Euzebya pacifica strain DY32-46 plasmid pEDY32-46I, complete sequence.
Bacteria; Actinomycetota; Nitriliruptoria; Euzebyales.
Complete genome sequence of Euzebya sp. DY32-46 isolated from seawater of Pacific Ocean
Submitted (07-SEP-2018) College of Life Sciences, Zhejiang Sci-Tech University, Street 2, Hangzhou, Zhejiang 310000, China
Submitted (20-JUL-2018) College of Life Sciences, Zhejiang Sci-Tech University, Street 2, Hangzhou, Zhejiang 310000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP031166.1.\nBacteria and source DNA available from Second Institute of\nOceanography, State Oceanic Administration, PR China.\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##Genome-Assembly-Data-START##\nAssembly Method :: Celera Assembler v. 8.3; Pbdagcon v.\n MAY-2018; GATK v. 4.0.2.0; SOAPindel v. 2\nAssembly Name :: ESDY_1.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 204.0x\nSequencing Technology :: PacBio RSII; Illumina HiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/05/2023 01:57:58\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) :: 5,638\nCDSs (total) :: 5,549\nGenes (coding) :: 5,519\nCDSs (with protein) :: 5,519\nGenes (RNA) :: 89\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 80\nncRNAs :: 3\nPseudo Genes (total) :: 30\nCDSs (without protein) :: 30\nPseudo Genes (ambiguous residues) :: 0 of 30\nPseudo Genes (frameshifted) :: 7 of 30\nPseudo Genes (incomplete) :: 26 of 30\nPseudo Genes (internal stop) :: 2 of 30\nPseudo Genes (multiple problems) :: 4 of 30\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF021378.2
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: protein motif:HMM:NF016047.2
cell wall-binding repeat-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015798153.1
GO:0003676 - nucleic acid binding [Evidence IEA]; GO:0004523 - RNA-DNA hybrid ribonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012772.2
GO:0071111 - cyclic-guanylate-specific phosphodiesterase activity [Evidence IEA]; GO:0052621 - diguanylate cyclase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
bifunctional diguanylate cyclase/phosphodiesterase
GGDEF domain-containing phosphodiesterase
COORDINATES: protein motif:HMM:NF024776.2
helix-turn-helix domain-containing protein
GO:0004518 - nuclease activity [Evidence IEA]
GO:0042546 - cell wall biogenesis [Evidence IEA]
COORDINATES: protein motif:HMM:NF025602.2
COORDINATES: protein motif:HMM:NF025447.2
COORDINATES: similar to AA sequence:RefSeq:WP_013126520.1
GO:0004170 - dUTP diphosphatase activity [Evidence IEA]; GO:0000287 - magnesium ion binding [Evidence IEA]
GO:0006226 - dUMP biosynthetic process [Evidence IEA]; GO:0046081 - dUTP catabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00621.2
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: protein motif:HMM:NF014533.2
GO:0009294 - DNA-mediated transformation [Evidence IEA]
COORDINATES: protein motif:HMM:NF015692.2
GO:0016799 - hydrolase activity, hydrolyzing N-glycosyl compounds [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
ADP-ribosylglycohydrolase family protein
COORDINATES: protein motif:HMM:TIGR00663.1
GO:0009360 - DNA polymerase III complex [Evidence IEA]
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012787245.1
COORDINATES: protein motif:HMM:NF037501.2
Swt1 family HEPN domain-containing protein
COORDINATES: protein motif:HMM:NF014520.2
COORDINATES: protein motif:HMM:NF014566.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
GO:0071586 - CAAX-box protein processing [Evidence IEA]
CPBP family intramembrane metalloprotease
COORDINATES: similar to AA sequence:RefSeq:WP_018949030.1
COORDINATES: protein motif:HMM:NF019575.2
prepilin-type N-terminal cleavage/methylation domain-containing protein
dual specificity protein phosphatase family protein
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024423.2
COORDINATES: protein motif:HMM:NF017183.2
COORDINATES: protein motif:HMM:NF013593.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01587.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: protein motif:HMM:NF021030.2
type I-E CRISPR-associated protein Cse1/CasA
COORDINATES: protein motif:HMM:NF021034.2
type I-E CRISPR-associated protein Cse2/CasB
COORDINATES: protein motif:HMM:NF020902.2
GO:0003674 - molecular_function [Evidence IEA]
type I-E CRISPR-associated protein Cas7/Cse4/CasC
COORDINATES: protein motif:HMM:NF021240.2
type I-E CRISPR-associated protein Cas5/CasD
COORDINATES: protein motif:HMM:NF020377.2
type I-E CRISPR-associated protein Cas6/Cse3/CasE
COORDINATES: protein motif:HMM:NF013984.2
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
GO:0051607 - defense response to virus [Evidence IEA]; GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: protein motif:HMM:NF021242.2
GO:0004521 - endoribonuclease activity [Evidence IEA]
type I-E CRISPR-associated endoribonuclease Cas2e
COORDINATES: protein motif:HMM:NF012514.2
COORDINATES: protein motif:HMM:TIGR00254.1
GGDEF domain-containing response regulator
COORDINATES: protein motif:HMM:NF012234.2
COORDINATES: similar to AA sequence:RefSeq:WP_019550596.1
COORDINATES: protein motif:HMM:NF012792.2
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015210.2
COORDINATES: similar to AA sequence:RefSeq:WP_020616686.1
GO:0030261 - chromosome condensation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024197.2
COORDINATES: similar to AA sequence:RefSeq:WP_018504416.1
COORDINATES: protein motif:HMM:NF024783.2
COORDINATES: similar to AA sequence:RefSeq:WP_007032431.1
GO:0008829 - dCTP deaminase activity [Evidence IEA]
GO:0009394 - 2'-deoxyribonucleotide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014738217.1
helix-hairpin-helix domain-containing protein
COORDINATES: protein motif:HMM:NF014560.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0050797 - thymidylate synthase (FAD) activity [Evidence IEA]
GO:0006231 - dTMP biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024803.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024589.2
COORDINATES: protein motif:HMM:NF012630.2
GO:0031012 - extracellular matrix [Evidence IEA]
GO:0004222 - metalloendopeptidase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF004226.0
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011210568.1
COORDINATES: protein motif:HMM:NF024139.2
COORDINATES: protein motif:HMM:NF012451.2
COORDINATES: protein motif:HMM:NF012301.2
GO:0000156 - phosphorelay response regulator activity [Evidence IEA]
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
ParB/Srx family N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024949.2
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:NF012403.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0140658 - ATP-dependent chromatin remodeler activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025669.2
GO:0008270 - zinc ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020591400.1
COORDINATES: protein motif:HMM:TIGR02612.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF017760.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01391.1
GO:0003896 - DNA primase activity [Evidence IEA]
GO:0006269 - DNA replication, synthesis of RNA primer [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012609881.1
COORDINATES: protein motif:HMM:NF015338.2
endonuclease/exonuclease/phosphatase family protein
COORDINATES: protein motif:HMM:NF013252.2
COORDINATES: similar to AA sequence:RefSeq:WP_007962365.1
COORDINATES: protein motif:HMM:NF012632.2
COORDINATES: protein motif:HMM:TIGR02228.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008455511.1
COORDINATES: similar to AA sequence:RefSeq:WP_012397534.1
COORDINATES: protein motif:HMM:NF023331.2
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_019980646.1
COORDINATES: similar to AA sequence:RefSeq:WP_006541595.1
COORDINATES: protein motif:HMM:NF017170.2
COORDINATES: protein motif:HMM:NF015232.2
COORDINATES: protein motif:HMM:NF019974.2
nitrate- and nitrite sensing domain-containing protein
COORDINATES: protein motif:HMM:NF025451.2
COORDINATES: protein motif:HMM:TIGR02937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF014516.2
COORDINATES: protein motif:HMM:TIGR00619.1
COORDINATES: protein motif:HMM:NF013871.2
COORDINATES: similar to AA sequence:RefSeq:WP_006350092.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF010588.0
GO:0005524 - ATP binding [Evidence IEA]; GO:0003952 - NAD+ synthase (glutamine-hydrolyzing) activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013053.2
COORDINATES: protein motif:HMM:NF006698.0
GO:0004516 - nicotinate phosphoribosyltransferase activity [Evidence IEA]; GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF005932.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003911 - DNA ligase (NAD+) activity [Evidence IEA]
GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015834604.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0009378 - four-way junction helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]
Holliday junction branch migration DNA helicase RuvB
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: protein motif:HMM:NF012321.2
COORDINATES: similar to AA sequence:RefSeq:WP_015977169.1
COORDINATES: protein motif:HMM:NF014069.2
COORDINATES: protein motif:HMM:NF013964.2
GO:0004519 - endonuclease activity [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
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: similar to AA sequence:RefSeq:WP_012623093.1
COORDINATES: similar to AA sequence:RefSeq:WP_013977113.1
COORDINATES: protein motif:HMM:NF016724.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012271.2
GO:0005515 - protein binding [Evidence IEA]
fibronectin type III domain-containing protein
COORDINATES: protein motif:HMM:TIGR02532.1
GO:0005886 - plasma membrane [Evidence IEA]
COORDINATES: protein motif:HMM:NF013700.2
GO:0046872 - metal ion binding [Evidence IEA]; GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012415.2
COORDINATES: protein motif:HMM:TIGR01420.1
GO:0043107 - type IV pilus-dependent motility [Evidence IEA]
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF014759.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
5'-3' exonuclease H3TH domain-containing protein
COORDINATES: protein motif:HMM:NF016362.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00084.1
GO:0009379 - Holliday junction helicase complex [Evidence IEA]
GO:0009378 - four-way junction helicase activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
Holliday junction branch migration protein RuvA
COORDINATES: protein motif:HMM:NF012610.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017172484.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: protein motif:HMM:NF024703.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006359967.1
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF014177.2
COORDINATES: protein motif:HMM:NF017663.2
RusA family crossover junction endodeoxyribonuclease
COORDINATES: protein motif:HMM:NF013122.2
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013495855.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
amino acid ABC transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF039494.1
RlpA-like double-psi beta-barrel domain-containing protein
COORDINATES: protein motif:HMM:NF025744.2
COORDINATES: protein motif:HMM:NF019348.2
COORDINATES: protein motif:HMM:NF024601.2
COORDINATES: protein motif:HMM:NF025052.2
COORDINATES: similar to AA sequence:RefSeq:WP_010562001.1
COORDINATES: protein motif:HMM:NF039183.1
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: protein motif:HMM:NF014868.2
Catalyzes the rate-limiting step in dNTP synthesis; Derived by automated computational analysis using gene prediction method: Protein Homology.
vitamin B12-dependent ribonucleotide reductase
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF024752.2
COORDINATES: protein motif:HMM:NF019151.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF025001.2
COORDINATES: protein motif:HMM:NF024254.2
COORDINATES: protein motif:HMM:NF014605.2
COORDINATES: protein motif:HMM:NF022794.2
peptidoglycan DD-metalloendopeptidase family protein
COORDINATES: protein motif:HMM:NF025881.2
GO:0004519 - endonuclease activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019976.2
nuclease-related domain-containing protein
COORDINATES: protein motif:HMM:NF026240.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
DnaB-like helicase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2