Parasedimentitalea marina strain W43 plasmid pW43D, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Paracoccaceae; Parasedimentitalea.
Polyphasic taxonomic analysis of Parasedimentitalea marina gen. nov., sp. nov., a psychrotolerant bacterium isolated from deep sea water of the New Britain Trench
Submitted (23-OCT-2018) Shanghai Engineering Research Center of Hadal Scicence and Technology, College of Marine Sciences, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP033223.1.\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##Genome-Assembly-Data-START##\nAssembly Date :: JUL-2018\nAssembly Method :: Canu v. 1.3\nAssembly Name :: SHOU_W43\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 80.0x\nSequencing Technology :: Oxford Nanopore GridION\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/24/2023 00:06:54\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,919\nCDSs (total) :: 4,843\nGenes (coding) :: 4,696\nCDSs (with protein) :: 4,696\nGenes (RNA) :: 76\nrRNAs :: 5, 5, 5 (5S, 16S, 23S)\ncomplete rRNAs :: 5, 5, 5 (5S, 16S, 23S)\ntRNAs :: 58\nncRNAs :: 3\nPseudo Genes (total) :: 147\nCDSs (without protein) :: 147\nPseudo Genes (ambiguous residues) :: 0 of 147\nPseudo Genes (frameshifted) :: 111 of 147\nPseudo Genes (incomplete) :: 47 of 147\nPseudo Genes (internal stop) :: 23 of 147\nPseudo Genes (multiple problems) :: 28 of 147\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type material of Parasedimentitalea marina
COORDINATES: similar to AA sequence:RefSeq:WP_009806906.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012730.2
GO:0006811 - monoatomic ion transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF017409.2
GO:0003674 - molecular_function [Evidence IEA]
GO:0033103 - protein secretion by the type VI secretion system [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
type VI secretion system contractile sheath small subunit
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF017730.2
type VI secretion system contractile sheath large subunit
COORDINATES: protein motif:HMM:TIGR01646.1
type VI secretion system tip protein VgrG
COORDINATES: protein motif:HMM:TIGR03361.1
type VI secretion system tip protein TssI/VgrG
COORDINATES: similar to AA sequence:RefSeq:WP_008209783.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815950.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807589.1
type VI secretion system-associated FHA domain protein TagH
COORDINATES: similar to AA sequence:RefSeq:WP_009807588.1
type VI secretion system baseplate subunit TssK
COORDINATES: similar to AA sequence:RefSeq:WP_009806916.1
GO:0033104 - type VI protein secretion system complex [Evidence IEA]
type VI secretion system protein TssL, long form
COORDINATES: similar to AA sequence:RefSeq:WP_008209789.1
type VI secretion system membrane subunit TssM
COORDINATES: similar to AA sequence:RefSeq:WP_008209791.1
type VI secretion system-associated protein TagF
COORDINATES: similar to AA sequence:RefSeq:WP_009807584.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
protein phosphatase 2C domain-containing protein
COORDINATES: protein motif:HMM:NF012298.2
COORDINATES: similar to AA sequence:RefSeq:WP_008558458.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807707.1
COORDINATES: similar to AA sequence:RefSeq:WP_006937084.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536822.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536823.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014881836.1
COORDINATES: similar to AA sequence:RefSeq:WP_019297432.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536825.1
COORDINATES: similar to AA sequence:RefSeq:WP_008209329.1
COORDINATES: similar to AA sequence:RefSeq:WP_008563477.1
COORDINATES: similar to AA sequence:RefSeq:WP_014889359.1
GO:0007165 - signal transduction [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009807718.1
CheB methylesterase domain-containing protein
COORDINATES: protein motif:HMM:NF015908.2
COORDINATES: similar to AA sequence:RefSeq:WP_009177775.1
COORDINATES: similar to AA sequence:RefSeq:WP_005624316.1
COORDINATES: similar to AA sequence:RefSeq:WP_005624313.1
COORDINATES: similar to AA sequence:RefSeq:WP_019297598.1
COORDINATES: similar to AA sequence:RefSeq:WP_014881419.1
GO:0003723 - RNA binding [Evidence IEA]; GO:0004523 - RNA-DNA hybrid ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005624306.1
COORDINATES: similar to AA sequence:RefSeq:WP_011049133.1
adenylate/guanylate cyclase domain-containing protein
COORDINATES: protein motif:HMM:NF022995.2
COORDINATES: protein motif:HMM:NF012245.2
COORDINATES: similar to AA sequence:RefSeq:WP_009824246.1
COORDINATES: similar to AA sequence:RefSeq:WP_009814045.1
COORDINATES: similar to AA sequence:RefSeq:WP_008552597.1
COORDINATES: similar to AA sequence:RefSeq:WP_008203988.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982490.1
COORDINATES: similar to AA sequence:RefSeq:WP_008203991.1
COORDINATES: similar to AA sequence:RefSeq:WP_012061886.1
COORDINATES: similar to AA sequence:RefSeq:WP_008203993.1
GO:0140359 - ABC-type transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
COORDINATES: similar to AA sequence:RefSeq:WP_011537010.1
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007763955.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441248.1
COORDINATES: similar to AA sequence:RefSeq:WP_018689564.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008203998.1
COORDINATES: similar to AA sequence:RefSeq:WP_015501558.1
COORDINATES: protein motif:HMM:NF012692.2
COORDINATES: similar to AA sequence:RefSeq:WP_007006787.1
COORDINATES: similar to AA sequence:RefSeq:WP_007006788.1
COORDINATES: similar to AA sequence:RefSeq:WP_007006789.1
COORDINATES: similar to AA sequence:RefSeq:WP_006472821.1
GO:0004056 - argininosuccinate lyase activity [Evidence IEA]
GO:0042450 - arginine biosynthetic process via ornithine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007006791.1
COORDINATES: protein motif:HMM:NF012515.2
COORDINATES: similar to AA sequence:RefSeq:WP_014876555.1
COORDINATES: similar to AA sequence:RefSeq:WP_008209508.1
GO:0004047 - aminomethyltransferase activity [Evidence IEA]
GO:0006546 - glycine catabolic process [Evidence IEA]
glycine cleavage system aminomethyltransferase GcvT
COORDINATES: similar to AA sequence:RefSeq:WP_008557313.1
GO:0003824 - catalytic activity [Evidence IEA]
GO:0019464 - glycine decarboxylation via glycine cleavage system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009810508.1
GO:0004375 - glycine dehydrogenase (decarboxylating) activity [Evidence IEA]
aminomethyl-transferring glycine dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_011453438.1
GO:0046872 - metal ion binding [Evidence IEA]
zinc ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014881849.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008558409.1
metal ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009572321.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0042626 - ATPase-coupled transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014889367.1
COORDINATES: similar to AA sequence:RefSeq:WP_005614880.1
PhnD/SsuA/transferrin family substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_019294478.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016301 - kinase activity [Evidence IEA]
GO:0016310 - phosphorylation [Evidence IEA]
PEP/pyruvate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_010138048.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_009814835.1
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_018633989.1
COORDINATES: similar to AA sequence:RefSeq:WP_011538817.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019294472.1
GO:0051287 - NAD binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB
COORDINATES: similar to AA sequence:RefSeq:WP_005848978.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803648.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294469.1
ParB N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF014273.2
COORDINATES: similar to AA sequence:RefSeq:WP_010443420.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815972.1
COORDINATES: protein motif:HMM:NF025684.2
COORDINATES: similar to AA sequence:RefSeq:WP_008558463.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558392.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294464.1
MotA/TolQ/ExbB proton channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009806895.1
COORDINATES: similar to AA sequence:RefSeq:WP_008209764.1
COORDINATES: similar to AA sequence:RefSeq:WP_008209766.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558451.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294619.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294620.1
type VI secretion system tube protein Hcp
COORDINATES: similar to AA sequence:RefSeq:WP_008558475.1
type VI secretion system accessory protein TagJ
COORDINATES: similar to AA sequence:RefSeq:WP_019294622.1
type VI secretion system baseplate subunit TssE
COORDINATES: similar to AA sequence:RefSeq:WP_008558439.1
type VI secretion system baseplate subunit TssF
COORDINATES: similar to AA sequence:RefSeq:WP_008558464.1
type VI secretion system baseplate subunit TssG
COORDINATES: similar to AA sequence:RefSeq:WP_008558416.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]