Pseudosulfitobacter pseudonitzschiae strain H46 plasmid unnamed4, 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\nCP054603.1.\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: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_005862455.1
Lrp/AsnC family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007881002.1
COORDINATES: protein motif:HMM:NF024950.2
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007881001.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010658517.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006609314.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012092752.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008549461.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_009572144.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018066996.1
L-2-amino-thiazoline-4-carboxylic acid hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_006468579.1
GO:0016787 - hydrolase activity [Evidence IEA]; GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827129.1
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_003616132.1
COORDINATES: similar to AA sequence:RefSeq:WP_011911055.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820228.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187157.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807512.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327379.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187323.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503805.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859613.1
COORDINATES: similar to AA sequence:RefSeq:WP_003537745.1
COORDINATES: similar to AA sequence:RefSeq:WP_012559876.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
COORDINATES: similar to AA sequence:RefSeq:WP_008331014.1
COORDINATES: protein motif:HMM:NF022436.2
COORDINATES: similar to AA sequence:RefSeq:WP_006199482.1
sulfotransferase family 2 domain-containing protein
COORDINATES: protein motif:HMM:NF012888.2
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase domain-containing protein
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF015527.2
COORDINATES: similar to AA sequence:RefSeq:WP_015496681.1
COORDINATES: similar to AA sequence:RefSeq:WP_008225762.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
GO:0016757 - glycosyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012676863.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013636.2
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005848490.1
COORDINATES: protein motif:HMM:NF025314.2
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF014910.2
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
FAD-binding and (Fe-S)-binding domain-containing protein
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007564482.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_012640573.1
COORDINATES: similar to AA sequence:RefSeq:WP_026155209.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187375.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187427.1
COORDINATES: protein motif:HMM:NF020604.2
COORDINATES: similar to AA sequence:RefSeq:WP_007120210.1
tricarballylate utilization 4Fe-4S protein TcuB
COORDINATES: similar to AA sequence:RefSeq:WP_008888103.1
FAD-dependent tricarballylate dehydrogenase TcuA
COORDINATES: similar to AA sequence:RefSeq:WP_005856062.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005856061.1
COORDINATES: similar to AA sequence:RefSeq:WP_005856060.1
D-2-hydroxyacid dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008888049.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888275.1
GO:0032559 - adenyl ribonucleotide binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005856054.1
COORDINATES: similar to AA sequence:RefSeq:WP_005979208.1
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_008229818.1
COORDINATES: similar to AA sequence:RefSeq:WP_009826179.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008888213.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0000155 - phosphorelay sensor kinase activity [Evidence IEA]; GO:0004673 - protein histidine kinase activity [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013963446.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008887339.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009820064.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819736.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611562.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007256277.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004673796.1
COORDINATES: similar to AA sequence:RefSeq:WP_007771786.1
GO:0008697 - 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity [Evidence IEA]
GO:0045490 - pectin catabolic process [Evidence IEA]
5-dehydro-4-deoxy-D-glucuronate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_007771782.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]; GO:0000976 - transcription cis-regulatory region binding [Evidence IEA]
GO:0006351 - DNA-templated transcription [Evidence IEA]; GO:0045892 - negative regulation of DNA-templated transcription [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_007090681.1
GO:0008678 - 2-deoxy-D-gluconate 3-dehydrogenase activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
GO:0000272 - polysaccharide catabolic process [Evidence IEA]
2-dehydro-3-deoxy-D-gluconate 5-dehydrogenase KduD
COORDINATES: similar to AA sequence:RefSeq:WP_009794470.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0008643 - carbohydrate transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_010896874.1
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009110870.1
COORDINATES: similar to AA sequence:RefSeq:WP_012825883.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_009574209.1
COORDINATES: similar to AA sequence:RefSeq:WP_005617061.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807963.1
COORDINATES: protein motif:HMM:NF012656.2
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010234427.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009808361.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005848621.1
MarR family winged helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018871325.1
COORDINATES: similar to AA sequence:RefSeq:WP_011630037.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_005860815.1
COORDINATES: similar to AA sequence:RefSeq:WP_012254165.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011941571.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_013639493.1
GO:0043546 - molybdopterin cofactor binding [Evidence IEA]
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007812606.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0015343 - siderophore-iron transmembrane transporter activity [Evidence IEA]
GO:0015891 - siderophore transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011749771.1
COORDINATES: similar to AA sequence:RefSeq:WP_007762759.1
iron chelate uptake ABC transporter family permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_018000565.1
GO:0006826 - iron ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007812604.1
COORDINATES: protein motif:HMM:NF016818.2
GO:0055072 - obsolete iron ion homeostasis [Evidence IEA]
GO:0001216 - DNA-binding transcription activator activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065307.1
COORDINATES: protein motif:HMM:NF015366.2
GO:0042597 - periplasmic space [Evidence IEA]
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018065309.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010138116.1
COORDINATES: protein motif:HMM:NF020479.2
COORDINATES: similar to AA sequence:RefSeq:WP_009818011.1
GO:0005215 - transporter activity [Evidence IEA]
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010138120.1
GO:0050129 - N-formylglutamate deformylase activity [Evidence IEA]
GO:0019557 - histidine catabolic process to glutamate and formate [Evidence IEA]
COORDINATES: protein motif:HMM:NF006684.0
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: similar to AA sequence:RefSeq:WP_007803627.1
COORDINATES: similar to AA sequence:RefSeq:WP_008559410.1
GO:0008115 - sarcosine oxidase activity [Evidence IEA]
GO:0046653 - tetrahydrofolate metabolic process [Evidence IEA]
sarcosine oxidase subunit beta family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008281097.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803630.1
sarcosine oxidase subunit alpha family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008887997.1
COORDINATES: similar to AA sequence:RefSeq:WP_005851123.1
GO:0008864 - formyltetrahydrofolate deformylase activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009803663.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820261.1
COORDINATES: similar to AA sequence:RefSeq:WP_009803666.1
COORDINATES: similar to AA sequence:RefSeq:WP_008208328.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558172.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009803671.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00059
TPP riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_013963750.1
COORDINATES: similar to AA sequence:RefSeq:WP_013963749.1
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015496894.1
GO:1990107 - thiazole synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005605915.1
GO:0004789 - thiamine-phosphate diphosphorylase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009816697.1
COORDINATES: similar to AA sequence:RefSeq:WP_015496899.1