Rubrobacter indicoceani strain SCSIO 08198 plasmid unnamed1, complete sequence.
Bacteria; Actinomycetota; Rubrobacteria; Rubrobacterales; Rubrobacteraceae; Rubrobacter.
Whole genome sequence of Indioceanicola profundi
Submitted (18-JUL-2018) 164, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Chinese Academy of Sciences, Guangzhou 510301, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP031116.1.\nBacteria and source DNA available from Xin-Peng Tian.\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 Method :: FALCON v. V0.3.0; proovread v. 2.12;\n Celera Assembler v. 8.3; SMRT Analysis v.\n V2.3.0; GATK v. V1.6-13\nExpected Final Version :: yes\nGenome Coverage :: 444.0x\nSequencing Technology :: Illumina; PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/21/2023 02:09:43\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) :: 3,085\nCDSs (total) :: 3,033\nGenes (coding) :: 3,017\nCDSs (with protein) :: 3,017\nGenes (RNA) :: 52\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 46\nncRNAs :: 3\nPseudo Genes (total) :: 16\nCDSs (without protein) :: 16\nPseudo Genes (ambiguous residues) :: 0 of 16\nPseudo Genes (frameshifted) :: 2 of 16\nPseudo Genes (incomplete) :: 12 of 16\nPseudo Genes (internal stop) :: 2 of 16\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_007570464.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016530 - metallochaperone activity [Evidence IEA]
GO:0019627 - urea metabolic process [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013858.2
GO:0016151 - nickel cation binding [Evidence IEA]
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_017286272.1
GO:0016151 - nickel cation binding [Evidence IEA]; GO:0009039 - urease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008426011.1
GO:0035550 - urease complex [Evidence IEA]
GO:0043419 - urea catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015225581.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565584.1
COORDINATES: similar to AA sequence:RefSeq:WP_020221830.1
COORDINATES: similar to AA sequence:RefSeq:WP_008963882.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00442
guanidine-I (ykkC/yxkD leader) riboswitch; Guanidine-I riboswitches control genes whose products are involved in modification or pumping out guanidine as a toxic compound from bacteria; This is class of guanidine riboswitches is based on the ykkC/yxkD leader; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_009336057.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF013918.2
ferric reductase-like transmembrane domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012870730.1
COORDINATES: protein motif:HMM:NF014567.2
COORDINATES: similar to AA sequence:RefSeq:WP_011600471.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF015094.2
COORDINATES: similar to AA sequence:RefSeq:WP_011392156.1
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_011564343.1
GO:0004750 - D-ribulose-phosphate 3-epimerase activity [Evidence IEA]
GO:0006098 - pentose-phosphate shunt [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006552153.1
COORDINATES: similar to AA sequence:RefSeq:WP_006552154.1
GO:0004805 - trehalose-phosphatase activity [Evidence IEA]
GO:0005992 - trehalose biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011564053.1
glycerol-3-phosphate dehydrogenase/oxidase
COORDINATES: similar to AA sequence:RefSeq:WP_002528362.1
COORDINATES: similar to AA sequence:RefSeq:WP_014846859.1
GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009199880.1
COORDINATES: similar to AA sequence:RefSeq:WP_016666556.1
COORDINATES: similar to AA sequence:RefSeq:WP_009052506.1
GO:0004751 - ribose-5-phosphate isomerase activity [Evidence IEA]
GO:0009052 - pentose-phosphate shunt, non-oxidative branch [Evidence IEA]
COORDINATES: protein motif:HMM:NF013434.2
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006681419.1
COORDINATES: similar to AA sequence:RefSeq:WP_016444214.1
GO:0016787 - hydrolase activity [Evidence IEA]
GO:0008152 - metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009153005.1
COORDINATES: similar to AA sequence:RefSeq:WP_016444355.1
COORDINATES: protein motif:HMM:NF013916.2
COORDINATES: similar to AA sequence:RefSeq:WP_017954221.1
COORDINATES: similar to AA sequence:RefSeq:WP_016934401.1
COORDINATES: similar to AA sequence:RefSeq:WP_020722258.1
GO:0004802 - transketolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020514227.1
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_002147994.1
COORDINATES: similar to AA sequence:RefSeq:WP_015246385.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
redox-sensitive transcriptional activator SoxR
COORDINATES: similar to AA sequence:RefSeq:WP_020644412.1
COORDINATES: similar to AA sequence:RefSeq:WP_009945331.1
xanthine dehydrogenase family protein molybdopterin-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_009945332.1
xanthine dehydrogenase family protein subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_019607510.1
GO:0046872 - metal ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
2Fe-2S iron-sulfur cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013530979.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_007413240.1
COORDINATES: protein motif:HMM:NF024758.2
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: similar to AA sequence:RefSeq:WP_015927228.1
trypsin-like peptidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017300844.1
COORDINATES: similar to AA sequence:RefSeq:WP_018557530.1
GO:0050043 - lactate racemase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011563658.1
COORDINATES: similar to AA sequence:RefSeq:WP_006219667.1
GO:0016829 - lyase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007917020.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565320.1
COORDINATES: similar to AA sequence:RefSeq:WP_006942120.1
COORDINATES: similar to AA sequence:RefSeq:WP_007779429.1
pyridoxal phosphate-dependent aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_016859773.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563670.1
COORDINATES: similar to AA sequence:RefSeq:WP_012642239.1
COORDINATES: protein motif:HMM:NF015331.2
COORDINATES: similar to AA sequence:RefSeq:WP_015489180.1
COORDINATES: protein motif:HMM:NF012257.2
Crp/Fnr family transcriptional regulator
COORDINATES: protein motif:HMM:NF021098.2
PRC and DUF2382 domain-containing protein
COORDINATES: protein motif:HMM:NF017373.2
COORDINATES: protein motif:HMM:NF013672.2
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: protein motif:HMM:NF017238.2
GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity [Evidence IEA]
GO:0009877 - nodulation [Evidence IEA]; GO:0009312 - oligosaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF019604.2
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: protein motif:HMM:TIGR01509.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565800.1
COORDINATES: similar to AA sequence:RefSeq:WP_003543957.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_012521997.1
GO:0003674 - molecular_function [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012873818.1
COORDINATES: similar to AA sequence:RefSeq:WP_011417387.1
COORDINATES: similar to AA sequence:RefSeq:WP_019328137.1
COORDINATES: protein motif:HMM:NF005750.0
GO:0008863 - formate dehydrogenase (NAD+) activity [Evidence IEA]; GO:0051287 - NAD binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007168768.1
COORDINATES: similar to AA sequence:RefSeq:WP_012950101.1
COORDINATES: similar to AA sequence:RefSeq:WP_015236150.1
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF019310.2
COORDINATES: similar to AA sequence:RefSeq:WP_018610922.1
GO:0018578 - protocatechuate 3,4-dioxygenase activity [Evidence IEA]
GO:0046278 - 3,4-dihydroxybenzoate metabolic process [Evidence IEA]
protocatechuate 3,4-dioxygenase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_009942208.1
protocatechuate 3,4-dioxygenase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_003222404.1
COORDINATES: similar to AA sequence:RefSeq:WP_019811469.1
COORDINATES: similar to AA sequence:RefSeq:WP_011564561.1
COORDINATES: protein motif:HMM:NF021637.2
COORDINATES: similar to AA sequence:RefSeq:WP_011563707.1
GO:0003824 - catalytic activity [Evidence IEA]
NAD-dependent epimerase/dehydratase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011563708.1
COORDINATES: similar to AA sequence:RefSeq:WP_017563665.1
four-helix bundle copper-binding protein
COORDINATES: protein motif:HMM:NF012870.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004112207.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565666.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565665.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF012298.2
GO:0004672 - protein kinase activity [Evidence IEA]
GO:0006468 - protein phosphorylation [Evidence IEA]
COORDINATES: protein motif:HMM:NF024703.2
COORDINATES: similar to AA sequence:RefSeq:WP_005451542.1
COORDINATES: similar to AA sequence:RefSeq:WP_011581211.1
COORDINATES: similar to AA sequence:RefSeq:WP_011564671.1
COORDINATES: similar to AA sequence:RefSeq:WP_011564672.1
hydantoinase B/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011564673.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_012893067.1
COORDINATES: similar to AA sequence:RefSeq:WP_012121969.1
COORDINATES: similar to AA sequence:RefSeq:WP_008593321.1
COORDINATES: similar to AA sequence:RefSeq:WP_012782860.1
COORDINATES: protein motif:HMM:NF012946.2
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF014126.2
GO:0071705 - nitrogen compound transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF041518.1
choice-of-anchor Q domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017653860.1
COORDINATES: similar to AA sequence:RefSeq:WP_009473998.1
GO:0008150 - biological_process [Evidence IEA]
TIGR03557 family F420-dependent LLM class oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_020375479.1
GO:0016811 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011565917.1
lactate racemase domain-containing protein
COORDINATES: protein motif:HMM:NF024771.2
mandelate racemase/muconate lactonizing enzyme family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011565928.1
COORDINATES: protein motif:HMM:NF012335.2
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004967956.1
COORDINATES: similar to AA sequence:RefSeq:WP_015041295.1
COORDINATES: similar to AA sequence:RefSeq:WP_018832338.1
COORDINATES: similar to AA sequence:RefSeq:WP_011565801.1
COORDINATES: similar to AA sequence:RefSeq:WP_011563528.1
COORDINATES: protein motif:HMM:NF019349.2
FadR/GntR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011565911.1
COORDINATES: protein motif:HMM:NF014628.2
COORDINATES: similar to AA sequence:RefSeq:WP_011565913.1
GO:0009055 - electron transfer activity [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0019516 - lactate oxidation [Evidence IEA]
LutB/LldF family L-lactate oxidation iron-sulfur protein
COORDINATES: similar to AA sequence:RefSeq:WP_006675952.1
COORDINATES: protein motif:HMM:NF018682.2
four-carbon acid sugar kinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011565907.1
GO:0050570 - 4-hydroxythreonine-4-phosphate dehydrogenase activity [Evidence IEA]
GO:0008615 - pyridoxine biosynthetic process [Evidence IEA]
4-hydroxythreonine-4-phosphate dehydrogenase PdxA
COORDINATES: similar to AA sequence:RefSeq:WP_003386443.1
COORDINATES: protein motif:HMM:NF013741.2
COORDINATES: similar to AA sequence:RefSeq:WP_017870604.1
COORDINATES: protein motif:HMM:NF013810.2
COORDINATES: protein motif:HMM:NF013899.2