Dyadobacter chenhuakuii strain CY22 plasmid unnamed, complete sequence.
Bacteria; Bacteroidota; Cytophagia; Cytophagales; Spirosomaceae; Dyadobacter.
Submitted (21-JUN-2022) National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 ChangBai Road, Changping District, Beijing 102206, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP099631.1.\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 :: SMRT Link v. 6.0.0.47841\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 468.13x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/20/2023 12:08:31\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) :: 5,119\nCDSs (total) :: 5,068\nGenes (coding) :: 5,054\nCDSs (with protein) :: 5,054\nGenes (RNA) :: 51\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 40\nncRNAs :: 2\nPseudo Genes (total) :: 14\nCDSs (without protein) :: 14\nPseudo Genes (ambiguous residues) :: 0 of 14\nPseudo Genes (frameshifted) :: 6 of 14\nPseudo Genes (incomplete) :: 7 of 14\nPseudo Genes (internal stop) :: 2 of 14\nPseudo Genes (multiple problems) :: 1 of 14\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_012931429.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012931428.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_015813492.1
COORDINATES: similar to AA sequence:RefSeq:WP_005041560.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF012425.2
COORDINATES: protein motif:HMM:NF024242.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019505535.1
COORDINATES: protein motif:HMM:NF012371.2
serine hydrolase domain-containing protein
COORDINATES: protein motif:HMM:NF015531.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF013328.2
GO:0019104 - DNA N-glycosylase activity [Evidence IEA]; GO:0003906 - DNA-(apurinic or apyrimidinic site) endonuclease activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0006284 - base-excision repair [Evidence IEA]
DNA-formamidopyrimidine glycosylase family protein
COORDINATES: protein motif:HMM:NF018533.2
COORDINATES: protein motif:HMM:NF040155.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_003485985.1
COORDINATES: similar to AA sequence:RefSeq:WP_020214362.1
GO:0006303 - double-strand break repair via nonhomologous end joining [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010601930.1
GO:0008853 - exodeoxyribonuclease III activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008236954.1
COORDINATES: similar to AA sequence:RefSeq:WP_018478502.1
COORDINATES: protein motif:HMM:NF014626.2
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006974 - cellular response to DNA damage stimulus [Evidence IEA]; GO:0018142 - protein-DNA covalent cross-linking [Evidence IEA]
SOS response-associated peptidase family protein
COORDINATES: protein motif:HMM:TIGR02258.1
GO:0008664 - 2'-5'-RNA ligase activity [Evidence IEA]
GO:0008033 - tRNA processing [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015811811.1
COORDINATES: similar to AA sequence:RefSeq:WP_015811812.1
COORDINATES: similar to AA sequence:RefSeq:WP_015811813.1
COORDINATES: similar to AA sequence:RefSeq:WP_015811814.1
GO:0008408 - 3'-5' exonuclease activity [Evidence IEA]; GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF025391.2
COORDINATES: protein motif:HMM:NF020123.2
COORDINATES: protein motif:HMM:NF013353.2
GO:0036361 - racemase activity, acting on amino acids and derivatives [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015810813.1
COORDINATES: protein motif:HMM:NF019284.2
COORDINATES: similar to AA sequence:RefSeq:WP_020214376.1
PDDEXK nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF012464.2
COORDINATES: similar to AA sequence:RefSeq:WP_012931166.1
COORDINATES: similar to AA sequence:RefSeq:WP_019942681.1
COORDINATES: similar to AA sequence:RefSeq:WP_012931167.1
COORDINATES: similar to AA sequence:RefSeq:WP_017805079.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076611505.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020601537.1
GO:0004801 - transaldolase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018614878.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018948255.1
COORDINATES: similar to AA sequence:RefSeq:WP_019940934.1
COORDINATES: similar to AA sequence:RefSeq:WP_018343595.1
COORDINATES: similar to AA sequence:RefSeq:WP_012790547.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012791882.1
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: similar to AA sequence:RefSeq:WP_018620407.1
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF024143.2
COORDINATES: similar to AA sequence:RefSeq:WP_009281931.1
COORDINATES: protein motif:HMM:NF014510.2
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_015026235.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]