Hymenobacter yonginensis strain KCTC 22745 plasmid unnamed2, complete sequence.
Bacteria; Bacteroidota; Cytophagia; Cytophagales; Hymenobacteraceae; Hymenobacter.
Hymenobacter yonginensis sp. nov., isolated from a mesotrophic artificial lake
Int J Syst Evol Microbiol 61 (Pt 7), 1511-1514 (2011)
Submitted (28-DEC-2022) Division of Life Sciences, Korea Polar Research Institute, 26, Songdomirae-ro, Yeonsu-gu, Incheon 21990, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP115397.1.\nBacteria and source DNA available from Hymenobacter yonginensis\nKCTC 22745.\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 Date :: 11-NOV-2022\nAssembly Method :: Unicyler v. 3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 230.0x\nSequencing Technology :: Illumina; Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 01/10/2023 15:16:16\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) :: 4,217\nCDSs (total) :: 4,154\nGenes (coding) :: 4,131\nCDSs (with protein) :: 4,131\nGenes (RNA) :: 63\nrRNAs :: 4, 4, 4 (5S, 16S, 23S)\ncomplete rRNAs :: 4, 4, 4 (5S, 16S, 23S)\ntRNAs :: 48\nncRNAs :: 3\nPseudo Genes (total) :: 23\nCDSs (without protein) :: 23\nPseudo Genes (ambiguous residues) :: 0 of 23\nPseudo Genes (frameshifted) :: 5 of 23\nPseudo Genes (incomplete) :: 15 of 23\nPseudo Genes (internal stop) :: 6 of 23\nPseudo Genes (multiple problems) :: 3 of 23\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:NF040570.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017729772.1
COORDINATES: similar to AA sequence:RefSeq:WP_013769167.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013453211.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949129.1
COORDINATES: similar to AA sequence:RefSeq:WP_015212131.1
COORDINATES: protein motif:HMM:NF039593.1
heavy metal-binding domain-containing protein
COORDINATES: protein motif:HMM:NF015658.2
COORDINATES: protein motif:HMM:NF014385.2
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01730.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019949138.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_012511111.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025041.2
HipA N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007836250.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:NF014081.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012806832.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
PDDEXK nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF012321.2
carboxypeptidase-like regulatory domain-containing protein
COORDINATES: protein motif:HMM:NF013395.2
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019949042.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949041.1
translesion error-prone DNA polymerase V autoproteolytic subunit
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: protein motif:HMM:NF024736.2
COORDINATES: similar to AA sequence:RefSeq:WP_013668004.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013668005.1
COORDINATES: similar to AA sequence:RefSeq:WP_019505535.1
COORDINATES: similar to AA sequence:RefSeq:WP_019948932.1
COORDINATES: protein motif:HMM:NF014567.2
HAMP domain-containing sensor histidine kinase
COORDINATES: protein motif:HMM:NF013718.2
COORDINATES: similar to AA sequence:RefSeq:WP_004658161.1
COORDINATES: similar to AA sequence:RefSeq:WP_010585551.1
COORDINATES: similar to AA sequence:RefSeq:WP_011530830.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019948029.1
nuclear transport factor 2 family protein
COORDINATES: protein motif:HMM:NF024242.2
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF024949.2
COORDINATES: similar to AA sequence:RefSeq:WP_012504664.1
COORDINATES: protein motif:HMM:NF012789.2
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: protein motif:HMM:NF013727.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006563075.1
phosphoadenosine phosphosulfate reductase family protein
COORDINATES: protein motif:HMM:NF024580.2
COORDINATES: similar to AA sequence:RefSeq:WP_008514347.1
COORDINATES: similar to AA sequence:RefSeq:WP_020605767.1
HNH endonuclease domain-containing protein
COORDINATES: protein motif:HMM:NF020387.2
COORDINATES: similar to AA sequence:RefSeq:WP_013921609.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949649.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019949650.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_009281303.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002995334.1
COORDINATES: protein motif:HMM:NF025471.2
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:NF039424.1
COORDINATES: similar to AA sequence:RefSeq:WP_012793414.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF039751.1
COORDINATES: protein motif:HMM:NF039748.1
COORDINATES: protein motif:HMM:NF039752.1
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_013427186.1
COORDINATES: similar to AA sequence:RefSeq:WP_012791350.1
COORDINATES: similar to AA sequence:RefSeq:WP_010853765.1
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: protein motif:HMM:NF014536.2
COORDINATES: similar to AA sequence:RefSeq:WP_006745188.1
type II toxin-antitoxin system Y4mF family antitoxin
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF014453.2
COORDINATES: protein motif:HMM:NF012301.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012791346.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF013767.2
LytTR family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:TIGR00229.1
PAS domain-containing hybrid sensor histidine kinase/response regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002191568.1
COORDINATES: protein motif:HMM:NF028012.2
COORDINATES: protein motif:HMM:NF020904.2
COORDINATES: protein motif:HMM:NF039704.1
COORDINATES: protein motif:HMM:NF019339.2
COORDINATES: protein motif:HMM:NF015692.2
ADP-ribosylglycohydrolase family protein
COORDINATES: protein motif:HMM:TIGR04183.1
T9SS type A sorting domain-containing protein
COORDINATES: protein motif:HMM:NF020766.2
GO:0015643 - toxic substance binding [Evidence IEA]
GO:0030153 - bacteriocin immunity [Evidence IEA]
colicin immunity domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014937324.1
COORDINATES: protein motif:HMM:TIGR02937.1
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF019846.2
GO:0008168 - methyltransferase activity [Evidence IEA]
methyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007059695.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949108.1
COORDINATES: protein motif:HMM:NF024957.2
COORDINATES: protein motif:HMM:NF024777.2
GO:0005515 - protein binding [Evidence IEA]
LamG-like jellyroll fold domain-containing protein
COORDINATES: protein motif:HMM:NF037660.2
GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015531.2
COORDINATES: protein motif:HMM:NF039197.1
COORDINATES: protein motif:HMM:NF013955.2
COORDINATES: protein motif:HMM:NF019205.2
COORDINATES: similar to AA sequence:RefSeq:WP_013914169.1
COORDINATES: protein motif:HMM:NF040192.1
COORDINATES: similar to AA sequence:RefSeq:WP_019946757.1
COORDINATES: similar to AA sequence:RefSeq:WP_020531259.1
COORDINATES: similar to AA sequence:RefSeq:WP_013763376.1
COORDINATES: similar to AA sequence:RefSeq:WP_019947094.1
COORDINATES: similar to AA sequence:RefSeq:WP_011330355.1
COORDINATES: similar to AA sequence:RefSeq:WP_017314146.1
mechanosensitive ion channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019949488.1
COORDINATES: similar to AA sequence:RefSeq:WP_015814083.1
COORDINATES: similar to AA sequence:RefSeq:WP_019949486.1
COORDINATES: similar to AA sequence:RefSeq:WP_012927486.1
COORDINATES: protein motif:HMM:NF013739.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012825705.1
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012382.2
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_020602483.1