Alistipes indistinctus strain 2BBH45 plasmid p2BBH45, complete sequence.
Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Rikenellaceae; Alistipes.
Complete Genome Sequence of Alistipes indistinctus Strain 2BBH45, Isolated from the Feces of a Healthy Japanese Male
Microbiol Resour Announc 10, e01284-20 (2021)
DOI:10.1128/MRA.01284-20 Publication Status: Online-Only
Submitted (15-APR-2020) Contact:Yusuke Ogata RIKEN, Center for Integrative Medical Sciences, Laboratory for Microbiome Sciences; 1-7-22, Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
REFSEQ INFORMATION: The reference sequence is identical to\nAP023050.1.\nAnnotated by DFAST v.1.2.6 (https://dfast.nig.ac.jp).\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 :: Unicycler v. 0.4.6\nGenome Coverage :: 251x\nSequencing Technology :: Illumina MiSeq; PacBio Sequel\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 10/06/2022 13:25:41\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 2,518\nCDSs (total) :: 2,466\nGenes (coding) :: 2,444\nCDSs (with protein) :: 2,444\nGenes (RNA) :: 52\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 43\nncRNAs :: 3\nPseudo Genes (total) :: 22\nCDSs (without protein) :: 22\nPseudo Genes (ambiguous residues) :: 0 of 22\nPseudo Genes (frameshifted) :: 2 of 22\nPseudo Genes (incomplete) :: 19 of 22\nPseudo Genes (internal stop) :: 4 of 22\nPseudo Genes (multiple problems) :: 2 of 22\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:NF012360.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013884.2
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: similar to AA sequence:RefSeq:WP_005798399.1
COORDINATES: similar to AA sequence:RefSeq:WP_017494941.1
GO:0008761 - UDP-N-acetylglucosamine 2-epimerase activity [Evidence IEA]
GO:0006047 - UDP-N-acetylglucosamine metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012022411.1
GO:0016051 - carbohydrate biosynthetic process [Evidence IEA]
N-acetylneuraminate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010231917.1
acylneuraminate cytidylyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019246756.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019246839.1
COORDINATES: similar to AA sequence:RefSeq:WP_019246840.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009135148.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_019246953.1
COORDINATES: similar to AA sequence:RefSeq:WP_015547107.1
COORDINATES: similar to AA sequence:RefSeq:WP_005636834.1
COORDINATES: protein motif:HMM:NF014581.2
TraM recognition domain-containing protein
COORDINATES: protein motif:HMM:NF024554.2
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF012493.2
COORDINATES: protein motif:HMM:NF024866.2
COORDINATES: protein motif:HMM:NF037110.2
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF016820.2
COORDINATES: protein motif:HMM:NF023922.2
COORDINATES: protein motif:HMM:NF024982.2
COORDINATES: similar to AA sequence:RefSeq:WP_014776537.1
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016662419.1
COORDINATES: similar to AA sequence:RefSeq:WP_005930817.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: protein motif:HMM:NF039835.1
COORDINATES: protein motif:HMM:NF015648.2
COORDINATES: similar to AA sequence:RefSeq:WP_011499693.1
COORDINATES: protein motif:HMM:NF040570.1
RNA-guided endonuclease TnpB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018668203.1
COORDINATES: similar to AA sequence:RefSeq:WP_018696897.1
COORDINATES: protein motif:HMM:NF028182.2
putative phage abortive infection protein
COORDINATES: protein motif:HMM:NF023742.2
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009750616.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013665076.1
WbbJ; catalyzes the transfer of the O-acetyl moiety to the O antigen; part of the lipopolysaccharide biosynthetic pathway; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF024122.2
COORDINATES: protein motif:HMM:NF025017.2