Ilyobacter polytropus DSM 2926 plasmid pILYOP02, complete sequence.
Bacteria; Fusobacteriota; Fusobacteriia; Fusobacteriales; Fusobacteriaceae; Ilyobacter.
Complete genome sequence of Ilyobacter polytropus type strain (CuHbu1)
The complete plasmid2 of Ilyobacter polytrpous DSM 2926
Submitted (18-OCT-2010) US DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP002283.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4085717\nSource DNA and organism available from Hans-Peter Klenk at the\nGerman Collection of Microorganisms and Cell Cultures (DSMZ)\n(hans-peter.klenk@dsmz.de)\nContacts: Jonathan A. Eisen (jaeisen@ucdavis.edu)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LANL\nAnnotation by JGI-ORNL and JGI-PGF\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 :: Ilyobacter polytropus CuHBu1, DSM 2926\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Germany\nenvironment :: Marine\nnum_replicons :: 1\nref_biomaterial :: DSM 2926\nbiotic_relationship :: Free living\ntrophic_level :: Chemoorganotroph\nrel_to_oxygen :: Anaerobe\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi02536\nType Strain :: Yes\nFunding Program :: DOE-GEBA 2007\nGene Calling Method :: Prodigal, GenePRIMP\nIsolation Site :: Marine mud from Germany\nCell Shape :: Rod-shaped\nMotility :: Nonmotile\nSporulation :: Nonsporulating\nTemperature Range :: Mesophile\nTemperature Optimum :: 30C\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\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 02:11:53\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) :: 3,063\nCDSs (total) :: 2,955\nGenes (coding) :: 2,932\nCDSs (with protein) :: 2,932\nGenes (RNA) :: 108\nrRNAs :: 10, 8, 8 (5S, 16S, 23S)\ncomplete rRNAs :: 10, 8, 8 (5S, 16S, 23S)\ntRNAs :: 79\nncRNAs :: 3\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 7 of 23\nPseudo Genes (incomplete) :: 15 of 23\nPseudo Genes (internal stop) :: 4 of 23\nPseudo Genes (multiple problems) :: 2 of 23\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF022077.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014904200.1
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
nucleotidyltransferase domain-containing protein
COORDINATES: protein motif:HMM:NF014043.2
COORDINATES: similar to AA sequence:RefSeq:WP_013387401.1
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity [Evidence IEA]
GGDEF domain-containing phosphodiesterase
COORDINATES: similar to AA sequence:RefSeq:WP_013387325.1
COORDINATES: nucleotide motif:Rfam:14.4:RF01051
cyclic di-GMP riboswitch class I; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013388733.1
COORDINATES: similar to AA sequence:RefSeq:WP_013135111.1
GO:0008168 - methyltransferase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005951609.1
GO:0005506 - iron ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013388878.1
COORDINATES: similar to AA sequence:RefSeq:WP_013387527.1
GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0016661 - oxidoreductase activity, acting on other nitrogenous compounds as donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012058496.1
COORDINATES: similar to AA sequence:RefSeq:WP_013388879.1
tetratricopeptide domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008011886.1
COORDINATES: similar to AA sequence:RefSeq:WP_013387232.1
COORDINATES: protein motif:HMM:NF019351.2
GO:0005507 - copper ion binding [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005009483.1
frameshifted; internal stop; 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:NF024864.2
COORDINATES: similar to AA sequence:RefSeq:WP_020405305.1
carboxymuconolactone decarboxylase family protein
COORDINATES: protein motif:HMM:NF012621.2
COORDINATES: protein motif:HMM:NF012612.2
COORDINATES: similar to AA sequence:RefSeq:WP_005949556.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_005489076.1
COORDINATES: protein motif:HMM:NF012738.2
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0006826 - iron ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008498225.1
Fe(3+) ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF013132.2
GO:0005886 - plasma membrane [Evidence IEA]
GO:0008509 - monoatomic anion transmembrane transporter activity [Evidence IEA]
GO:0006820 - monoatomic anion transport [Evidence IEA]
DASS family sodium-coupled anion symporter
COORDINATES: similar to AA sequence:RefSeq:WP_002073964.1
GO:0004020 - adenylylsulfate kinase activity [Evidence IEA]
GO:0006790 - sulfur compound metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011928319.1
adenylyl-sulfate reductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_015393055.1
COORDINATES: similar to AA sequence:RefSeq:WP_014313517.1
GO:0009336 - sulfate adenylyltransferase complex (ATP) [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0004781 - sulfate adenylyltransferase (ATP) activity [Evidence IEA]
GO:0070814 - hydrogen sulfide biosynthetic process [Evidence IEA]; GO:0019419 - sulfate reduction [Evidence IEA]
sulfate adenylyltransferase subunit CysD
COORDINATES: similar to AA sequence:RefSeq:WP_013278893.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0003924 - GTPase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015171985.1
GO:0051213 - dioxygenase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
class III extradiol ring-cleavage dioxygenase
COORDINATES: protein motif:HMM:NF016121.2
COORDINATES: protein motif:HMM:NF013068.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
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:NF017534.2
COORDINATES: similar to AA sequence:RefSeq:WP_005957372.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF020036.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00254.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010520896.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]; GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_013389259.1
COORDINATES: similar to AA sequence:RefSeq:WP_019262209.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: protein motif:HMM:NF013579.2
COORDINATES: similar to AA sequence:RefSeq:WP_009266597.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: similar to AA sequence:RefSeq:WP_014559586.1
COORDINATES: similar to AA sequence:RefSeq:WP_020588557.1
COORDINATES: similar to AA sequence:RefSeq:WP_007951733.1
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: similar to AA sequence:RefSeq:WP_003495892.1
COORDINATES: similar to AA sequence:RefSeq:WP_017755004.1
COORDINATES: similar to AA sequence:RefSeq:WP_011878730.1
COORDINATES: similar to AA sequence:RefSeq:WP_017895072.1
COORDINATES: protein motif:HMM:NF037521.2
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF018152.2
COORDINATES: protein motif:HMM:NF015354.2
COORDINATES: similar to AA sequence:RefSeq:WP_006323635.1
HI0074 family nucleotidyltransferase substrate-binding subunit
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF014581.2
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008800951.1
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: protein motif:HMM:NF040179.1
zonular occludens toxin domain-containing protein
COORDINATES: protein motif:HMM:NF033516.0
Conjugal transfer/entry exclusion protein
COORDINATES: protein motif:HMM:NF016491.2
GO:0030255 - protein secretion by the type IV secretion system [Evidence IEA]
COORDINATES: protein motif:HMM:NF021981.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010968273.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013387465.1
COORDINATES: similar to AA sequence:RefSeq:WP_019038320.1
COORDINATES: similar to AA sequence:RefSeq:WP_013360432.1
COORDINATES: similar to AA sequence:RefSeq:WP_013387945.1
COORDINATES: similar to AA sequence:RefSeq:WP_012465865.1
COORDINATES: protein motif:HMM:NF014981.2
COORDINATES: similar to AA sequence:RefSeq:WP_015812324.1
COORDINATES: protein motif:HMM:NF014021.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017020.2
COORDINATES: similar to AA sequence:RefSeq:WP_013725793.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014820.2
COORDINATES: protein motif:HMM:NF024212.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020588282.1
COORDINATES: similar to AA sequence:RefSeq:WP_019999221.1
COORDINATES: similar to AA sequence:RefSeq:WP_007062411.1
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:NF014126.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0071705 - nitrogen compound transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF013539.2
GO:0097367 - carbohydrate derivative binding [Evidence IEA]
GO:1901135 - carbohydrate derivative metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012145190.1
COORDINATES: similar to AA sequence:RefSeq:WP_018395016.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013386936.1
GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013405094.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF013200.2
GO:0009055 - electron transfer activity [Evidence IEA]
electron transfer flavoprotein subunit beta/FixA family protein
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
electron transfer flavoprotein subunit alpha/FixB family protein
COORDINATES: protein motif:HMM:NF016000.2
COORDINATES: similar to AA sequence:RefSeq:WP_016361838.1
2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
COORDINATES: similar to AA sequence:RefSeq:WP_003365739.1
GO:0008697 - 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity [Evidence IEA]
GO:0045490 - pectin catabolic process [Evidence IEA]
5-dehydro-4-deoxy-D-glucuronate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_002569694.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008721406.1
COORDINATES: similar to AA sequence:RefSeq:WP_005899851.1
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF019349.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011022934.1
PDDEXK nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF024806.2