Parasedimentitalea marina strain W43 plasmid pW43C, 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\nCP033222.1.\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_009177840.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014879182.1
COORDINATES: similar to AA sequence:RefSeq:WP_014879183.1
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_014879184.1
COORDINATES: similar to AA sequence:RefSeq:WP_014879186.1
GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_008207428.1
COORDINATES: similar to AA sequence:RefSeq:WP_008207427.1
COORDINATES: similar to AA sequence:RefSeq:WP_019298142.1
COORDINATES: similar to AA sequence:RefSeq:WP_008555689.1
WecB/TagA/CpsF family glycosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008557571.1
COORDINATES: similar to AA sequence:RefSeq:WP_007119353.1
COORDINATES: similar to AA sequence:RefSeq:WP_014873624.1
CpsD/CapB family tyrosine-protein kinase
COORDINATES: similar to AA sequence:RefSeq:WP_008555159.1
COORDINATES: similar to AA sequence:RefSeq:WP_008204397.1
COORDINATES: protein motif:HMM:NF013539.2
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013531143.1
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_008835849.1
COORDINATES: similar to AA sequence:RefSeq:WP_008204923.1
sarcosine oxidase subunit alpha family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF015905.2
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020184970.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020184969.1
COORDINATES: similar to AA sequence:RefSeq:WP_012330118.1
The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc.; The N-terminal region of this protein, as described by TIGR01726, is a three transmembrane segment that identifies a subfamily of ABC transporter permease subunits, which specificities that include histidine, arginine, glutamine, glutamate, L-cystine (sic), the opines (in Agrobacterium) octopine and nopaline, etc; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008279972.1
amino acid ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF012432.2
COORDINATES: similar to AA sequence:RefSeq:WP_009812984.1
COORDINATES: similar to AA sequence:RefSeq:WP_008207229.1
COORDINATES: similar to AA sequence:RefSeq:WP_010437473.1
COORDINATES: similar to AA sequence:RefSeq:WP_008207233.1
COORDINATES: protein motif:HMM:NF025343.2
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF016180.2
sarcosine oxidase subunit gamma family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007068461.1
COORDINATES: similar to AA sequence:RefSeq:WP_020086982.1
COORDINATES: similar to AA sequence:RefSeq:WP_003821029.1
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008836883.1
trimethylamine methyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019307614.1
COORDINATES: protein motif:HMM:NF013434.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005633419.1
GO:0008108 - UDP-glucose:hexose-1-phosphate uridylyltransferase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
UDP-glucose--hexose-1-phosphate uridylyltransferase
COORDINATES: protein motif:HMM:NF012673.2
COORDINATES: protein motif:HMM:NF015000.2
GO:0008081 - phosphoric diester hydrolase activity [Evidence IEA]
GO:0006629 - lipid metabolic process [Evidence IEA]
glycerophosphodiester phosphodiesterase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008185087.1
COORDINATES: similar to AA sequence:RefSeq:WP_008185089.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008185091.1
COORDINATES: similar to AA sequence:RefSeq:WP_009469636.1
COORDINATES: protein motif:HMM:NF012692.2
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF019421.2
COORDINATES: similar to AA sequence:RefSeq:WP_009808479.1
GO:0008784 - alanine racemase activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009808480.1
GO:0004180 - carboxypeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009808481.1
COORDINATES: similar to AA sequence:RefSeq:WP_020043424.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808483.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808484.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808485.1
COORDINATES: similar to AA sequence:RefSeq:WP_010658696.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808487.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808488.1
COORDINATES: similar to AA sequence:RefSeq:WP_009831022.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]
GO:0044237 - cellular metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008209144.1
COORDINATES: similar to AA sequence:RefSeq:WP_008207224.1
COORDINATES: similar to AA sequence:RefSeq:WP_020590317.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819397.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819398.1
COORDINATES: similar to AA sequence:RefSeq:WP_020057438.1
COORDINATES: similar to AA sequence:RefSeq:WP_008596791.1
COORDINATES: similar to AA sequence:RefSeq:WP_008036443.1
COORDINATES: similar to AA sequence:RefSeq:WP_010511570.1
COORDINATES: protein motif:HMM:NF013044.2
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_011750300.1
COORDINATES: similar to AA sequence:RefSeq:WP_012178270.1
COORDINATES: similar to AA sequence:RefSeq:WP_007254157.1
COORDINATES: similar to AA sequence:RefSeq:WP_008834980.1
COORDINATES: similar to AA sequence:RefSeq:WP_014889453.1
GO:0004148 - dihydrolipoyl dehydrogenase activity [Evidence IEA]
GO:0045454 - cell redox homeostasis [Evidence IEA]; GO:0051068 - dihydrolipoamide metabolic process [Evidence IEA]; GO:0006096 - glycolytic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008758654.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016992 - lipoate synthase activity [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009107 - lipoate biosynthetic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_019294833.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441645.1
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_014889456.1
GO:0004375 - glycine dehydrogenase (decarboxylating) activity [Evidence IEA]
aminomethyl-transferring glycine dehydrogenase
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008209391.1
aspartate/glutamate racemase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008558284.1
COORDINATES: similar to AA sequence:RefSeq:WP_008546666.1
COORDINATES: similar to AA sequence:RefSeq:WP_008558279.1
TAXI family TRAP transporter solute-binding subunit
COORDINATES: protein motif:HMM:NF012354.2
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_011910866.1
COORDINATES: similar to AA sequence:RefSeq:WP_006023449.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008208466.1
COORDINATES: protein motif:HMM:NF024375.2
COORDINATES: similar to AA sequence:RefSeq:WP_010442421.1
COORDINATES: similar to AA sequence:RefSeq:WP_008208462.1
glycine betaine/L-proline ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:NF015995.2
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]
GO:0022857 - transmembrane transporter activity [Evidence IEA]
glycine betaine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009760116.1
COORDINATES: similar to AA sequence:RefSeq:WP_008281096.1
COORDINATES: similar to AA sequence:RefSeq:WP_008556467.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441275.1
frameshifted; internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013720.2
COORDINATES: similar to AA sequence:RefSeq:WP_008280802.1
COORDINATES: similar to AA sequence:RefSeq:WP_010437799.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008280800.1
COORDINATES: similar to AA sequence:RefSeq:WP_006204494.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818612.1
dimethylamine monooxygenase subunit DmmA
COORDINATES: similar to AA sequence:RefSeq:WP_011047316.1
COORDINATES: protein motif:HMM:NF013104.2
internal stop; 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_010437786.1
COORDINATES: similar to AA sequence:RefSeq:WP_008557088.1
glutamine amidotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008759548.1
COORDINATES: protein motif:HMM:NF013784.2
GO:0015930 - glutamate synthase activity [Evidence IEA]; GO:0016638 - oxidoreductase activity, acting on the CH-NH2 group of donors [Evidence IEA]
GO:0006537 - glutamate biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013960551.1
GO:0004356 - glutamate-ammonia ligase activity [Evidence IEA]
GO:0006542 - glutamine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008557626.1
COORDINATES: similar to AA sequence:RefSeq:WP_019296933.1
COORDINATES: similar to AA sequence:RefSeq:WP_011047303.1
COORDINATES: similar to AA sequence:RefSeq:WP_011570289.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_008208299.1
COORDINATES: similar to AA sequence:RefSeq:WP_013963483.1
COORDINATES: similar to AA sequence:RefSeq:WP_008557544.1
COORDINATES: protein motif:HMM:NF012532.2
GO:0008964 - phosphoenolpyruvate carboxylase activity [Evidence IEA]
GO:0015977 - carbon fixation [Evidence IEA]; GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: protein motif:HMM:NF012677.2
GO:0004372 - glycine hydroxymethyltransferase activity [Evidence IEA]
GO:0019264 - glycine biosynthetic process from serine [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011567431.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815511.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187363.1