Parasedimentitalea marina strain W43 plasmid pW43B, 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\nCP033221.1.\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_010515367.1
GO:0008115 - sarcosine oxidase activity [Evidence IEA]
GO:0046653 - tetrahydrofolate metabolic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
sarcosine oxidase subunit beta family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008204924.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008876466.1
sarcosine oxidase subunit alpha family protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_009830098.1
GO:0051920 - peroxiredoxin activity [Evidence IEA]
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011048398.1
serine hydrolase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011048399.1
COORDINATES: similar to AA sequence:RefSeq:WP_009829608.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010443825.1
COORDINATES: similar to AA sequence:RefSeq:WP_011048402.1
COORDINATES: similar to AA sequence:RefSeq:WP_009827507.1
COORDINATES: similar to AA sequence:RefSeq:WP_011048404.1
COORDINATES: similar to AA sequence:RefSeq:WP_011048405.1
3-keto-5-aminohexanoate cleavage protein
COORDINATES: similar to AA sequence:RefSeq:WP_020044230.1
COORDINATES: similar to AA sequence:RefSeq:WP_009830730.1
GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004097330.1
COORDINATES: similar to AA sequence:RefSeq:WP_013046988.1
LLM class flavin-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_010443812.1
COORDINATES: similar to AA sequence:RefSeq:WP_010443810.1
COORDINATES: similar to AA sequence:RefSeq:WP_011048412.1
COORDINATES: similar to AA sequence:RefSeq:WP_011048413.1
GO:0008410 - CoA-transferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010443804.1
COORDINATES: similar to AA sequence:RefSeq:WP_009022216.1
COORDINATES: similar to AA sequence:RefSeq:WP_008279973.1
GO:0016829 - lyase activity [Evidence IEA]
GO:0006099 - tricarboxylic acid cycle [Evidence IEA]
COORDINATES: protein motif:HMM:NF012913.2
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_009831845.1
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: protein motif:HMM:NF015445.2
GO:0055085 - transmembrane transport [Evidence IEA]
TRAP transporter substrate-binding protein DctP
COORDINATES: similar to AA sequence:RefSeq:WP_020287583.1
COORDINATES: protein motif:HMM:NF014068.2
COORDINATES: protein motif:HMM:NF012437.2
adenylate/guanylate cyclase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008206340.1
carbon-nitrogen hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008206353.1
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008206354.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008206359.1
COORDINATES: similar to AA sequence:RefSeq:WP_003942035.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
crotonase/enoyl-CoA hydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007118451.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0008987 - quinolinate synthetase A activity [Evidence IEA]
GO:0009435 - NAD biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007118450.1
GO:0008734 - L-aspartate oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005977330.1
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_009810986.1
heme ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010140614.1
COORDINATES: similar to AA sequence:RefSeq:WP_008203609.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005848657.1
ChuX/HutX family heme-like substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008203613.1
COORDINATES: similar to AA sequence:RefSeq:WP_009810992.1
MotA/TolQ/ExbB proton channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009810993.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007801316.1
COORDINATES: protein motif:HMM:NF018252.2
GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011454447.1
GO:0071949 - FAD binding [Evidence IEA]; GO:0010181 - FMN binding [Evidence IEA]; GO:0050661 - NADP binding [Evidence IEA]; GO:0003959 - NADPH dehydrogenase activity [Evidence IEA]
bifunctional salicylyl-CoA 5-hydroxylase/oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_009828921.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_009829841.1
COORDINATES: similar to AA sequence:RefSeq:WP_009829212.1
COORDINATES: similar to AA sequence:RefSeq:WP_011454451.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861464.1
COORDINATES: similar to AA sequence:RefSeq:WP_008233091.1
COORDINATES: similar to AA sequence:RefSeq:WP_011566868.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_008233075.1
COORDINATES: similar to AA sequence:RefSeq:WP_011539555.1
COORDINATES: similar to AA sequence:RefSeq:WP_011539554.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120020.1
COORDINATES: protein motif:HMM:NF024832.2
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: protein motif:HMM:NF012888.2
GO:0008146 - sulfotransferase activity [Evidence IEA]
sulfotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008562520.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441812.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_010441811.1
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_010396664.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396675.1
COORDINATES: similar to AA sequence:RefSeq:WP_018689969.1
COORDINATES: similar to AA sequence:RefSeq:WP_007197843.1
COORDINATES: similar to AA sequence:RefSeq:WP_004689045.1
COORDINATES: similar to AA sequence:RefSeq:WP_010396667.1
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: protein motif:HMM:NF019491.2
COORDINATES: similar to AA sequence:RefSeq:WP_007603153.1
GO:0050660 - flavin adenine dinucleotide binding [Evidence IEA]; GO:0016614 - oxidoreductase activity, acting on CH-OH group of donors [Evidence IEA]
GMC family oxidoreductase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008204991.1
zinc-binding alcohol dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008560942.1
COORDINATES: similar to AA sequence:RefSeq:WP_006699940.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067224.1
glycerol-3-phosphate dehydrogenase/oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_018067225.1
COORDINATES: similar to AA sequence:RefSeq:WP_008559998.1
COORDINATES: similar to AA sequence:RefSeq:WP_006932337.1
COORDINATES: similar to AA sequence:RefSeq:WP_011538528.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006932339.1
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013335.2
COORDINATES: similar to AA sequence:RefSeq:WP_008551028.1
COORDINATES: similar to AA sequence:RefSeq:WP_008551185.1
COORDINATES: similar to AA sequence:RefSeq:WP_008551176.1
COORDINATES: similar to AA sequence:RefSeq:WP_008551082.1
COORDINATES: protein motif:HMM:NF019322.2
COORDINATES: protein motif:HMM:NF009498.0
COORDINATES: protein motif:HMM:NF014753.2
COORDINATES: protein motif:HMM:NF014754.2
GO:0004371 - glycerone kinase activity [Evidence IEA]
GO:0006071 - glycerol metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013429.2
sugar phosphate isomerase/epimerase family protein
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: protein motif:HMM:NF012336.2
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_019294910.1
COORDINATES: similar to AA sequence:RefSeq:WP_013167429.1
4-hydroxyphenylacetate 3-hydroxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011049359.1
COORDINATES: similar to AA sequence:RefSeq:WP_009831017.1
COORDINATES: similar to AA sequence:RefSeq:WP_008208414.1
COORDINATES: similar to AA sequence:RefSeq:WP_011049356.1
COORDINATES: similar to AA sequence:RefSeq:WP_009814528.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013167428.1
GO:0008777 - acetylornithine deacetylase activity [Evidence IEA]
GO:0006592 - ornithine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013960317.1
COORDINATES: similar to AA sequence:RefSeq:WP_013960314.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294919.1
COORDINATES: similar to AA sequence:RefSeq:WP_008208408.1
COORDINATES: similar to AA sequence:RefSeq:WP_009816845.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0009055 - electron transfer activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008205199.1
COORDINATES: similar to AA sequence:RefSeq:WP_004212703.1
COORDINATES: similar to AA sequence:RefSeq:WP_011241969.1
GO:0004129 - cytochrome-c oxidase activity [Evidence IEA]
cytochrome-c oxidase, cbb3-type subunit I
COORDINATES: similar to AA sequence:RefSeq:WP_014875442.1
cytochrome-c oxidase, cbb3-type subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_011241967.1
CcoQ/FixQ family Cbb3-type cytochrome c oxidase assembly chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_011241966.1
cytochrome-c oxidase, cbb3-type subunit III
COORDINATES: similar to AA sequence:RefSeq:WP_009817291.1
GO:0008535 - respiratory chain complex IV assembly [Evidence IEA]
cbb3-type cytochrome oxidase assembly protein CcoS
COORDINATES: similar to AA sequence:RefSeq:WP_008205216.1
formate/nitrite transporter family protein
COORDINATES: protein motif:HMM:NF014667.2
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:NF012344.2
COORDINATES: similar to AA sequence:RefSeq:WP_008205206.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008555745.1
COORDINATES: similar to AA sequence:RefSeq:WP_018319857.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_009573265.1
COORDINATES: similar to AA sequence:RefSeq:WP_013069339.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573263.1
COORDINATES: protein motif:HMM:NF015366.2
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: protein motif:HMM:NF014073.2
tripartite tricarboxylate transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_013165028.1
COORDINATES: similar to AA sequence:RefSeq:WP_010089693.1
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611339.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_010138494.1
COORDINATES: protein motif:HMM:NF015297.2
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013849875.1
COORDINATES: protein motif:HMM:NF015411.2
COORDINATES: similar to AA sequence:RefSeq:WP_008945311.1
COORDINATES: similar to AA sequence:RefSeq:WP_018062964.1
COORDINATES: protein motif:HMM:NF017494.2
GO:0016836 - hydro-lyase activity [Evidence IEA]
fumarate hydratase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF007342.0
COORDINATES: protein motif:HMM:TIGR02122.1
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_014992767.1
COORDINATES: protein motif:HMM:NF012488.2
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_013530808.1
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.
spermidine/putrescine ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_007598161.1
COORDINATES: similar to AA sequence:RefSeq:WP_002252250.1
COORDINATES: protein motif:HMM:NF012698.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
winged helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011047911.1
COORDINATES: protein motif:HMM:NF017747.2
COORDINATES: similar to AA sequence:RefSeq:WP_011047916.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008283108.1
GO:0050480 - imidazolonepropionase activity [Evidence IEA]
GO:0006548 - histidine catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008283109.1
GO:0004397 - histidine ammonia-lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008756129.1
GO:0050129 - N-formylglutamate deformylase activity [Evidence IEA]
GO:0019557 - histidine catabolic process to glutamate and formate [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009813150.1
GO:0016153 - urocanate hydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014873197.1
COORDINATES: similar to AA sequence:RefSeq:WP_014873196.1
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_014873194.1
tripartite tricarboxylate transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF020897.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009831456.1
aspartate aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007256784.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294510.1
COORDINATES: similar to AA sequence:RefSeq:WP_009816496.1
COORDINATES: similar to AA sequence:RefSeq:WP_009830388.1
COORDINATES: similar to AA sequence:RefSeq:WP_008279759.1
COORDINATES: similar to AA sequence:RefSeq:WP_011540012.1
COORDINATES: similar to AA sequence:RefSeq:WP_015494171.1
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012354.2
COORDINATES: similar to AA sequence:RefSeq:WP_011241947.1
COORDINATES: similar to AA sequence:RefSeq:WP_008283006.1
COORDINATES: protein motif:HMM:NF040249.1
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
COORDINATES: similar to AA sequence:RefSeq:WP_019294536.1
COORDINATES: protein motif:HMM:NF014795.2
COORDINATES: protein motif:HMM:NF014794.2
GO:0003824 - catalytic activity [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011242193.1
aspartate/glutamate racemase family protein
COORDINATES: protein motif:HMM:NF033563.0
COORDINATES: protein motif:HMM:NF012512.2
COORDINATES: similar to AA sequence:RefSeq:WP_006931434.1
COORDINATES: similar to AA sequence:RefSeq:WP_014874722.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611355.1
frameshifted; internal stop; 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_009811590.1
GO:0030638 - polyketide metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008204933.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008204932.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0033286 - ATPase-coupled ectoine transmembrane transporter activity [Evidence IEA]; GO:0033288 - ATPase-coupled hydroxyectoine transmembrane transporter activity [Evidence IEA]
GO:0051470 - ectoine transport [Evidence IEA]; GO:0033308 - hydroxyectoine transport [Evidence IEA]
ectoine/hydroxyectoine ABC transporter permease subunit EhuC
COORDINATES: similar to AA sequence:RefSeq:WP_008204931.1
ectoine/hydroxyectoine ABC transporter permease subunit EhuD
COORDINATES: similar to AA sequence:RefSeq:WP_020593989.1
GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0005524 - ATP binding [Evidence IEA]; GO:0033286 - ATPase-coupled ectoine transmembrane transporter activity [Evidence IEA]; GO:0033288 - ATPase-coupled hydroxyectoine transmembrane transporter activity [Evidence IEA]
ectoine/hydroxyectoine ABC transporter ATP-binding protein EhuA
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008204927.1
COORDINATES: protein motif:HMM:NF036686.2