Allocoleopsis franciscana PCC 7113 plasmid pMIC7113.04, complete sequence.
Allocoleopsis franciscana PCC 7113 (Microcoleus sp. PCC 7113)
Bacteria; Cyanobacteriota; Cyanophyceae; Oscillatoriophycideae; Oscillatoriales; Coleofasciculaceae; Allocoleopsis; Allocoleopsis franciscana.
Finished plasmid 4 of genome of Microcoleus sp. PCC 7113
Submitted (01-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\nCP003634.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089897\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 :: Microcoleus sp. PCC 7113\ncollection_date :: 1971\nlat_lon :: 37.774 122.419\ndepth :: Missing\nalt_elev :: Missing\ncountry :: USA\nenvironment :: Soil\nnum_replicons :: 9\nref_biomaterial :: PCC 7113, ATCC 29206\nbiotic_relationship :: Free living\ntrophic_level :: Chemoheterotroph\nrel_to_oxygen :: Anaerobe\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 :: Gi05876\nType Strain :: No\nFunding Program :: DOE-GEBA 2009\nGene Calling Method :: GenePrimp, Prodigal 1.4\nIsolation Site :: Soil, orchid house, San Francisco, USA, 1971\nMotility :: Motile\nTemperature Range :: Mesophile\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 :: 02/05/2023 19:26:01\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) :: 6,773\nCDSs (total) :: 6,686\nGenes (coding) :: 6,571\nCDSs (with protein) :: 6,571\nGenes (RNA) :: 87\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 71\nncRNAs :: 4\nPseudo Genes (total) :: 115\nCDSs (without protein) :: 115\nPseudo Genes (ambiguous residues) :: 0 of 115\nPseudo Genes (frameshifted) :: 37 of 115\nPseudo Genes (incomplete) :: 84 of 115\nPseudo Genes (internal stop) :: 3 of 115\nPseudo Genes (multiple problems) :: 9 of 115\nCRISPR Arrays :: 11\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Soil, orchid house, San Francisco, USA, 1971
reference strain of Allocoleopsis franciscana
COORDINATES: similar to AA sequence:RefSeq:WP_013313399.1
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_012412053.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_015185455.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006098269.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612115.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
ISKra4-like element ISMic1 family transposase
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015182548.1
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_006198663.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_006198662.1
COORDINATES: similar to AA sequence:RefSeq:WP_009786246.1
COORDINATES: similar to AA sequence:RefSeq:WP_017292326.1
COORDINATES: similar to AA sequence:RefSeq:WP_020710111.1
GO:0004066 - asparagine synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0006529 - asparagine biosynthetic process [Evidence IEA]
asparagine synthase (glutamine-hydrolyzing)
COORDINATES: similar to AA sequence:RefSeq:WP_015217614.1
COORDINATES: similar to AA sequence:RefSeq:WP_009630953.1
COORDINATES: similar to AA sequence:RefSeq:WP_015184907.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017740966.1
TnsA endonuclease N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017740967.1
GO:0015074 - DNA integration [Evidence IEA]
DDE-type integrase/transposase/recombinase
COORDINATES: similar to AA sequence:RefSeq:WP_017740968.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_017299072.1
CDP-alcohol phosphatidyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007354631.1
COORDINATES: similar to AA sequence:RefSeq:WP_002803482.1
COORDINATES: protein motif:HMM:NF013124.2
COORDINATES: protein motif:HMM:NF013328.2
DNA-formamidopyrimidine glycosylase family protein
COORDINATES: protein motif:HMM:NF024367.2
COORDINATES: protein motif:HMM:NF024986.2
COORDINATES: similar to AA sequence:RefSeq:WP_015188489.1
COORDINATES: protein motif:HMM:NF025056.2
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015131460.1
COORDINATES: protein motif:HMM:NF024816.2
COORDINATES: similar to AA sequence:RefSeq:WP_006509991.1
COORDINATES: similar to AA sequence:RefSeq:WP_017316806.1
COORDINATES: protein motif:HMM:NF017834.2
COORDINATES: protein motif:HMM:NF012464.2
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_015186210.1
COORDINATES: protein motif:HMM:NF013561.2
ribbon-helix-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015186814.1