Geoalkalibacter subterraneus strain Red1 plasmid pGSUB1, complete sequence.
Bacteria; Proteobacteria; Deltaproteobacteria; Desulfuromonadales; Geobacteraceae; Geoalkalibacter.
Genomes of Geoalkalibacter ferrihydriticus Z-0531T and Geoalkalibacter subterraneus Red1T, Two Haloalkaliphilic Metal-Reducing Deltaproteobacteria
Submitted (15-DEC-2014) BioTechnology Institute, University of Minnesota - Twin Cities, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP010312.1.\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 :: HGAP v. 2 in SMRT Analysis v. 2.1\nGenome Coverage :: 430x\nSequencing Technology :: PacBio RSII\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 12/12/2022 18:41:11\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) :: 3,614\nCDSs (total) :: 3,544\nGenes (coding) :: 3,500\nCDSs (with protein) :: 3,500\nGenes (RNA) :: 70\nrRNAs :: 3, 3, 3 (5S, 16S, 23S)\ncomplete rRNAs :: 3, 3, 3 (5S, 16S, 23S)\ntRNAs :: 53\nncRNAs :: 8\nPseudo Genes (total) :: 44\nCDSs (without protein) :: 44\nPseudo Genes (ambiguous residues) :: 0 of 44\nPseudo Genes (frameshifted) :: 11 of 44\nPseudo Genes (incomplete) :: 37 of 44\nPseudo Genes (internal stop) :: 4 of 44\nPseudo Genes (multiple problems) :: 7 of 44\nCRISPR Arrays :: 2\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
type strain of Geoalkalibacter subterraneus
COORDINATES: protein motif:HMM:TIGR02740.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008933076.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
MerR family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004086683.1
RNA-guided endonuclease TnpB family protein
COORDINATES: protein motif:HMM:NF025125.2
COORDINATES: similar to AA sequence:RefSeq:WP_014406917.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF040570.1
COORDINATES: protein motif:HMM:NF018836.2
type IV conjugative transfer system protein TraL
COORDINATES: protein motif:HMM:NF017152.2
TraE/TraK family type IV conjugative transfer system protein
COORDINATES: protein motif:HMM:NF019575.2
prepilin-type N-terminal cleavage/methylation domain-containing protein
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012485.2
COORDINATES: protein motif:HMM:NF018894.2
COORDINATES: similar to AA sequence:RefSeq:WP_015351907.1
type IV pilus twitching motility protein PilT
COORDINATES: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: protein motif:HMM:NF012652.2
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: protein motif:HMM:NF018714.2
COORDINATES: similar to AA sequence:RefSeq:WP_009546178.1
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:NF019153.2
COORDINATES: protein motif:HMM:TIGR03743.1
GO:0003674 - molecular_function [Evidence IEA]
GO:0015074 - DNA integration [Evidence IEA]
Members of this protein family are the putative conjugative coupling factor, TraD, as the term is used for the SXT and TOL plasmid systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
conjugative transfer system coupling protein TraD
COORDINATES: protein motif:HMM:NF025706.2
COORDINATES: similar to AA sequence:RefSeq:WP_018574284.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF018311.2
type-F conjugative transfer system secretin TraK
COORDINATES: similar to AA sequence:RefSeq:WP_011899400.1
COORDINATES: protein motif:HMM:NF024498.2
COORDINATES: protein motif:HMM:NF021212.2
COORDINATES: protein motif:HMM:NF016820.2
TraA family conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_001896378.1
COORDINATES: protein motif:HMM:NF021981.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF012772.2
COORDINATES: protein motif:HMM:NF021209.2
TrbC family F-type conjugative pilus assembly protein
COORDINATES: similar to AA sequence:RefSeq:WP_019091819.1
COORDINATES: similar to AA sequence:RefSeq:WP_001278583.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF015146.2
COORDINATES: similar to AA sequence:RefSeq:WP_019866532.1
COORDINATES: protein motif:HMM:NF018666.2
COORDINATES: similar to AA sequence:RefSeq:WP_011341420.1
COORDINATES: protein motif:HMM:NF020354.2
COORDINATES: protein motif:HMM:NF040127.1
COORDINATES: protein motif:HMM:TIGR00644.1
GO:0008297 - single-stranded DNA exodeoxyribonuclease activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
single-stranded-DNA-specific exonuclease RecJ
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_006000770.1
COORDINATES: protein motif:HMM:NF017411.2
COORDINATES: similar to AA sequence:RefSeq:WP_013786003.1
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: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_011254780.1
COORDINATES: protein motif:HMM:NF023742.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020682663.1
COORDINATES: similar to AA sequence:RefSeq:WP_011733829.1
COORDINATES: protein motif:HMM:NF024117.2
COORDINATES: similar to AA sequence:RefSeq:WP_020481823.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
COORDINATES: protein motif:HMM:NF013790.2
helix-hairpin-helix domain-containing protein
COORDINATES: protein motif:HMM:NF019348.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: protein motif:HMM:NF022792.2
COORDINATES: protein motif:HMM:NF017973.2
COORDINATES: similar to AA sequence:RefSeq:WP_013403960.1
GO:0008998 - ribonucleoside-triphosphate reductase activity [Evidence IEA]
GO:0006260 - DNA replication [Evidence IEA]
COORDINATES: protein motif:HMM:NF024755.2
COORDINATES: protein motif:HMM:NF013594.2
GO:0004222 - metalloendopeptidase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF016214.2
COORDINATES: protein motif:HMM:NF012920.2
COORDINATES: protein motif:HMM:NF025073.2
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
GO:0044780 - bacterial-type flagellum assembly [Evidence IEA]; GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]
flagellar transcriptional regulator FlhD
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018942.2
COORDINATES: protein motif:HMM:NF013793.2
COORDINATES: protein motif:HMM:NF012774.2
COORDINATES: protein motif:HMM:NF037161.2
COORDINATES: protein motif:HMM:NF039622.1
COORDINATES: protein motif:HMM:NF019945.2
COORDINATES: protein motif:HMM:NF016724.2
COORDINATES: similar to AA sequence:RefSeq:WP_017977244.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_008080804.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007331471.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF033550.5
COORDINATES: similar to AA sequence:RefSeq:WP_013006583.1
COORDINATES: similar to AA sequence:RefSeq:WP_012208625.1
COORDINATES: protein motif:HMM:NF019146.2
COORDINATES: similar to AA sequence:RefSeq:WP_013345601.1
COORDINATES: protein motif:HMM:NF012372.2
GO:0008168 - methyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF014752.2
COORDINATES: similar to AA sequence:RefSeq:WP_003596608.1
COORDINATES: similar to AA sequence:RefSeq:WP_020717129.1
COORDINATES: similar to AA sequence:RefSeq:WP_006964932.1
COORDINATES: protein motif:HMM:NF019106.2
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012700209.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015930158.1
COORDINATES: protein motif:HMM:NF013658.2
COORDINATES: protein motif:HMM:NF014442.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: protein motif:HMM:TIGR03115.1
GO:0043571 - maintenance of CRISPR repeat elements [Evidence IEA]
COORDINATES: protein motif:HMM:NF024703.2
COORDINATES: similar to AA sequence:RefSeq:WP_008537710.1
COORDINATES: similar to AA sequence:RefSeq:WP_004594496.1
COORDINATES: protein motif:HMM:NF014062.2
COORDINATES: similar to AA sequence:RefSeq:WP_005997907.1
COORDINATES: protein motif:HMM:TIGR00254.1
COORDINATES: protein motif:HMM:NF015758.2
nucleoside triphosphate pyrophosphohydrolase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013006858.1
GO:0050797 - thymidylate synthase (FAD) activity [Evidence IEA]
GO:0009265 - 2'-deoxyribonucleotide biosynthetic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF024949.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_018411101.1
COORDINATES: similar to AA sequence:RefSeq:WP_015162932.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019568970.1
GO:0003824 - catalytic activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
Eco57I restriction-modification methylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011415923.1
nuclease-related domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_003326144.1
COORDINATES: similar to AA sequence:RefSeq:WP_019692577.1
COORDINATES: protein motif:HMM:NF016281.2
COORDINATES: similar to AA sequence:RefSeq:WP_019584421.1
COORDINATES: similar to AA sequence:RefSeq:WP_015081054.1
COORDINATES: similar to AA sequence:RefSeq:WP_012448893.1
COORDINATES: similar to AA sequence:RefSeq:WP_012448894.1
internal stop; 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:NF022224.2
COORDINATES: similar to AA sequence:RefSeq:WP_017173669.1
COORDINATES: protein motif:HMM:NF039653.1
COORDINATES: similar to AA sequence:RefSeq:WP_007527980.1
GO:0004798 - thymidylate kinase activity [Evidence IEA]
GO:0015949 - nucleobase-containing small molecule interconversion [Evidence IEA]
COORDINATES: protein motif:HMM:NF013540.2
COORDINATES: similar to AA sequence:RefSeq:WP_011980398.1
COORDINATES: similar to AA sequence:RefSeq:WP_007294181.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025447.2
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF013094.2
GO:0008641 - ubiquitin-like modifier activating enzyme activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF021235.2
COORDINATES: similar to AA sequence:RefSeq:WP_009546327.1
COORDINATES: protein motif:HMM:NF012632.2
COORDINATES: protein motif:HMM:NF024106.2