Pseudosulfitobacter pseudonitzschiae strain H46 plasmid unnamed3, 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\nCP054602.1.\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_005979896.1
GO:0008902 - hydroxymethylpyrimidine kinase activity [Evidence IEA]; GO:0008972 - phosphomethylpyrimidine kinase activity [Evidence IEA]
GO:0009228 - thiamine biosynthetic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
bifunctional hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase
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_009827309.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179468.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819660.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009804189.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009574084.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: protein motif:HMM:NF033545.0
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF041025.1
GO:0019239 - deaminase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013094.2
COORDINATES: similar to AA sequence:RefSeq:WP_015146106.1
multiubiquitin domain-containing protein
sigma-70 family RNA polymerase sigma factor
COORDINATES: protein motif:HMM:NF017885.2
COORDINATES: similar to AA sequence:RefSeq:WP_007120616.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819650.1
COORDINATES: similar to AA sequence:RefSeq:WP_009179475.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009179414.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120612.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574112.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804200.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804201.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009574108.1
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120605.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335578.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120603.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120602.1
COORDINATES: similar to AA sequence:RefSeq:WP_008561424.1
GO:0042834 - peptidoglycan binding [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005645232.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807491.1
GO:0008324 - monoatomic cation transmembrane transporter activity [Evidence IEA]
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_008282972.1
COORDINATES: similar to AA sequence:RefSeq:WP_005645239.1
GO:0006812 - monoatomic cation transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018303599.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820107.1
protein-disulfide reductase DsbD family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820108.1
GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0017004 - cytochrome complex assembly [Evidence IEA]
c-type cytochrome biogenesis protein CcmI
COORDINATES: similar to AA sequence:RefSeq:WP_009820109.1
cytochrome c-type biogenesis protein CcmH
COORDINATES: similar to AA sequence:RefSeq:WP_012180067.1
DsbE family thiol:disulfide interchange protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282980.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959866.1
GO:0031966 - mitochondrial membrane [Evidence IEA]
GO:0033617 - mitochondrial cytochrome c oxidase assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009815483.1
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001721.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647556.1
GO:0016531 - copper chaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803468.1
COORDINATES: similar to AA sequence:RefSeq:WP_005647562.1
GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013959872.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803463.1
GO:0046873 - metal ion transmembrane transporter activity [Evidence IEA]
GO:0030001 - metal ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803461.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006508 - proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018303609.1
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008282832.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282833.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0017000 - antibiotic biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824428.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820125.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0046983 - protein dimerization activity [Evidence IEA]; GO:0046914 - transition metal ion binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
manganese-binding transcriptional regulator MntR
COORDINATES: similar to AA sequence:RefSeq:WP_017927567.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820127.1
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282839.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009824422.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_009815495.1
GO:0016740 - transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803450.1
COORDINATES: similar to AA sequence:RefSeq:WP_005613342.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503854.1
GO:0016746 - acyltransferase activity [Evidence IEA]; GO:0071972 - peptidoglycan L,D-transpeptidase activity [Evidence IEA]
GO:0018104 - peptidoglycan-protein cross-linking [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008282828.1
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_009573642.1
GO:0015036 - disulfide oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820136.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820137.1
COORDINATES: similar to AA sequence:RefSeq:WP_014763450.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120881.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120882.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820143.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
ABC transporter transmembrane domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120884.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
plastocyanin/azurin family copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007120885.1
COORDINATES: similar to AA sequence:RefSeq:WP_010968681.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820147.1
GO:0015562 - efflux transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009824197.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282876.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120889.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187038.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0019829 - ATPase-coupled monoatomic cation transmembrane transporter activity [Evidence IEA]
GO:0006812 - monoatomic cation transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007120891.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - intracellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009503819.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820198.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121398.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503821.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121400.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820200.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121402.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503826.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503827.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820202.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121580.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820203.1
COORDINATES: similar to AA sequence:RefSeq:WP_014332191.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121516.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120831.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820205.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120830.1
COORDINATES: similar to AA sequence:RefSeq:WP_007117802.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820206.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120629.1
COORDINATES: protein motif:HMM:NF014273.2
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_007068978.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505437.1
COORDINATES: similar to AA sequence:RefSeq:WP_015075038.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009574268.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574267.1
COORDINATES: similar to AA sequence:RefSeq:WP_009574266.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859468.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018301019.1
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_008327530.1
energy-coupling factor transporter transmembrane component T
COORDINATES: similar to AA sequence:RefSeq:WP_008327529.1
COORDINATES: similar to AA sequence:RefSeq:WP_015497142.1
GO:0016491 - oxidoreductase activity [Evidence IEA]; GO:0016657 - oxidoreductase activity, acting on NAD(P)H, nitrogenous group as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008758846.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_009803649.1
GO:0004592 - pantoate-beta-alanine ligase activity [Evidence IEA]
GO:0015940 - pantothenate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827075.1
GO:0003864 - 3-methyl-2-oxobutanoate hydroxymethyltransferase activity [Evidence IEA]
3-methyl-2-oxobutanoate hydroxymethyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_009827076.1
GO:0004514 - nicotinate-nucleotide diphosphorylase (carboxylating) activity [Evidence IEA]
GO:0019363 - pyridine nucleotide biosynthetic process [Evidence IEA]
carboxylating nicotinate-nucleotide diphosphorylase
COORDINATES: similar to AA sequence:RefSeq:WP_009827077.1
GO:0008734 - L-aspartate oxidase activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009827078.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0008987 - quinolinate synthetase A activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007600452.1
COORDINATES: similar to AA sequence:RefSeq:WP_018516728.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013500664.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187165.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536558.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011567058.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013963746.1
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011567056.1
GO:0004789 - thiamine-phosphate diphosphorylase activity [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_013963749.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013963750.1