Trichlorobacter lovleyi SZ plasmid pGLOV01, complete sequence.
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae; Trichlorobacter.
Complete sequence of plasmid of Geobacter lovleyi SZ
Submitted (23-MAY-2008) US DOE Joint Genome Institute, 2800 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001090.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4002885\nSource DNA and bacteria available from Frank Loeffler\n(ce.gatech.edu)\nContacts: Frank Loeffler (ce.gatech.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\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 :: 12/12/2022 13:51:51\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) :: 3,738\nCDSs (total) :: 3,684\nGenes (coding) :: 3,651\nCDSs (with protein) :: 3,651\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 4\nPseudo Genes (total) :: 33\nCDSs (without protein) :: 33\nPseudo Genes (ambiguous residues) :: 0 of 33\nPseudo Genes (frameshifted) :: 3 of 33\nPseudo Genes (incomplete) :: 29 of 33\nPseudo Genes (internal stop) :: 3 of 33\nPseudo Genes (multiple problems) :: 2 of 33\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: nucleotide motif:Rfam:14.4:RF00174
cobalamin riboswitch; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: protein motif:HMM:TIGR02467.1
GO:0046025 - precorrin-6Y C5,15-methyltransferase (decarboxylating) activity [Evidence IEA]
GO:0046140 - corrin biosynthetic process [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
precorrin-6y C5,15-methyltransferase (decarboxylating) subunit CbiE
COORDINATES: protein motif:HMM:TIGR00715.1
GO:0016994 - precorrin-6A reductase activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011340155.1
GO:0030789 - precorrin-3B C17-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006000193.1
COORDINATES: similar to AA sequence:RefSeq:WP_011340157.1
GO:0046026 - precorrin-4 C11-methyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011340159.1
cobalt-precorrin-5B (C(1))-methyltransferase CbiD
COORDINATES: similar to AA sequence:RefSeq:WP_011340160.1
GO:0030788 - precorrin-2 C20-methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017944.2
GO:0016852 - sirohydrochlorin cobaltochelatase activity [Evidence IEA]
GO:0019251 - anaerobic cobalamin biosynthetic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005038294.1
COORDINATES: similar to AA sequence:RefSeq:WP_005985496.1
GO:0042242 - cobyrinic acid a,c-diamide synthase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF004790.0
GO:0004851 - uroporphyrin-III C-methyltransferase activity [Evidence IEA]
GO:0019354 - siroheme biosynthetic process [Evidence IEA]
uroporphyrinogen-III C-methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008443321.1
COORDINATES: protein motif:HMM:NF014420.2
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0032778 - P-type cobalt transporter activity [Evidence IEA]
GO:0006824 - cobalt ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011735163.1
GO:0015087 - cobalt ion transmembrane transporter activity [Evidence IEA]
GO:0009236 - cobalamin biosynthetic process [Evidence IEA]; GO:0006824 - cobalt ion transport [Evidence IEA]
energy-coupling factor ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_011735149.1
GO:0043190 - ATP-binding cassette (ABC) transporter complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0000041 - transition metal ion transport [Evidence IEA]
energy-coupling factor ABC transporter permease
COORDINATES: similar to AA sequence:RefSeq:WP_011342416.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF027890.2
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_076611644.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
IS3-like element ISGlo6 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_012471683.1
IS5-like element ISGlo4 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_011735151.1
TonB-dependent receptor plug domain-containing protein
COORDINATES: protein motif:HMM:NF024503.2
COORDINATES: similar to AA sequence:RefSeq:WP_013163076.1
COORDINATES: similar to AA sequence:RefSeq:WP_011735171.1
GO:0015078 - proton transmembrane transporter activity [Evidence IEA]; GO:0015291 - secondary active transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011937706.1
COORDINATES: similar to AA sequence:RefSeq:WP_013705349.1
COORDINATES: similar to AA sequence:RefSeq:WP_011937708.1
MotA/TolQ/ExbB proton channel family protein
COORDINATES: similar to AA sequence:RefSeq:WP_011937709.1
COORDINATES: similar to AA sequence:RefSeq:WP_011735160.1
COORDINATES: protein motif:HMM:NF013087.2
COORDINATES: similar to AA sequence:RefSeq:WP_006000218.1
COORDINATES: similar to AA sequence:RefSeq:WP_012471113.1
GO:0008939 - nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity [Evidence IEA]
nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_009106854.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012442.2
COORDINATES: protein motif:HMM:NF016670.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: similar to AA sequence:RefSeq:WP_012469973.1
COORDINATES: similar to AA sequence:RefSeq:YP_002516242.1
class I SAM-dependent DNA methyltransferase
COORDINATES: protein motif:HMM:NF024252.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011733917.1
type II toxin-antitoxin system HipA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013549246.1
COORDINATES: similar to AA sequence:RefSeq:WP_013743247.1
COORDINATES: similar to AA sequence:RefSeq:WP_012468375.1
COORDINATES: similar to AA sequence:RefSeq:WP_008288827.1
COORDINATES: similar to AA sequence:RefSeq:WP_020678113.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015155287.1
COORDINATES: similar to AA sequence:RefSeq:WP_006869880.1
COORDINATES: protein motif:HMM:NF015325.2
COORDINATES: similar to AA sequence:RefSeq:WP_005446033.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_015904272.1
TetR/AcrR family transcriptional regulator
COORDINATES: protein motif:HMM:NF019100.2
COORDINATES: similar to AA sequence:RefSeq:WP_008516298.1
COORDINATES: similar to AA sequence:RefSeq:WP_004511815.1
COORDINATES: similar to AA sequence:RefSeq:WP_013011314.1
COORDINATES: similar to AA sequence:RefSeq:WP_012471725.1
IS481-like element ISGlo3 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015710008.1
GO:0034257 - nicotinamide riboside transmembrane transporter activity [Evidence IEA]
GO:0034258 - nicotinamide riboside transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007019889.1
2-hydroxychromene-2-carboxylate isomerase
COORDINATES: similar to AA sequence:RefSeq:WP_008172450.1
SDR family NAD(P)-dependent oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_076611347.1
IS3-like element ISGlo1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_013516320.1
COORDINATES: similar to AA sequence:RefSeq:WP_058167704.1
COORDINATES: similar to AA sequence:RefSeq:WP_019621397.1
COORDINATES: similar to AA sequence:RefSeq:WP_008295921.1
GO:0008817 - corrinoid adenosyltransferase activity [Evidence IEA]
cob(I)yrinic acid a,c-diamide adenosyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_007276781.1
2-oxoacid:ferredoxin oxidoreductase subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_013156077.1
2-oxoacid:acceptor oxidoreductase subunit alpha
COORDINATES: similar to AA sequence:RefSeq:WP_020158880.1
5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase
COORDINATES: protein motif:HMM:NF038050.1
COORDINATES: similar to AA sequence:RefSeq:WP_020677599.1
GO:0005525 - GTP binding [Evidence IEA]; GO:0043022 - ribosome binding [Evidence IEA]
ribosome small subunit-dependent GTPase A
COORDINATES: similar to AA sequence:RefSeq:WP_013945876.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_010388770.1
GO:0018784 - (S)-2-haloacid dehalogenase activity [Evidence IEA]
GO:0006805 - xenobiotic metabolic process [Evidence IEA]