Gemmobacter fulva strain con5 plasmid p5, complete sequence.
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales; Rhodobacteraceae; Gemmobacter.
Submitted (01-JUN-2021) College of Biology and the Environment, Nanjing Forestry University, Longpan 59, Nanjing, Jiangsu 210000, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP076366.1.\nBacteria and source DNA available from KCTC 82246.\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 :: HGAP v. 3.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 200.0x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/20/2022 07:36:12\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 4,524\nCDSs (total) :: 4,463\nGenes (coding) :: 4,393\nCDSs (with protein) :: 4,393\nGenes (RNA) :: 61\nrRNAs :: 3, 2, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 2, 3 (5S, 16S, 23S)\ntRNAs :: 50\nncRNAs :: 3\nPseudo Genes (total) :: 70\nCDSs (without protein) :: 70\nPseudo Genes (ambiguous residues) :: 0 of 70\nPseudo Genes (frameshifted) :: 18 of 70\nPseudo Genes (incomplete) :: 60 of 70\nPseudo Genes (internal stop) :: 6 of 70\nPseudo Genes (multiple problems) :: 12 of 70\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
16S ribosomal RNA rRNA prediction is too short
COORDINATES: protein motif:HMM:NF012573.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_122332868.1
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: protein motif:HMM:NF012258.2
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_007205237.1
COORDINATES: similar to AA sequence:RefSeq:WP_011750432.1
ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_008563530.1
COORDINATES: similar to AA sequence:RefSeq:WP_011455257.1
heme ABC transporter ATP-binding protein
COORDINATES: protein motif:HMM:TIGR01785.1
COORDINATES: similar to AA sequence:RefSeq:WP_080363108.1
sulfate ABC transporter, periplasmic sulfate-binding protein
COORDINATES: protein motif:HMM:TIGR03661.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327468.1
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: similar to AA sequence:RefSeq:WP_007205247.1
COORDINATES: protein motif:HMM:NF021364.2
COORDINATES: similar to AA sequence:RefSeq:WP_011423960.1
COORDINATES: similar to AA sequence:RefSeq:WP_014818595.1
COORDINATES: similar to AA sequence:RefSeq:WP_012386042.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0016987 - sigma factor activity [Evidence IEA]
GO:0006352 - DNA-templated transcription initiation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
sigma-70 family RNA polymerase sigma factor
COORDINATES: similar to AA sequence:RefSeq:WP_009807320.1
COORDINATES: similar to AA sequence:RefSeq:WP_013844003.1
COORDINATES: protein motif:HMM:NF022436.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_003634465.1
COORDINATES: similar to AA sequence:RefSeq:WP_008283135.1
COORDINATES: similar to AA sequence:RefSeq:WP_006939306.1
acylneuraminate cytidylyltransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_003634460.1
COORDINATES: protein motif:HMM:NF014075.2
COORDINATES: similar to AA sequence:RefSeq:WP_011331385.1
GO:0008446 - GDP-mannose 4,6-dehydratase activity [Evidence IEA]
GO:0000271 - polysaccharide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF012888.2
sulfotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008227870.1
COORDINATES: similar to AA sequence:RefSeq:WP_002721020.1
GO:0004476 - mannose-6-phosphate isomerase activity [Evidence IEA]; GO:0008905 - mannose-phosphate guanylyltransferase activity [Evidence IEA]
GO:0009103 - lipopolysaccharide biosynthetic process [Evidence IEA]
mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase
COORDINATES: protein motif:HMM:NF012745.2
COORDINATES: protein motif:HMM:NF025025.2
COORDINATES: similar to AA sequence:RefSeq:WP_018388331.1
COORDINATES: similar to AA sequence:RefSeq:WP_012642359.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_017929929.1
COORDINATES: similar to AA sequence:RefSeq:WP_007396306.1
COORDINATES: similar to AA sequence:RefSeq:WP_008281360.1
COORDINATES: protein motif:HMM:NF025659.2
COORDINATES: similar to AA sequence:RefSeq:WP_007427780.1
GO:0008879 - glucose-1-phosphate thymidylyltransferase activity [Evidence IEA]
GO:0019305 - dTDP-rhamnose biosynthetic process [Evidence IEA]; GO:0009243 - O antigen biosynthetic process [Evidence IEA]
glucose-1-phosphate thymidylyltransferase RfbA
COORDINATES: similar to AA sequence:RefSeq:WP_008281614.1
GO:0008831 - dTDP-4-dehydrorhamnose reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007204439.1
GO:0008460 - dTDP-glucose 4,6-dehydratase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007121512.1
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019294884.1
COORDINATES: similar to AA sequence:RefSeq:WP_007426517.1
COORDINATES: similar to AA sequence:RefSeq:WP_014876631.1
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF020459.2
COORDINATES: similar to AA sequence:RefSeq:WP_010397262.1
GO:0003978 - UDP-glucose 4-epimerase activity [Evidence IEA]
GO:0006012 - galactose metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002721875.1
COORDINATES: similar to AA sequence:RefSeq:WP_008335646.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007121138.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187055.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_018327596.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001709.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398645.1
COORDINATES: similar to AA sequence:RefSeq:WP_008336115.1
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_076611431.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030567.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019956934.1
COORDINATES: similar to AA sequence:RefSeq:WP_011441264.1
GO:0000160 - phosphorelay signal transduction system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008030571.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001746.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030576.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004425185.1
COORDINATES: protein motif:HMM:NF021039.2
COORDINATES: similar to AA sequence:RefSeq:WP_015822074.1
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_006953641.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
GO:0006878 - cellular copper ion homeostasis [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
Cu(I)-responsive transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018715880.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030632.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006726580.1
COORDINATES: protein motif:HMM:NF024853.2
GO:0015035 - protein-disulfide reductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014875535.1
COORDINATES: similar to AA sequence:RefSeq:WP_005619181.1
COORDINATES: protein motif:HMM:NF013487.2
COORDINATES: similar to AA sequence:RefSeq:WP_018065818.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820153.1
ferric reductase-like transmembrane domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008204324.1
GO:0003824 - catalytic activity [Evidence IEA]
GO:0009252 - peptidoglycan biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019956944.1
COORDINATES: similar to AA sequence:RefSeq:WP_011242139.1
COORDINATES: similar to AA sequence:RefSeq:WP_009805271.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030994.1
COORDINATES: similar to AA sequence:RefSeq:WP_010398612.1
GO:0005507 - copper ion binding [Evidence IEA]; GO:0016491 - oxidoreductase activity [Evidence IEA]
multicopper oxidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005613366.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817281.1
COORDINATES: protein motif:HMM:NF013700.2
COORDINATES: similar to AA sequence:RefSeq:WP_008889345.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030626.1
COORDINATES: similar to AA sequence:RefSeq:WP_008030624.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503847.1
COORDINATES: similar to AA sequence:RefSeq:WP_009573590.1
GO:0016021 - integral component of membrane [Evidence IEA]
GO:0016410 - N-acyltransferase activity [Evidence IEA]
GO:0042158 - lipoprotein biosynthetic process [Evidence IEA]; GO:0006497 - protein lipidation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_047389784.1
COORDINATES: protein motif:HMM:NF013257.2
COORDINATES: protein motif:HMM:NF018877.2
COORDINATES: similar to AA sequence:RefSeq:WP_011509812.1
COORDINATES: similar to AA sequence:RefSeq:WP_019832297.1
GO:0016773 - phosphotransferase activity, alcohol group as acceptor [Evidence IEA]
GO:0009244 - lipopolysaccharide core region biosynthetic process [Evidence IEA]
D-glycero-beta-D-manno-heptose-7-phosphate kinase
COORDINATES: similar to AA sequence:RefSeq:WP_017999668.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294852.1
COORDINATES: similar to AA sequence:RefSeq:WP_014876615.1
COORDINATES: similar to AA sequence:RefSeq:WP_019294850.1
COORDINATES: protein motif:HMM:NF025063.2
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_060768813.1
COORDINATES: similar to AA sequence:RefSeq:WP_015914912.1
COORDINATES: similar to AA sequence:RefSeq:WP_008495843.1
COORDINATES: similar to AA sequence:RefSeq:WP_018009737.1
COORDINATES: protein motif:HMM:NF033516.0
COORDINATES: similar to AA sequence:RefSeq:WP_007817478.1
COORDINATES: protein motif:HMM:NF017528.2
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.; 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_012975328.1
COORDINATES: similar to AA sequence:RefSeq:WP_007602188.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817370.1
Derived by automated computational analysis using gene prediction method: tRNAscan-SE.
COORDINATES: nucleotide motif:Rfam:14.4:RF00001
Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: nucleotide motif:Rfam:14.4:RF02541