Salipiger abyssi strain JLT2014 plasmid pPABY2, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Salipiger.
Deep-sea bacteria in the southern Pacific
Submitted (06-APR-2016) State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Zhoulongquan Building A2-319, Xianan, Xiamen 361005, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP015090.1.\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-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/06/2023 04:28:10\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) :: 5,147\nCDSs (total) :: 5,091\nGenes (coding) :: 5,023\nCDSs (with protein) :: 5,023\nGenes (RNA) :: 56\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 4\nPseudo Genes (total) :: 68\nCDSs (without protein) :: 68\nPseudo Genes (ambiguous residues) :: 0 of 68\nPseudo Genes (frameshifted) :: 32 of 68\nPseudo Genes (incomplete) :: 33 of 68\nPseudo Genes (internal stop) :: 6 of 68\nPseudo Genes (multiple problems) :: 2 of 68\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_003526610.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013247.2
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF013046.2
COORDINATES: protein motif:HMM:NF013228.2
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: protein motif:HMM:NF020090.2
COORDINATES: similar to AA sequence:RefSeq:WP_009451250.1
GO:0016624 - oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002966546.1
GO:0045254 - pyruvate dehydrogenase complex [Evidence IEA]
GO:0004742 - dihydrolipoyllysine-residue acetyltransferase activity [Evidence IEA]; GO:0004738 - pyruvate dehydrogenase activity [Evidence IEA]
GO:0006086 - acetyl-CoA biosynthetic process from pyruvate [Evidence IEA]
pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_009572125.1
isochorismatase family cysteine hydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_009572126.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572127.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067533.1
COORDINATES: similar to AA sequence:RefSeq:WP_018067532.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018067531.1
COORDINATES: protein motif:HMM:NF018952.2
COORDINATES: similar to AA sequence:RefSeq:WP_009025463.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010102930.1
COORDINATES: similar to AA sequence:RefSeq:WP_007756810.1
COORDINATES: similar to AA sequence:RefSeq:WP_007435657.1
COORDINATES: similar to AA sequence:RefSeq:WP_009486586.1
COORDINATES: similar to AA sequence:RefSeq:WP_014807874.1
COORDINATES: similar to AA sequence:RefSeq:WP_006904563.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_009176260.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014879814.1
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_010547788.1
COORDINATES: similar to AA sequence:RefSeq:WP_014329271.1
COORDINATES: similar to AA sequence:RefSeq:WP_005853356.1
COORDINATES: similar to AA sequence:RefSeq:WP_005614371.1
COORDINATES: similar to AA sequence:RefSeq:WP_007794744.1
GO:0018659 - 4-hydroxybenzoate 3-monooxygenase activity [Evidence IEA]
GO:0018874 - benzoate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008886111.1
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]
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF015048.2
COORDINATES: similar to AA sequence:RefSeq:WP_009503032.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046470.1
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008387032.1
COORDINATES: similar to AA sequence:RefSeq:WP_008831923.1
GO:0016747 - acyltransferase activity, transferring groups other than amino-acyl groups [Evidence IEA]
GO:0019619 - 3,4-dihydroxybenzoate catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011746548.1
GO:0070403 - NAD+ binding [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_013654541.1
COORDINATES: similar to AA sequence:RefSeq:WP_013654540.1
COORDINATES: similar to AA sequence:RefSeq:WP_012356301.1
COORDINATES: similar to AA sequence:RefSeq:WP_018315124.1
COORDINATES: similar to AA sequence:RefSeq:WP_011811795.1
COORDINATES: similar to AA sequence:RefSeq:WP_008071293.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008071297.1
COORDINATES: protein motif:HMM:NF015445.2
GO:0055085 - transmembrane transport [Evidence IEA]
TRAP transporter substrate-binding protein DctP
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_008944058.1
COORDINATES: similar to AA sequence:RefSeq:WP_006403979.1
COORDINATES: protein motif:HMM:NF019590.2
COORDINATES: similar to AA sequence:RefSeq:WP_018633664.1
COORDINATES: similar to AA sequence:RefSeq:WP_004259956.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009572696.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803668.1
COORDINATES: similar to AA sequence:RefSeq:WP_009809155.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801620.1
COORDINATES: similar to AA sequence:RefSeq:WP_013762241.1
COORDINATES: similar to AA sequence:RefSeq:WP_009176074.1
COORDINATES: similar to AA sequence:RefSeq:WP_020010194.1
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005610350.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801630.1
COORDINATES: similar to AA sequence:RefSeq:WP_019964922.1
GO:0005515 - protein binding [Evidence IEA]; GO:0004856 - xylulokinase activity [Evidence IEA]
GO:0042732 - D-xylose metabolic process [Evidence IEA]; GO:0005997 - xylulose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010973745.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504656.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815512.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859462.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327482.1
COORDINATES: similar to AA sequence:RefSeq:WP_005859475.1
GO:0051304 - chromosome separation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008593388.1
COORDINATES: similar to AA sequence:RefSeq:WP_109614505.1
COORDINATES: similar to AA sequence:RefSeq:WP_216331782.1
COORDINATES: similar to AA sequence:RefSeq:WP_008593382.1
GO:0005215 - transporter activity [Evidence IEA]
TAXI family TRAP transporter solute-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008593380.1
COORDINATES: protein motif:HMM:NF012791.2
COORDINATES: similar to AA sequence:RefSeq:WP_007689010.1
COORDINATES: similar to AA sequence:RefSeq:WP_007689008.1
fumarylacetoacetate hydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007689006.1
COORDINATES: similar to AA sequence:RefSeq:WP_007689004.1
COORDINATES: protein motif:HMM:NF019013.2
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007689021.1
COORDINATES: similar to AA sequence:RefSeq:WP_007689019.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504370.1
COORDINATES: similar to AA sequence:RefSeq:WP_007689012.1
COORDINATES: protein motif:HMM:NF024644.2
COORDINATES: similar to AA sequence:RefSeq:WP_012402843.1
COORDINATES: protein motif:HMM:NF012655.2
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_019198728.1
COORDINATES: similar to AA sequence:RefSeq:WP_012321606.1
COORDINATES: protein motif:HMM:NF019640.2
COORDINATES: protein motif:HMM:NF037009.2
COORDINATES: similar to AA sequence:RefSeq:WP_013425672.1
COORDINATES: protein motif:HMM:NF015316.2
outer membrane protein transport protein
COORDINATES: similar to AA sequence:RefSeq:WP_018698530.1
COORDINATES: protein motif:HMM:NF013706.2
COORDINATES: protein motif:HMM:NF024966.2
COORDINATES: similar to AA sequence:RefSeq:WP_006049809.1
COORDINATES: similar to AA sequence:RefSeq:WP_007744060.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007586867.1
xanthine dehydrogenase family protein subunit M
COORDINATES: protein motif:HMM:NF017999.2
COORDINATES: protein motif:HMM:NF013866.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013959617.1
COORDINATES: similar to AA sequence:RefSeq:WP_007436734.1
COORDINATES: similar to AA sequence:RefSeq:WP_008165114.1
CDP-6-deoxy-delta-3,4-glucoseen reductase
LysR substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008887779.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887668.1
COORDINATES: similar to AA sequence:RefSeq:WP_009450123.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887780.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887816.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008887748.1
COORDINATES: protein motif:HMM:NF018513.2
TRAP transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008887664.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887658.1
LLM class flavin-dependent oxidoreductase
COORDINATES: protein motif:HMM:NF012706.2
COORDINATES: similar to AA sequence:RefSeq:WP_006462162.1
COORDINATES: similar to AA sequence:RefSeq:WP_020202516.1
COORDINATES: similar to AA sequence:RefSeq:WP_007923777.1
COORDINATES: similar to AA sequence:RefSeq:WP_009451183.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012251054.1
COORDINATES: similar to AA sequence:RefSeq:WP_012111908.1
GO:0004121 - cystathionine beta-lyase activity [Evidence IEA]
GO:0009086 - methionine biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012790.2
COORDINATES: protein motif:HMM:NF024859.2
COORDINATES: similar to AA sequence:RefSeq:WP_009571806.1
COORDINATES: protein motif:HMM:NF014585.2
COORDINATES: similar to AA sequence:RefSeq:WP_007181206.1
COORDINATES: protein motif:HMM:NF013672.2
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007104136.1
COORDINATES: similar to AA sequence:RefSeq:WP_007768410.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861696.1
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_020043699.1
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_020043034.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_008887440.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_008887554.1
COORDINATES: similar to AA sequence:RefSeq:WP_002719725.1
GO:0004024 - alcohol dehydrogenase activity, zinc-dependent [Evidence IEA]; GO:0051903 - S-(hydroxymethyl)glutathione dehydrogenase activity [Evidence IEA]
GO:0006113 - fermentation [Evidence IEA]; GO:0009404 - toxin metabolic process [Evidence IEA]
S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_009506463.1
GO:0018738 - S-formylglutathione hydrolase activity [Evidence IEA]
GO:0046292 - formaldehyde metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011567179.1
COORDINATES: similar to AA sequence:RefSeq:WP_009817311.1
methanol/ethanol family PQQ-dependent dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_008887384.1
c-type cytochrome, methanol metabolism-related
COORDINATES: similar to AA sequence:RefSeq:WP_012177156.1
substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020039920.1
PQQ-dependent catabolism-associated CXXCW motif protein
COORDINATES: similar to AA sequence:RefSeq:WP_011567184.1
quinoprotein dehydrogenase-associated SoxYZ-like carrier
COORDINATES: similar to AA sequence:RefSeq:WP_007802686.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802688.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887446.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887402.1
COORDINATES: similar to AA sequence:RefSeq:WP_003528747.1
YVTN family beta-propeller repeat protein
COORDINATES: similar to AA sequence:RefSeq:WP_007802697.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802698.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802699.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802606.1
COORDINATES: similar to AA sequence:RefSeq:WP_011567175.1
quinoprotein relay system zinc metallohydrolase 2
COORDINATES: similar to AA sequence:RefSeq:WP_008887377.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887526.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802630.1
COORDINATES: similar to AA sequence:RefSeq:WP_020039909.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802634.1
FIST N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008887426.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802638.1
GO:0051907 - S-(hydroxymethyl)glutathione synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001435.1
COORDINATES: similar to AA sequence:RefSeq:WP_007802649.1
GO:0018149 - peptide cross-linking [Evidence IEA]; GO:0018189 - pyrroloquinoline quinone biosynthetic process [Evidence IEA]
pyrroloquinoline quinone biosynthesis protein PqqE
COORDINATES: similar to AA sequence:RefSeq:WP_008281623.1
GO:0048038 - quinone binding [Evidence IEA]
GO:0018189 - pyrroloquinoline quinone biosynthetic process [Evidence IEA]
pyrroloquinoline quinone biosynthesis peptide chaperone PqqD
COORDINATES: similar to AA sequence:RefSeq:WP_008887406.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887512.1
pyrroloquinoline quinone biosynthesis protein PqqB
COORDINATES: similar to AA sequence:RefSeq:WP_012177128.1
pyrroloquinoline quinone precursor peptide PqqA
COORDINATES: similar to AA sequence:RefSeq:WP_012113594.1
COORDINATES: similar to AA sequence:RefSeq:WP_003290281.1
COORDINATES: similar to AA sequence:RefSeq:WP_010927182.1
COORDINATES: similar to AA sequence:RefSeq:WP_011811944.1
COORDINATES: similar to AA sequence:RefSeq:WP_013958623.1