Pseudosulfitobacter pseudonitzschiae strain H46 plasmid unnamed9, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Pseudosulfitobacter.
De novo assembly of human genomes with massively parallel short read sequencing
Submitted (05-JUN-2020) Ministry of natural resources, The first Institute of Oceanography, ZhongHan Street, QingDao 266100, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP054608.1.\nBacteria and source DNA available from China Qingdao Laoshan\nDistrict The first Institute of Oceanography Zheng Li.\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 Method :: CLC NGS Cell v. February-2020\nGenome Representation :: Full\nExpected Final Version :: No\nGenome Coverage :: 103.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 06/01/2023 23:18:00\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) :: 4,846\nCDSs (total) :: 4,793\nGenes (coding) :: 4,747\nCDSs (with protein) :: 4,747\nGenes (RNA) :: 53\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 3\nPseudo Genes (total) :: 46\nCDSs (without protein) :: 46\nPseudo Genes (ambiguous residues) :: 0 of 46\nPseudo Genes (frameshifted) :: 19 of 46\nPseudo Genes (incomplete) :: 23 of 46\nPseudo Genes (internal stop) :: 9 of 46\nPseudo Genes (multiple problems) :: 4 of 46\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
shallow sea, symbosis with harmful algal bloom algae
COORDINATES: similar to AA sequence:RefSeq:WP_007206089.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013797701.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005857581.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011580181.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011580180.1
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015925.2
COORDINATES: similar to AA sequence:RefSeq:WP_013039894.1
GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: protein motif:HMM:NF024180.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012318.2
GO:0008233 - peptidase activity [Evidence IEA]; GO:0004252 - serine-type endopeptidase activity [Evidence IEA]; GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012862.2
GO:0008234 - cysteine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008226752.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: protein motif:HMM:NF012343.2
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
GO:0009060 - aerobic respiration [Evidence IEA]
cbb3-type cytochrome c oxidase subunit I
COORDINATES: protein motif:HMM:NF013862.2
GO:0006629 - lipid metabolic process [Evidence IEA]
patatin-like phospholipase family protein
COORDINATES: protein motif:HMM:NF014567.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0000156 - phosphorelay response regulator activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_010142109.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001702.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009504820.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887984.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_008885607.1
IclR family transcriptional regulator C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008885015.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002966000.1
COORDINATES: similar to AA sequence:RefSeq:WP_003564118.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807928.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011748648.1
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009176543.1
GO:0005515 - protein binding [Evidence IEA]
GO:0006749 - glutathione metabolic process [Evidence IEA]
glutathione S-transferase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007121066.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009209233.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121068.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121069.1
TAXI family TRAP transporter solute-binding subunit
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_007121453.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121454.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0006189 - 'de novo' IMP biosynthetic process [Evidence IEA]
nickel pincer cofactor biosynthesis protein LarB
COORDINATES: similar to AA sequence:RefSeq:WP_007091578.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007121456.1
COORDINATES: similar to AA sequence:RefSeq:WP_014189208.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013789920.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013065900.1
COORDINATES: similar to AA sequence:RefSeq:WP_012667786.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009804139.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804137.1
COORDINATES: similar to AA sequence:RefSeq:WP_011095453.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_019074512.1
COORDINATES: protein motif:HMM:NF025607.2
COORDINATES: similar to AA sequence:RefSeq:WP_009828794.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF019310.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012607.2
COORDINATES: similar to AA sequence:RefSeq:WP_018304729.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121105.1
COORDINATES: similar to AA sequence:RefSeq:WP_009208055.1
GO:0009436 - glyoxylate catabolic process [Evidence IEA]; GO:0071704 - organic substance metabolic process [Evidence IEA]
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009812250.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009812249.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_007854771.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004103505.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121110.1
GO:0050043 - lactate racemase activity [Evidence IEA]
lactate racemase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013168274.1
COORDINATES: protein motif:HMM:NF017088.2
COORDINATES: similar to AA sequence:RefSeq:WP_008031527.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_008184927.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009504426.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005611164.1
COORDINATES: similar to AA sequence:RefSeq:WP_007820070.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016651 - oxidoreductase activity, acting on NAD(P)H [Evidence IEA]