Ahniella affigens strain D13 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales; Rhodanobacteraceae; Ahniella.
Ahniella affigens gen. nov., sp. nov., a gammaproteobacterium isolated from sandy soil near a stream
Submitted (17-MAR-2018) Microbiology, Dankook University, 119, Dandae-ro, Dongnam-gu, Cheonan-si 31116, Korea, Republic of
REFSEQ INFORMATION: The reference sequence is identical to\nCP027861.1.\nBacteria and source DNA available from JCM 31634.\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/\nThis genome has a base modification file available.\n\n##Genome-Assembly-Data-START##\nAssembly Date :: MAR-2018\nAssembly Method :: PreAssembler v. 2\nAssembly Name :: Ahniella affigens\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 146.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/23/2023 03:02:14\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) :: 4,657\nCDSs (total) :: 4,598\nGenes (coding) :: 4,553\nCDSs (with protein) :: 4,553\nGenes (RNA) :: 59\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 49\nncRNAs :: 4\nPseudo Genes (total) :: 45\nCDSs (without protein) :: 45\nPseudo Genes (ambiguous residues) :: 0 of 45\nPseudo Genes (frameshifted) :: 8 of 45\nPseudo Genes (incomplete) :: 34 of 45\nPseudo Genes (internal stop) :: 5 of 45\nPseudo Genes (multiple problems) :: 2 of 45\nCRISPR Arrays :: 6\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:NF016820.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:TIGR03736.1
COORDINATES: protein motif:HMM:TIGR03735.1
COORDINATES: protein motif:HMM:TIGR03737.1
COORDINATES: protein motif:HMM:NF025810.2
COORDINATES: protein motif:HMM:TIGR03734.1
COORDINATES: protein motif:HMM:NF012298.2
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:TIGR02762.1
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF040570.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: protein motif:HMM:TIGR03743.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF041494.1
COORDINATES: protein motif:HMM:NF019843.2
COORDINATES: protein motif:HMM:NF012492.2
lytic transglycosylase domain-containing protein
COORDINATES: protein motif:HMM:NF013528.2
GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR00041.1
GO:0004798 - thymidylate kinase activity [Evidence IEA]
GO:0015949 - nucleobase-containing small molecule interconversion [Evidence IEA]
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF020384.2
COORDINATES: protein motif:HMM:TIGR02520.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: protein motif:HMM:NF022136.2
COORDINATES: protein motif:HMM:NF013506.2
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF014273.2
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF024503.2
TonB C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019464268.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF024754.2
COORDINATES: similar to AA sequence:RefSeq:WP_012578907.1
COORDINATES: similar to AA sequence:RefSeq:WP_000611894.1
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: protein motif:HMM:NF020387.2
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_014161724.1
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_006484960.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013595.2
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:TIGR02293.1
COORDINATES: similar to AA sequence:RefSeq:WP_017460187.1
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:NF024755.2
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_014075685.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: protein motif:HMM:NF018536.2
COORDINATES: protein motif:HMM:NF014638.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: protein motif:HMM:NF021981.2