Gemmobacter aquarius strain HYN0069 plasmid unnamed1, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Gemmobacter.
Submitted (17-APR-2018) College of Health Science, Korea University, Anam-ro 145, Seoul 02841, South Korea
REFSEQ INFORMATION: The reference sequence is identical to\nCP028919.1.\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 Method :: PacBio SMRT Analysis v. v2.3\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 221.67x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/16/2022 03:16:07\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.3\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,135\nCDSs (total) :: 4,070\nGenes (coding) :: 3,916\nCDSs (with protein) :: 3,916\nGenes (RNA) :: 65\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 3\nPseudo Genes (total) :: 154\nCDSs (without protein) :: 154\nPseudo Genes (ambiguous residues) :: 0 of 154\nPseudo Genes (frameshifted) :: 105 of 154\nPseudo Genes (incomplete) :: 61 of 154\nPseudo Genes (internal stop) :: 9 of 154\nPseudo Genes (multiple problems) :: 17 of 154\nCRISPR Arrays :: 1\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+.
leukotoxin LktA family filamentous adhesin
COORDINATES: protein motif:HMM:NF015803.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF025082.2
COORDINATES: similar to AA sequence:RefSeq:WP_005854422.1
FdtA/QdtA family cupin domain-containing protein
COORDINATES: protein motif:HMM:NF016464.2
COORDINATES: similar to AA sequence:RefSeq:WP_011057184.1
DegT/DnrJ/EryC1/StrS family aminotransferase
COORDINATES: similar to AA sequence:RefSeq:WP_013418108.1
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_019516846.1
COORDINATES: protein motif:HMM:NF012744.2
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: similar to AA sequence:RefSeq:WP_008029453.1
COORDINATES: similar to AA sequence:RefSeq:WP_011909218.1
COORDINATES: similar to AA sequence:RefSeq:WP_009449181.1
GO:0005886 - plasma membrane [Evidence IEA]
GO:0009410 - response to xenobiotic stimulus [Evidence IEA]; GO:0006855 - xenobiotic transmembrane transport [Evidence IEA]
DHA2 family efflux MFS transporter permease subunit
COORDINATES: protein motif:HMM:NF027567.2
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002721800.1
COORDINATES: protein motif:HMM:NF013740.2
COORDINATES: protein motif:HMM:NF019174.2
COORDINATES: similar to AA sequence:RefSeq:WP_008283223.1
COORDINATES: similar to AA sequence:RefSeq:WP_013067999.1
COORDINATES: similar to AA sequence:RefSeq:WP_007426532.1
COORDINATES: similar to AA sequence:RefSeq:WP_018147495.1
COORDINATES: similar to AA sequence:RefSeq:WP_009806115.1
COORDINATES: protein motif:HMM:NF012760.2
GO:0016742 - hydroxymethyl-, formyl- and related transferase activity [Evidence IEA]
GO:0009058 - biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013882.2
polysaccharide pyruvyl transferase family protein
COORDINATES: protein motif:HMM:NF019850.2
COORDINATES: protein motif:HMM:NF025072.2
COORDINATES: protein motif:HMM:NF015417.2
COORDINATES: protein motif:HMM:NF024583.2
GO:0005515 - protein binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019923188.1
COORDINATES: similar to AA sequence:RefSeq:WP_009816029.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011950286.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010973575.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001056.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001055.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018064026.1
COORDINATES: similar to AA sequence:RefSeq:WP_015314573.1
COORDINATES: protein motif:HMM:NF012576.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LacI family DNA-binding transcriptional regulator
COORDINATES: protein motif:HMM:TIGR00229.1
COORDINATES: protein motif:HMM:NF013830.2
COORDINATES: protein motif:HMM:NF025663.2
ATP-grasp fold amidoligase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611342.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
frameshifted; 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_011749306.1
frameshifted; 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.
COORDINATES: similar to AA sequence:RefSeq:WP_012643394.1
GSU2403 family nucleotidyltransferase fold protein
COORDINATES: protein motif:HMM:NF012698.2
COORDINATES: similar to AA sequence:RefSeq:WP_003290589.1
COORDINATES: similar to AA sequence:RefSeq:WP_011090936.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF019316.2
COORDINATES: protein motif:HMM:NF012711.2
COORDINATES: similar to AA sequence:RefSeq:WP_008329810.1
COORDINATES: protein motif:HMM:NF015737.2
autotransporter outer membrane beta-barrel domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007117613.1
COORDINATES: protein motif:HMM:NF017003.2
Lpg1974 family pore-forming outer membrane protein
COORDINATES: protein motif:HMM:NF024109.2
COORDINATES: protein motif:HMM:NF012296.2
COORDINATES: protein motif:HMM:NF024860.2
COORDINATES: similar to AA sequence:RefSeq:WP_017971791.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_076612405.1
frameshifted; internal stop; 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.
COORDINATES: similar to AA sequence:RefSeq:WP_076611807.1
GO:0015074 - DNA integration [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: similar to AA sequence:RefSeq:WP_011970376.1
TnpB, as the term is used for proteins encoded by IS66 family insertion elements, is considered an accessory protein, since TnpC, encoded by a neighboring gene, is a DDE family transposase; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS66 family insertion sequence element accessory protein TnpB
COORDINATES: similar to AA sequence:RefSeq:WP_007811349.1
COORDINATES: similar to AA sequence:RefSeq:WP_028710025.1
COORDINATES: protein motif:HMM:NF016852.2
COORDINATES: protein motif:HMM:NF013621.2
GO:0003824 - catalytic activity [Evidence IEA]
adenylyltransferase/cytidyltransferase family protein
COORDINATES: protein motif:HMM:NF012334.2
COORDINATES: similar to AA sequence:RefSeq:WP_008071823.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807635.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008071821.1
COORDINATES: similar to AA sequence:RefSeq:WP_005863909.1
COORDINATES: protein motif:HMM:NF016800.2
COORDINATES: protein motif:HMM:NF012376.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR01007.1
GO:0045226 - extracellular polysaccharide biosynthetic process [Evidence IEA]
polysaccharide biosynthesis tyrosine autokinase
COORDINATES: similar to AA sequence:RefSeq:WP_009565458.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_007802592.1
COORDINATES: protein motif:HMM:NF024871.2
COORDINATES: protein motif:HMM:NF014298.2
COORDINATES: protein motif:HMM:NF016145.2
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_017483972.1
COORDINATES: similar to AA sequence:RefSeq:WP_007702345.1
COORDINATES: similar to AA sequence:RefSeq:WP_015888291.1
COORDINATES: similar to AA sequence:RefSeq:WP_014331129.1
COORDINATES: similar to AA sequence:RefSeq:WP_015888289.1
COORDINATES: similar to AA sequence:RefSeq:WP_015241412.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018238420.1
COORDINATES: similar to AA sequence:RefSeq:WP_004431840.1
COORDINATES: similar to AA sequence:RefSeq:WP_009467461.1
COORDINATES: similar to AA sequence:RefSeq:WP_019965595.1
SMP-30/gluconolactonase/LRE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019965598.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
sugar ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011654420.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427775.1
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF019009.2
type II toxin-antitoxin system CcdA family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010324111.1
COORDINATES: similar to AA sequence:RefSeq:WP_018387323.1
COORDINATES: similar to AA sequence:RefSeq:WP_018387324.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0015411 - ABC-type taurine transporter transporter activity [Evidence IEA]; GO:0030977 - taurine binding [Evidence IEA]
GO:0015734 - taurine transport [Evidence IEA]
taurine ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005848978.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803648.1
COORDINATES: similar to AA sequence:RefSeq:WP_009562030.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_018001705.1
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.
COORDINATES: similar to AA sequence:RefSeq:WP_007121138.1
COORDINATES: similar to AA sequence:RefSeq:WP_007121139.1
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: protein motif:HMM:NF023697.2
COORDINATES: protein motif:HMM:NF018980.2
COORDINATES: similar to AA sequence:RefSeq:WP_014880317.1
COORDINATES: similar to AA sequence:RefSeq:WP_007118181.1
GO:0019867 - outer membrane [Evidence IEA]
glycine zipper 2TM domain-containing protein
COORDINATES: protein motif:HMM:NF012257.2
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011582758.1
COORDINATES: similar to AA sequence:RefSeq:WP_018690306.1
COORDINATES: protein motif:HMM:NF012925.2
GO:0004553 - hydrolase activity, hydrolyzing O-glycosyl compounds [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_007658931.1
COORDINATES: similar to AA sequence:RefSeq:WP_012257099.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016867130.1
COORDINATES: similar to AA sequence:RefSeq:WP_012257101.1
GO:0047343 - glucose-1-phosphate cytidylyltransferase activity [Evidence IEA]
glucose-1-phosphate cytidylyltransferase
COORDINATES: protein motif:HMM:NF024914.2
COORDINATES: similar to AA sequence:RefSeq:WP_019341869.1
COORDINATES: similar to AA sequence:RefSeq:WP_007292324.1
COORDINATES: protein motif:HMM:NF014606.2
GO:0015159 - polysaccharide transmembrane transporter activity [Evidence IEA]
GO:0015774 - polysaccharide transport [Evidence IEA]
polysaccharide biosynthesis/export family protein
COORDINATES: protein motif:HMM:NF025179.2
COORDINATES: similar to AA sequence:RefSeq:WP_009563200.1
GO:0003983 - UTP:glucose-1-phosphate uridylyltransferase activity [Evidence IEA]
GO:0009225 - nucleotide-sugar metabolic process [Evidence IEA]
UTP--glucose-1-phosphate uridylyltransferase GalU
COORDINATES: similar to AA sequence:RefSeq:WP_010686507.1
COORDINATES: similar to AA sequence:RefSeq:WP_008872471.1
COORDINATES: protein motif:HMM:TIGR01845.1
GO:0009279 - cell outer membrane [Evidence IEA]
GO:0015288 - porin activity [Evidence IEA]
efflux transporter outer membrane subunit
COORDINATES: similar to AA sequence:RefSeq:WP_011501042.1
GO:0004096 - catalase activity [Evidence IEA]; GO:0020037 - heme binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF024950.2
COORDINATES: similar to AA sequence:RefSeq:WP_018388293.1
COORDINATES: similar to AA sequence:RefSeq:WP_018913083.1
COORDINATES: similar to AA sequence:RefSeq:WP_018097911.1
COORDINATES: similar to AA sequence:RefSeq:WP_011908910.1
COORDINATES: similar to AA sequence:RefSeq:WP_007536710.1
COORDINATES: similar to AA sequence:RefSeq:WP_011427511.1
glutathione-dependent formaldehyde dehydrogenase
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF020037.2
COORDINATES: similar to AA sequence:RefSeq:WP_017485318.1
COORDINATES: protein motif:HMM:NF013767.2
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: protein motif:HMM:NF023204.2
COORDINATES: protein motif:HMM:NF012655.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019954029.1
COORDINATES: similar to AA sequence:RefSeq:WP_008027393.1
COORDINATES: similar to AA sequence:RefSeq:WP_012748735.1
COORDINATES: similar to AA sequence:RefSeq:WP_006931376.1
COORDINATES: similar to AA sequence:RefSeq:WP_007254660.1
COORDINATES: protein motif:HMM:NF012335.2
COORDINATES: protein motif:HMM:NF019845.2
alcohol dehydrogenase catalytic domain-containing protein
COORDINATES: protein motif:HMM:NF019736.2
COORDINATES: protein motif:HMM:NF012515.2
COORDINATES: similar to AA sequence:RefSeq:WP_018064440.1
COORDINATES: similar to AA sequence:RefSeq:WP_009810403.1
COORDINATES: similar to AA sequence:RefSeq:WP_019726969.1
COORDINATES: similar to AA sequence:RefSeq:WP_015243442.1
COORDINATES: similar to AA sequence:RefSeq:WP_015342471.1
COORDINATES: similar to AA sequence:RefSeq:WP_019860081.1
dihydrodipicolinate synthase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_008282008.1
transporter substrate-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007528825.1
COORDINATES: similar to AA sequence:RefSeq:WP_003528591.1
COORDINATES: similar to AA sequence:RefSeq:WP_017271789.1
amino acid ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004110222.1
COORDINATES: similar to AA sequence:RefSeq:WP_011982644.1
COORDINATES: similar to AA sequence:RefSeq:WP_009818132.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120757.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00177
Derived by automated computational analysis using gene prediction method: cmsearch.
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: nucleotide motif:Rfam:14.4:RF02541
COORDINATES: nucleotide motif:Rfam:14.4:RF00001
COORDINATES: similar to AA sequence:RefSeq:WP_076611345.1
COORDINATES: protein motif:HMM:NF012730.2
GO:0006811 - ion transport [Evidence IEA]; GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012593.2
GO:0015293 - symporter activity [Evidence IEA]
cation:dicarboxylase symporter family transporter
COORDINATES: protein motif:HMM:TIGR00035.1
GO:0047689 - aspartate racemase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012707.2
COORDINATES: similar to AA sequence:RefSeq:WP_015153200.1
COORDINATES: similar to AA sequence:RefSeq:WP_015153198.1
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_017743991.1
COORDINATES: protein motif:HMM:NF018777.2
COORDINATES: similar to AA sequence:RefSeq:WP_015153197.1
COORDINATES: similar to AA sequence:RefSeq:WP_015153196.1
COORDINATES: similar to AA sequence:RefSeq:WP_014415632.1
COORDINATES: similar to AA sequence:RefSeq:WP_006528428.1
COORDINATES: similar to AA sequence:RefSeq:WP_010476406.1
GO:0004133 - glycogen debranching enzyme activity [Evidence IEA]
GO:0005980 - glycogen catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016877524.1
COORDINATES: similar to AA sequence:RefSeq:WP_013617820.1
COORDINATES: protein motif:HMM:NF012695.2
GO:0016779 - nucleotidyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016652.2
GO:0016972 - thiol oxidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013654810.1
frameshifted; 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:NF018435.2
COORDINATES: protein motif:HMM:NF016408.2
COORDINATES: similar to AA sequence:RefSeq:WP_008030597.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820205.1
COORDINATES: similar to AA sequence:RefSeq:WP_007424471.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187454.1
COORDINATES: similar to AA sequence:RefSeq:WP_020038226.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820101.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803302.1
COORDINATES: similar to AA sequence:RefSeq:WP_012778788.1
COORDINATES: similar to AA sequence:RefSeq:WP_012849318.1
COORDINATES: similar to AA sequence:RefSeq:WP_012073918.1
GO:0008783 - agmatinase activity [Evidence IEA]
GO:0008295 - spermidine biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002722058.1
COORDINATES: similar to AA sequence:RefSeq:WP_013068595.1
COORDINATES: similar to AA sequence:RefSeq:WP_000809131.1
M10 family metallopeptidase C-terminal domain-containing protein
COORDINATES: protein motif:HMM:TIGR01965.1
COORDINATES: protein motif:HMM:NF037016.2
COORDINATES: protein motif:HMM:NF018928.2