:RefSeq:WP_006183460.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR04474.1
COORDINATES: similar to AA sequence:RefSeq:WP_014030602.1
COORDINATES: similar to AA sequence:RefSeq:WP_006078726.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003824 - catalytic activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004060441.1
COORDINATES: similar to AA sequence:RefSeq:WP_006054782.1
COORDINATES: similar to AA sequence:RefSeq:WP_006054783.1
COORDINATES: similar to AA sequence:RefSeq:WP_006825217.1
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_007143101.1
COORDINATES: similar to AA sequence:RefSeq:WP_007977256.1
COORDINATES: similar to AA sequence:RefSeq:WP_006054543.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012600.2
transcription initiation factor IIB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014865019.1
COORDINATES: similar to AA sequence:RefSeq:WP_006653182.1
COORDINATES: similar to AA sequence:RefSeq:WP_009487145.1
COORDINATES: protein motif:HMM:NF013277.2
COORDINATES: similar to AA sequence:RefSeq:WP_013881832.1
COORDINATES: similar to AA sequence:RefSeq:WP_004043407.1
COORDINATES: similar to AA sequence:RefSeq:WP_008444947.1
COORDINATES: similar to AA sequence:RefSeq:WP_004594499.1
COORDINATES: similar to AA sequence:RefSeq:WP_006183361.1
COORDINATES: similar to AA sequence:RefSeq:WP_004048585.1
COORDINATES: similar to AA sequence:RefSeq:WP_013875818.1
COORDINATES: similar to AA sequence:RefSeq:WP_008580586.1
COORDINATES: similar to AA sequence:RefSeq:WP_015911446.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024784.2
HNH endonuclease signature motif containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006112452.1
metal ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006883124.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
metal ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_015790295.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008849224.1
metal-dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008458763.1
COORDINATES: similar to AA sequence:RefSeq:WP_006183343.1
COORDINATES: similar to AA sequence:RefSeq:WP_006183342.1
COORDINATES: similar to AA sequence:RefSeq:WP_004517739.1
COORDINATES: similar to AA sequence:RefSeq:WP_006183341.1
COORDINATES: similar to AA sequence:RefSeq:WP_013881869.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008446344.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422485.1
orc1/cdc6 family replication initiation protein
COORDINATES: similar to AA sequence:RefSeq:WP_006825220.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
DNA polymerase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004048351.1
COORDINATES: similar to AA sequence:RefSeq:WP_004966492.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667188.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012945283.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006111137.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012945285.1
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004048654.1
COORDINATES: similar to AA sequence:RefSeq:WP_007981700.1
GO:0016783 - sulfurtransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014863928.1
rhodanese-like domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006114975.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892556.1
GO:0032559 - adenyl ribonucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006066811.1
COORDINATES: similar to AA sequence:RefSeq:WP_008388501.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422815.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008422813.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892555.1
COORDINATES: similar to AA sequence:RefSeq:WP_008453948.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892553.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422924.1
COORDINATES: similar to AA sequence:RefSeq:WP_015300178.1
COORDINATES: similar to AA sequence:RefSeq:WP_007189213.1
GO:0016208 - AMP binding [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007693163.1
COORDINATES: similar to AA sequence:RefSeq:WP_006650739.1
COORDINATES: similar to AA sequence:RefSeq:WP_015298644.1
twin-arginine translocation signal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007143485.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006088442.1
COORDINATES: similar to AA sequence:RefSeq:WP_006179435.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422774.1
COORDINATES: similar to AA sequence:RefSeq:WP_007107578.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007140796.1
COORDINATES: similar to AA sequence:RefSeq:WP_004214322.1
COORDINATES: similar to AA sequence:RefSeq:WP_015300019.1
COORDINATES: similar to AA sequence:RefSeq:WP_004214328.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422783.1
COORDINATES: similar to AA sequence:RefSeq:WP_004267008.1
COORDINATES: similar to AA sequence:RefSeq:WP_008163141.1
COORDINATES: similar to AA sequence:RefSeq:WP_008423678.1
GO:0030554 - adenyl nucleotide binding [Evidence IEA]; GO:0008888 - glycerol dehydrogenase [NAD+] activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007258674.1
COORDINATES: similar to AA sequence:RefSeq:WP_015322814.1
GO:0016853 - isomerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008419737.1
COORDINATES: similar to AA sequence:RefSeq:WP_004267007.1
COORDINATES: similar to AA sequence:RefSeq:WP_007739973.1
COORDINATES: similar to AA sequence:RefSeq:WP_006180700.1
COORDINATES: similar to AA sequence:RefSeq:WP_008422788.1
COORDINATES: similar to AA sequence:RefSeq:WP_005576489.1
COORDINATES: similar to AA sequence:RefSeq:WP_006088406.1
COORDINATES: similar to AA sequence:RefSeq:WP_006053938.1
COORDINATES: similar to AA sequence:RefSeq:WP_007700385.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004595175.1
COORDINATES: similar to AA sequence:RefSeq:WP_006182375.1
COORDINATES: similar to AA sequence:RefSeq:WP_012945328.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892537.1
GO:0005384 - manganese ion transmembrane transporter activity [Evidence IEA]
GO:0030026 - cellular manganese ion homeostasis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008453971.1
COORDINATES: similar to AA sequence:RefSeq:WP_006092932.1
COORDINATES: similar to AA sequence:RefSeq:WP_007107580.1
GO:0005388 - P-type calcium transporter activity [Evidence IEA]
GO:0006816 - calcium ion transport [Evidence IEA]
calcium-translocating P-type ATPase, PMCA-type
COORDINATES: similar to AA sequence:RefSeq:WP_008014743.1
COORDINATES: protein motif:HMM:NF012780.2
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_012945314.1
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015323316.1
COORDINATES: similar to AA sequence:RefSeq:WP_007261650.1
COORDINATES: similar to AA sequence:RefSeq:WP_007259193.1
COORDINATES: similar to AA sequence:RefSeq:WP_015320603.1
bacterio-opsin activator domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012945336.1
COORDINATES: similar to AA sequence:RefSeq:WP_006087860.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_006650508.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006667180.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667179.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006667178.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667177.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667176.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111127.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007143725.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892522.1
COORDINATES: similar to AA sequence:RefSeq:WP_007143724.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667182.1
bifunctional metallophosphatase/5'-nucleotidase
COORDINATES: similar to AA sequence:RefSeq:WP_012945355.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006087850.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667165.1
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007143721.1
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006111121.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667162.1
COORDINATES: similar to AA sequence:RefSeq:WP_008383592.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006650526.1
COORDINATES: similar to AA sequence:RefSeq:WP_006667575.1
COORDINATES: similar to AA sequence:RefSeq:WP_014555977.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006667151.1
COORDINATES: similar to AA sequence:RefSeq:WP_012945357.1
COORDINATES: similar to AA sequence:RefSeq:WP_006650528.1
COORDINATES: similar to AA sequence:RefSeq:WP_008892502.1
COORDINATES: protein motif:HMM:NF016831.2
COORDINATES: similar to AA sequence:RefSeq:WP_012945363.1
GO:0005267 - potassium channel activity [Evidence IEA]
GO:0034220 - monoatomic ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006431758.1
COORDINATES: similar to AA sequence:RefSeq:WP_014865459.1
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_013879090.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008419694.1
COORDINATES: similar to AA sequence:RefSeq:WP_013881969.1
GO:0000166 - nucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006650532.1
COORDINATES: similar to AA sequence:RefSeq:WP_006431764.1
COORDINATES: similar to AA sequence:RefSeq:WP_006091024.1
COORDINATES: similar to AA sequence:RefSeq:WP_013881973.1
COORDINATES: similar to AA sequence:RefSeq:WP_007741191.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111098.1
COORDINATES: similar to AA sequence:RefSeq:WP_006179406.1
GO:0006817 - phosphate ion transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006431770.1
COORDINATES: similar to AA sequence:RefSeq:WP_004966622.1
COORDINATES: similar to AA sequence:RefSeq:WP_006187446.1
COORDINATES: similar to AA sequence:RefSeq:WP_006111093.1
COORDINATES: similar to AA sequence:RefSeq:WP_012945379.1
COORDINATES: similar to AA sequence:RefSeq:WP_006068046.1
COORDINATES: similar to AA sequence:RefSeq:WP_013878928.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0005215 - transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF036897.2
COORDINATES: similar to AA sequence:RefSeq:WP_006433044.1
COORDINATES: similar to AA sequence:RefSeq:WP_010890501.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.