Croceibacterium atlanticum strain 26DY36 plasmid unnamed, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales; Erythrobacteraceae; Croceibacterium.
The complete genome of Altererythrobacter atlanticus strain 26DY36
Submitted (10-AUG-2015) Second Institute of Oceanography, State Oceanic Administration, Baochubei Road No.36, Hangzhou, Zhejiang 310012, China
Submitted (13-MAY-2015) Second Institute of Oceanography, State Oceanic Administration, Baochubei Road No.36, Hangzhou, Zhejiang 310012, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP011453.2.\n\nOn Sep 16, 2015 this sequence version replaced NZ_CP011453.1.\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##MIGS:3.0-Data-START##\nsubmitted_to_insdc :: CP011452 and CP011453\ninvestigation_type :: bacteria_archaea\nproject_name :: Altererythrobacter atlanticus 26DY36\n genome sequencing and assembly\nlat_lon :: 5.9444 N, 33.1136 W\ndepth :: 2577 m\nalt_elev :: - 2577 m\ngeo_loc_name :: North Atlantic Mid-Ocean Ridge\ncollection_date :: 2012.07\nbiome :: ENVO:00002113\nfeature :: ENVO:00000406\nmaterial :: ENVO:00002007\nenv_package :: Deepsea calcareous oozes\nnum_replicons :: 2\nestimated_size :: 3475107 bp\nref_biomaterial :: PMID:24030689\nisol_growth_condt :: Marine agar 2216 (MA, BD) at 30 oc\nsamp_collect_device :: A television grab bucket operated from the\n vessel Da Yang Yi Hao\nnucl_acid_ext :: Qiagen DNA extraction kit\nlib_reads_seqd :: 30,213 reads\nlib_const_meth :: The large smrtbell gdna protocol (Pacific\n Biosciences, USA)\nseq_meth :: A pacbio RS II platform\nassembly :: missing\nassembly method :: De novo assembled using the PacBio\n hierarchical genome assembly process\n (HGAP)/Quiver software\nestimated error rate :: 99.99% (average reference consensus)\nmethod of calculation :: Estimation from HGAP Assembly quality\n scores\nassembly_name :: HGAP Assembly version 2 (Pacific\n Biosciences, USA)\nfinishing_strategy :: Complete, 110x, 2 contigs (one chromosome\n and one circular plasmid)\ntype strain :: 26DY36T =CGMCC 1.12411T=JCM 18865T\ngram staining :: Negative\ncell shape :: Rod\nmotility :: Motile\nsporulation :: Nonsporulating\ntemperature range :: 10-45 C\noptimum temperature :: 30-35 C\nsalinity :: Moderately halophilic, 0.5-5% NaCl\nrel_to_oxygen :: Strictly aerobic\nbiotic_relationship :: Free-living\npathogenicity :: Not reported\n##MIGS:3.0-Data-END##\n\n##Genome-Assembly-Data-START##\nAssembly Method :: HS HGAP Assembly v. 2\nGenome Coverage :: 102.33\nSequencing Technology :: Pacific Bioscience (SMRT)\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 02:08:42\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) :: 3,311\nCDSs (total) :: 3,255\nGenes (coding) :: 3,221\nCDSs (with protein) :: 3,221\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 34\nCDSs (without protein) :: 34\nPseudo Genes (ambiguous residues) :: 0 of 34\nPseudo Genes (frameshifted) :: 15 of 34\nPseudo Genes (incomplete) :: 18 of 34\nPseudo Genes (internal stop) :: 6 of 34\nPseudo Genes (multiple problems) :: 5 of 34\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Altererythrobacter atlanticus
COORDINATES: similar to AA sequence:RefSeq:WP_015460496.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012398.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012662508.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0004601 - peroxidase activity [Evidence IEA]
GO:0006979 - response to oxidative stress [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016508746.1
COORDINATES: similar to AA sequence:RefSeq:WP_013831354.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007015706.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_010124792.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0042578 - phosphoric ester hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_003414554.1
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF013508.2
COORDINATES: similar to AA sequence:RefSeq:WP_019183518.1
COORDINATES: similar to AA sequence:RefSeq:WP_009048847.1
COORDINATES: similar to AA sequence:RefSeq:WP_011635262.1
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_014074672.1
COORDINATES: similar to AA sequence:RefSeq:WP_015586570.1
COORDINATES: protein motif:HMM:NF024212.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF012801.2
GO:0015267 - channel activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF039360.1
COORDINATES: protein motif:HMM:NF021665.2
COORDINATES: similar to AA sequence:RefSeq:WP_004987432.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011993130.1
GO:0030272 - 5-formyltetrahydrofolate cyclo-ligase activity [Evidence IEA]
GO:0006730 - one-carbon metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011950582.1
GO:0016639 - oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008831344.1
COORDINATES: protein motif:HMM:NF025736.2
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF016145.2
GO:0016757 - glycosyltransferase activity [Evidence IEA]
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: protein motif:HMM:NF024603.2
COORDINATES: protein motif:HMM:NF016764.2
GO:0031267 - small GTPase binding [Evidence IEA]
GO:0006888 - endoplasmic reticulum to Golgi vesicle-mediated transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018066717.1
COORDINATES: similar to AA sequence:RefSeq:WP_018063521.1
COORDINATES: similar to AA sequence:RefSeq:WP_016835158.1
COORDINATES: similar to AA sequence:RefSeq:WP_002059143.1
GO:0003871 - 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity [Evidence IEA]; GO:0008270 - zinc ion binding [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018634429.1
GO:0010181 - FMN binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017181788.1
COORDINATES: similar to AA sequence:RefSeq:WP_017500560.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017500558.1
COORDINATES: similar to AA sequence:RefSeq:WP_017182735.1
COORDINATES: similar to AA sequence:RefSeq:WP_015665268.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017181775.1
COORDINATES: similar to AA sequence:RefSeq:WP_013166853.1
COORDINATES: similar to AA sequence:RefSeq:WP_017181778.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017181779.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017500553.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008973084.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017181782.1
GO:0009279 - cell outer membrane [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017181783.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_006967778.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0004174 - electron-transferring-flavoprotein dehydrogenase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0022900 - electron transport chain [Evidence IEA]
electron transfer flavoprotein-ubiquinone oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007681295.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]
electron transfer flavoprotein subunit alpha/FixB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010235569.1
GO:0009055 - electron transfer activity [Evidence IEA]
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017181774.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017181784.1
aromatic ring-hydroxylating dioxygenase subunit alpha