Salipiger abyssi strain JLT2014 plasmid pPABY1, 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\nCP015091.1.\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: similar to AA sequence:RefSeq:WP_007626654.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
sugar ABC transporter ATP-binding 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_012044835.1
SMP-30/gluconolactonase/LRE family protein
COORDINATES: protein motif:HMM:NF024799.2
sugar ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_018063091.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF027681.2
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006609955.1
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_006337153.1
COORDINATES: protein motif:HMM:NF014757.2
3-hydroxyacyl-CoA dehydrogenase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008335700.1
COORDINATES: similar to AA sequence:RefSeq:WP_011582240.1
COORDINATES: similar to AA sequence:RefSeq:WP_013945814.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008169282.1
COORDINATES: similar to AA sequence:RefSeq:WP_010397784.1
COORDINATES: protein motif:HMM:NF015431.2
LysR substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF013253.2
COORDINATES: similar to AA sequence:RefSeq:WP_012976514.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014795.2
GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011351538.1
COORDINATES: protein motif:HMM:NF013086.2
COORDINATES: protein motif:HMM:NF014658.2
COORDINATES: similar to AA sequence:RefSeq:WP_018386975.1
tripartite tricarboxylate transporter permease
COORDINATES: protein motif:HMM:NF018979.2
tripartite tricarboxylate transporter TctB family protein
COORDINATES: protein motif:HMM:NF015366.2
tripartite tricarboxylate transporter substrate binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_002614164.1
thiamine pyrophosphate-requiring protein
COORDINATES: similar to AA sequence:RefSeq:WP_013536466.1
COORDINATES: similar to AA sequence:RefSeq:WP_007751033.1
COORDINATES: similar to AA sequence:RefSeq:WP_013383127.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_009763795.1
COORDINATES: similar to AA sequence:RefSeq:WP_009763796.1
COORDINATES: similar to AA sequence:RefSeq:WP_018687425.1
COORDINATES: similar to AA sequence:RefSeq:WP_010395401.1
COORDINATES: similar to AA sequence:RefSeq:WP_008872356.1
COORDINATES: similar to AA sequence:RefSeq:WP_011747962.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009763797.1
COORDINATES: protein motif:HMM:NF013434.2
COORDINATES: protein motif:HMM:TIGR03453.1
COORDINATES: protein motif:HMM:TIGR03454.1
COORDINATES: protein motif:HMM:NF040974.1
COORDINATES: similar to AA sequence:RefSeq:WP_017998420.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_019956758.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0097351 - toxin sequestering activity [Evidence IEA]
GO:0001558 - regulation of cell growth [Evidence IEA]
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_008327527.1
COORDINATES: similar to AA sequence:RefSeq:WP_007816866.1
COORDINATES: similar to AA sequence:RefSeq:WP_018301020.1
energy-coupling factor transporter transmembrane component T
COORDINATES: similar to AA sequence:RefSeq:WP_002719325.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0015225 - biotin transmembrane transporter activity [Evidence IEA]
GO:0015878 - biotin transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008327528.1
COORDINATES: similar to AA sequence:RefSeq:WP_015934538.1
COORDINATES: similar to AA sequence:RefSeq:WP_018904841.1
COORDINATES: similar to AA sequence:RefSeq:WP_007005972.1
COORDINATES: similar to AA sequence:RefSeq:WP_007798570.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009571980.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009571981.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801612.1
branched-chain amino acid ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_009571983.1
COORDINATES: similar to AA sequence:RefSeq:WP_009571984.1
COORDINATES: similar to AA sequence:RefSeq:WP_008885348.1
COORDINATES: similar to AA sequence:RefSeq:WP_007801604.1
COORDINATES: protein motif:HMM:NF019349.2
COORDINATES: similar to AA sequence:RefSeq:WP_007801600.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_007801599.1
hydantoinase B/oxoprolinase family protein
TRAP transporter substrate-binding protein
COORDINATES: protein motif:HMM:NF016200.2
COORDINATES: similar to AA sequence:RefSeq:WP_007801589.1
GO:0005886 - plasma membrane [Evidence IEA]; GO:0031317 - tripartite ATP-independent periplasmic transporter complex [Evidence IEA]
GO:0015556 - C4-dicarboxylate transmembrane transporter activity [Evidence IEA]
GO:0015740 - C4-dicarboxylate transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007797881.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887385.1
hybrid-cluster NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007797887.1
aromatic ring-hydroxylating dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_003535578.1
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_020053005.1
COORDINATES: similar to AA sequence:RefSeq:WP_015458382.1
GO:0004488 - methylenetetrahydrofolate dehydrogenase (NADP+) activity [Evidence IEA]
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase FolD
COORDINATES: similar to AA sequence:RefSeq:WP_002965036.1
electron transfer flavoprotein subunit alpha/FixB family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006936816.1
electron transfer flavoprotein subunit beta/FixA family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019965754.1
COORDINATES: similar to AA sequence:RefSeq:WP_009572615.1
COORDINATES: similar to AA sequence:RefSeq:WP_008507740.1
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_008887495.1
COORDINATES: similar to AA sequence:RefSeq:WP_020010180.1
COORDINATES: similar to AA sequence:RefSeq:WP_007797906.1
GO:0005515 - protein binding [Evidence IEA]; GO:0008115 - sarcosine oxidase activity [Evidence IEA]
GO:1901053 - sarcosine catabolic process [Evidence IEA]
sarcosine oxidase subunit gamma family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009572621.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505681.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0003941 - L-serine ammonia-lyase activity [Evidence IEA]
GO:0009063 - amino acid catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018001668.1
GO:0008864 - formyltetrahydrofolate deformylase activity [Evidence IEA]
GO:0009152 - purine ribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007877084.1
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: similar to AA sequence:RefSeq:WP_008887810.1
COORDINATES: similar to AA sequence:RefSeq:WP_008887874.1
COORDINATES: similar to AA sequence:RefSeq:WP_019297003.1
COORDINATES: similar to AA sequence:RefSeq:WP_015340886.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_014875226.1
COORDINATES: similar to AA sequence:RefSeq:WP_020593578.1
glycine betaine/L-proline ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_020180779.1
COORDINATES: similar to AA sequence:RefSeq:WP_008028919.1
COORDINATES: similar to AA sequence:RefSeq:WP_008209036.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046470.1
COORDINATES: similar to AA sequence:RefSeq:WP_011046469.1
COORDINATES: similar to AA sequence:RefSeq:WP_010140544.1
COORDINATES: similar to AA sequence:RefSeq:WP_007791799.1
COORDINATES: similar to AA sequence:RefSeq:WP_014880916.1
COORDINATES: similar to AA sequence:RefSeq:WP_009465457.1
COORDINATES: similar to AA sequence:RefSeq:WP_007118458.1
COORDINATES: similar to AA sequence:RefSeq:WP_008597633.1
COORDINATES: similar to AA sequence:RefSeq:WP_007426042.1
COORDINATES: protein motif:HMM:NF024811.2
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF012707.2
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007813159.1
COORDINATES: protein motif:HMM:NF012738.2
COORDINATES: similar to AA sequence:RefSeq:WP_007817816.1
COORDINATES: similar to AA sequence:RefSeq:WP_019459378.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF012669.2
COORDINATES: similar to AA sequence:RefSeq:WP_014880630.1
COORDINATES: similar to AA sequence:RefSeq:WP_020087869.1
choline/ethanolamine kinase family protein
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: similar to AA sequence:RefSeq:WP_009178389.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_005613865.1
GO:0003867 - 4-aminobutyrate transaminase activity [Evidence IEA]
GO:0009448 - gamma-aminobutyric acid metabolic process [Evidence IEA]
4-aminobutyrate--2-oxoglutarate transaminase
COORDINATES: similar to AA sequence:RefSeq:WP_009178412.1
COORDINATES: protein motif:HMM:NF012422.2
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF013584.2
COORDINATES: protein motif:HMM:NF012766.2
COORDINATES: protein motif:HMM:NF024850.2
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: similar to AA sequence:RefSeq:WP_011928542.1
COORDINATES: protein motif:HMM:NF014684.2
COORDINATES: similar to AA sequence:RefSeq:WP_008305321.1
GO:0020037 - heme binding [Evidence IEA]; GO:0005506 - iron ion binding [Evidence IEA]; GO:0016705 - oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [Evidence IEA]
COORDINATES: protein motif:HMM:NF012655.2
COORDINATES: similar to AA sequence:RefSeq:WP_011873840.1
COORDINATES: similar to AA sequence:RefSeq:WP_005254735.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_008305320.1
COORDINATES: similar to AA sequence:RefSeq:WP_008302625.1
COORDINATES: protein motif:HMM:NF014164.2
GO:0004177 - aminopeptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008302617.1
COORDINATES: similar to AA sequence:RefSeq:WP_008302618.1
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: protein motif:HMM:NF012296.2
COORDINATES: protein motif:HMM:NF020039.2
COORDINATES: similar to AA sequence:RefSeq:WP_019655232.1
COORDINATES: protein motif:HMM:NF013757.2
COORDINATES: protein motif:HMM:NF024946.2
COORDINATES: similar to AA sequence:RefSeq:WP_076611302.1
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_007802443.1
GO:0003985 - acetyl-CoA C-acetyltransferase activity [Evidence IEA]
GO:0006631 - fatty acid metabolic process [Evidence IEA]
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025304.2
helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF021148.2
COORDINATES: similar to AA sequence:RefSeq:WP_008888059.1
sulfite exporter TauE/SafE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008888025.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888161.1
GO:0008484 - sulfuric ester hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008887783.1
COORDINATES: similar to AA sequence:RefSeq:WP_010142124.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888193.1
COORDINATES: similar to AA sequence:RefSeq:WP_008888057.1
tripartite tricarboxylate transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008888325.1
COORDINATES: similar to AA sequence:RefSeq:WP_016432971.1
formylglycine-generating enzyme family protein
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: protein motif:HMM:NF013080.2
COORDINATES: similar to AA sequence:RefSeq:WP_019016840.1
COORDINATES: similar to AA sequence:RefSeq:WP_012653182.1
COORDINATES: similar to AA sequence:RefSeq:WP_020592110.1
MurR/RpiR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020285544.1
COORDINATES: similar to AA sequence:RefSeq:WP_008594675.1
COORDINATES: similar to AA sequence:RefSeq:WP_018448592.1
COORDINATES: similar to AA sequence:RefSeq:WP_020285539.1
COORDINATES: similar to AA sequence:RefSeq:WP_018066188.1
amidohydrolase/deacetylase family metallohydrolase
COORDINATES: similar to AA sequence:RefSeq:WP_018066189.1
COORDINATES: similar to AA sequence:RefSeq:WP_012248503.1
COORDINATES: similar to AA sequence:RefSeq:WP_008594660.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861587.1
aminotransferase class V-fold PLP-dependent enzyme
COORDINATES: similar to AA sequence:RefSeq:WP_008335932.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009804126.1
NADPH:quinone oxidoreductase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011501192.1
GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors [Evidence IEA]
COORDINATES: protein motif:HMM:NF013775.2
COORDINATES: similar to AA sequence:RefSeq:WP_009804135.1
COORDINATES: similar to AA sequence:RefSeq:WP_016436023.1
COORDINATES: similar to AA sequence:RefSeq:WP_011389061.1
COORDINATES: similar to AA sequence:RefSeq:WP_009804129.1
COORDINATES: protein motif:HMM:NF025114.2
COORDINATES: similar to AA sequence:RefSeq:WP_008335498.1
GO:0005575 - cellular_component [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
YbhB/YbcL family Raf kinase inhibitor-like protein
COORDINATES: similar to AA sequence:RefSeq:WP_007682108.1
COORDINATES: protein motif:HMM:NF013722.2
MaoC/PaaZ C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014214265.1
COORDINATES: similar to AA sequence:RefSeq:WP_008833189.1
GO:0016746 - acyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012596.2
COORDINATES: similar to AA sequence:RefSeq:WP_009824378.1
COORDINATES: similar to AA sequence:RefSeq:WP_009823548.1
COORDINATES: protein motif:HMM:NF025694.2
COORDINATES: similar to AA sequence:RefSeq:WP_014747362.1
COORDINATES: similar to AA sequence:RefSeq:WP_006394735.1
COORDINATES: protein motif:HMM:NF020897.2
COORDINATES: similar to AA sequence:RefSeq:WP_013511910.1
COORDINATES: similar to AA sequence:RefSeq:WP_018065879.1