Cylindrospermum stagnale PCC 7417 plasmid pCYLST.02, complete sequence.
Bacteria; Cyanobacteriota; Cyanophyceae; Nostocales; Nostocaceae; Cylindrospermum.
Finished plasmid 2 of genome of Cylindrospermum stagnale PCC 7417
Submitted (04-JUN-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003644.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4091456\nSource DNA and Organism available from Cheryl A. Kerfeld\n(CKerfeld@lbl.gov)\n Contacts: Cheryl A. Kerfeld (CKerfeld@lbl.gov)\nWhole genome sequencing and draft assembly at JGI-PGF\nAnnotation by JGI-ORNL\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 :: Cylindrospermum stagnale PCC 7417\ncollection_date :: 1972\nlat_lon :: 59.332 18.064\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Sweden\nenvironment :: Missing\nnum_replicons :: 4\nref_biomaterial :: PCC 7417\nbiotic_relationship :: Free living\ntrophic_level :: Chemoheterotroph\nrel_to_oxygen :: Aerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release), VELVET v.\n 1.0.13, Parallel phrap v. 4.24 SPS\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi05619\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: Prodigal, GenePRIMP\nIsolation Site :: Soil, greenhouse, Stockholm, Sweden, 1972\nTemperature Range :: Mesophile\nGram Staining :: Gram-\nDiseases :: None\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3 (pre-release), VELVET v.\n 1.0.13, Parallel phrap v. 4.24 SPS\nGenome Coverage :: 30x\nSequencing Technology :: 454/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/03/2023 01:59:06\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) :: 6,575\nCDSs (total) :: 6,485\nGenes (coding) :: 6,298\nCDSs (with protein) :: 6,298\nGenes (RNA) :: 90\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 74\nncRNAs :: 4\nPseudo Genes (total) :: 187\nCDSs (without protein) :: 187\nPseudo Genes (ambiguous residues) :: 0 of 187\nPseudo Genes (frameshifted) :: 60 of 187\nPseudo Genes (incomplete) :: 131 of 187\nPseudo Genes (internal stop) :: 38 of 187\nPseudo Genes (multiple problems) :: 35 of 187\nCRISPR Arrays :: 10\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Soil, greenhouse, Stockholm, Sweden, 1972
COORDINATES: similar to AA sequence:RefSeq:WP_015364327.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_016953793.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364324.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_005650108.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015364320.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953800.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364318.1
COORDINATES: similar to AA sequence:RefSeq:WP_006196492.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006196493.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364314.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364313.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611326.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015186392.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186393.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186394.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186395.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015186396.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953817.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186398.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186399.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009630579.1
COORDINATES: similar to AA sequence:RefSeq:WP_006422811.1
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_012407368.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016953818.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364298.1
GO:0000166 - nucleotide binding [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015173899.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_015364295.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015208730.1
COORDINATES: similar to AA sequence:RefSeq:WP_017654896.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364293.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953829.1
COORDINATES: similar to AA sequence:RefSeq:WP_017749287.1
COORDINATES: similar to AA sequence:RefSeq:WP_017313955.1
COORDINATES: similar to AA sequence:RefSeq:WP_017654893.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017653118.1
GO:0003678 - DNA helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017654891.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953838.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015364280.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364279.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953841.1
COORDINATES: protein motif:HMM:NF013964.2
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF019984.2
group II intron maturase-specific domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017307605.1
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_016877593.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_017656191.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015129462.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186426.1
GO:0016020 - membrane [Evidence IEA]; GO:0046930 - pore complex [Evidence IEA]
GO:0015093 - ferrous iron transmembrane transporter activity [Evidence IEA]
GO:0033212 - iron import into cell [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017745666.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076611097.1
COORDINATES: similar to AA sequence:RefSeq:WP_015933337.1
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_015364312.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011317973.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_015163197.1
cation transporter dimerization domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015364310.1
COORDINATES: similar to AA sequence:RefSeq:WP_017655731.1
COORDINATES: similar to AA sequence:RefSeq:WP_017307554.1
COORDINATES: similar to AA sequence:RefSeq:WP_016877572.1
COORDINATES: similar to AA sequence:RefSeq:WP_017307563.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_015158981.1
COORDINATES: protein motif:HMM:NF024242.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Ada metal-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019497124.1
GO:0015116 - sulfate transmembrane transporter activity [Evidence IEA]
GO:0008272 - sulfate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF015029.2
COORDINATES: similar to AA sequence:RefSeq:WP_015364250.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364249.1
COORDINATES: similar to AA sequence:RefSeq:WP_010993925.1
COORDINATES: similar to AA sequence:RefSeq:WP_016877475.1
two-component system response regulator RppA
COORDINATES: similar to AA sequence:RefSeq:WP_019497169.1
two-component system sensor histidine kinase RppB
COORDINATES: similar to AA sequence:RefSeq:WP_006196472.1
COORDINATES: similar to AA sequence:RefSeq:WP_015180559.1
COORDINATES: similar to AA sequence:RefSeq:WP_009787766.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
reverse transcriptase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016869173.1
COORDINATES: similar to AA sequence:RefSeq:WP_017314029.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186448.1
GO:0003886 - DNA (cytosine-5-)-methyltransferase activity [Evidence IEA]; GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: protein motif:HMM:NF013691.2
COORDINATES: similar to AA sequence:RefSeq:WP_010994014.1
COORDINATES: similar to AA sequence:RefSeq:WP_010994015.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011153874.1
multiubiquitin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017299806.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574262.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015186453.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186454.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186455.1
COORDINATES: similar to AA sequence:RefSeq:WP_010993836.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953847.1
COORDINATES: similar to AA sequence:RefSeq:WP_017307666.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF020305.2
TnsA endonuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016948799.1
COORDINATES: similar to AA sequence:RefSeq:WP_017307665.1
COORDINATES: similar to AA sequence:RefSeq:WP_015186457.1
COORDINATES: similar to AA sequence:RefSeq:WP_017741147.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953669.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364363.1
COORDINATES: similar to AA sequence:RefSeq:WP_015130727.1
COORDINATES: similar to AA sequence:RefSeq:WP_015196268.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016864074.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015081665.1
COORDINATES: similar to AA sequence:RefSeq:WP_015081666.1
GO:0015074 - DNA integration [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016953740.1
COORDINATES: similar to AA sequence:RefSeq:WP_017313912.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953742.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953743.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364348.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364347.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953746.1
COORDINATES: similar to AA sequence:RefSeq:WP_019497712.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953748.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953749.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015364342.1
COORDINATES: similar to AA sequence:RefSeq:WP_019495045.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364341.1
COORDINATES: similar to AA sequence:RefSeq:WP_017307147.1
COORDINATES: similar to AA sequence:RefSeq:WP_012122688.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
type III-B CRISPR module RAMP protein Cmr4
COORDINATES: protein motif:HMM:TIGR02682.1
GO:0005575 - cellular_component [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015364337.1
COORDINATES: similar to AA sequence:RefSeq:WP_012031878.1
type III-B CRISPR module RAMP protein Cmr1
COORDINATES: similar to AA sequence:RefSeq:WP_016877671.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364335.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364334.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364333.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953786.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364331.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364330.1
COORDINATES: similar to AA sequence:RefSeq:WP_015364329.1
COORDINATES: similar to AA sequence:RefSeq:WP_016953791.1