Thioflavicoccus mobilis 8321 plasmid pTHIMO01, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; Thioflavicoccus.
Complete sequence of plasmid of Thioflavicoccus mobilis 8321
Submitted (09-SEP-2011) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003052.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4090915\nSource DNA and organism available from Donald A. Bryant\n(dab14@psu.edu)\nContacts: Donald A. Bryant (dab14@psu.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 :: Thioflavicoccus mobilis 8321\ncollection_date :: Missing\nlat_lon :: 41.526 -70.673\ndepth :: Missing\nalt_elev :: Missing\ncountry :: USA\nenvironment :: Marsh, Mat\nnum_replicons :: 2\nref_biomaterial :: ATCC 700959\nbiotic_relationship :: Missing\ntrophic_level :: Missing\nrel_to_oxygen :: Missing\nisol_growth_condt :: 11211246\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi06843\nType Strain :: Yes\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: GenePrimp 1.4, Prodigal\nIsolation Site :: flat, laminated microbial mat in a salt\n marsh near Woods Hole, Massachusetts, USA.\nCell Shape :: Coccus-shaped\nMotility :: Motile\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 :: 05/03/2023 01:11:57\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) :: 3,721\nCDSs (total) :: 3,664\nGenes (coding) :: 3,589\nCDSs (with protein) :: 3,589\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 75\nCDSs (without protein) :: 75\nPseudo Genes (ambiguous residues) :: 0 of 75\nPseudo Genes (frameshifted) :: 26 of 75\nPseudo Genes (incomplete) :: 60 of 75\nPseudo Genes (internal stop) :: 15 of 75\nPseudo Genes (multiple problems) :: 24 of 75\nCRISPR Arrays :: 3\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
flat, laminated microbial mat in a salt marsh
COORDINATES: similar to AA sequence:RefSeq:WP_011417544.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007192777.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009147190.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:TIGR00238.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016853 - isomerase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF019121.2
ATP-grasp enzyme, D-alanine-D-alanine ligase
COORDINATES: protein motif:HMM:NF014476.2
COORDINATES: protein motif:HMM:TIGR03945.1
GO:0030170 - pyridoxal phosphate binding [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
2,3-diaminopropionate biosynthesis protein SbnA
COORDINATES: similar to AA sequence:RefSeq:WP_015802946.1
diaminobutyrate--2-oxoglutarate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_006122509.1
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.
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015281876.1
COORDINATES: similar to AA sequence:RefSeq:WP_006119137.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_086558016.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017842785.1
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_000796541.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017524.2
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_007041943.1
COORDINATES: similar to AA sequence:RefSeq:WP_013964480.1
GO:0051983 - regulation of chromosome segregation [Evidence IEA]
type II toxin-antitoxin system ParD family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_018440969.1
GO:0008657 - DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity [Evidence IEA]; GO:0042803 - protein homodimerization activity [Evidence IEA]
GO:0030541 - plasmid partitioning [Evidence IEA]; GO:0051290 - protein heterotetramerization [Evidence IEA]
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_016487841.1
COORDINATES: protein motif:HMM:NF024554.2
GO:0006260 - DNA replication [Evidence IEA]
DUF3991 and TOPRIM domain-containing protein
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_017113439.1
COORDINATES: similar to AA sequence:RefSeq:WP_005965336.1
COORDINATES: similar to AA sequence:RefSeq:WP_007290786.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972391.1
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024039.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:TIGR00929.1
VirB4 family type IV secretion/conjugal transfer ATPase
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF038091.1
COORDINATES: protein motif:HMM:TIGR02788.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF019069.2
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: protein motif:HMM:NF025056.2
COORDINATES: similar to AA sequence:RefSeq:WP_018443219.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005963073.1
COORDINATES: protein motif:HMM:NF013122.2
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012979572.1
COORDINATES: protein motif:HMM:NF012307.2
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013219021.1
GO:0004176 - ATP-dependent peptidase activity [Evidence IEA]
GO:0030163 - protein catabolic process [Evidence IEA]
BREX system Lon protease-like protein BrxL
COORDINATES: protein motif:HMM:NF020249.2
COORDINATES: protein motif:HMM:NF023276.2
COORDINATES: similar to AA sequence:RefSeq:WP_011142654.1
COORDINATES: similar to AA sequence:RefSeq:WP_004146425.1
COORDINATES: protein motif:HMM:NF021564.2
COORDINATES: similar to AA sequence:RefSeq:WP_017836440.1
COORDINATES: similar to AA sequence:RefSeq:WP_004146424.1
COORDINATES: protein motif:HMM:NF033441.0
COORDINATES: protein motif:HMM:NF020329.2
COORDINATES: protein motif:HMM:NF020425.2
COORDINATES: protein motif:HMM:NF033447.1