Rahnella aquatilis CIP 78.65 = ATCC 33071 plasmid pRahaq202, complete sequence.
Rahnella aquatilis CIP 78.65 = ATCC 33071
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Yersiniaceae; Rahnella.
Complete genome sequence of Rahnella aquatilis CIP 78.65
Submitted (04-JAN-2012) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP003246.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4089211\nSource DNA and organism available from Robert Martinez\n(rmartinez@bama.ua.edu)\nContacts: Robert Martinez (rmartinez@bama.ua.edu)\n Tanja Woyke (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LANL\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##MIGS-Data-START##\ninvestigation_type :: bacteria_archaea\nproject_name :: Rahnella aquatilis CIP 78.65\ncollection_date :: Missing\nlat_lon :: Missing\ndepth :: Missing\nalt_elev :: Missing\ncountry :: Missing\nenvironment :: Host\nnum_replicons :: 4\nref_biomaterial :: Missing\nbiotic_relationship :: Missing\ntrophic_level :: Missing\nrel_to_oxygen :: Facultative\nisol_growth_condt :: Missing\nsequencing_meth :: WGS\nassembly :: Newbler v. 2.3 (pre-release)\nfinishing_strategy :: Finished\nGOLD Stamp ID :: Gi06369\nType Strain :: Yes\nFunding Program :: DOE-CSP 2010\nGene Calling Method :: Prodigal 1.4, GenePRIMP\nIsolation Site :: drinking water\nHost Name :: Water, humans\nCell Shape :: Rod-shaped\nTemperature Range :: Mesophile\nGram Staining :: Gram-\n##MIGS-Data-END##\n\n##Genome-Assembly-Data-START##\nFinishing Goal :: Finished\nCurrent Finishing Status :: Finished\nAssembly Method :: Newbler v. 2.3\nGenome Coverage :: 30x\nSequencing Technology :: 454/Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 02/22/2023 14:19:21\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) :: 4,999\nCDSs (total) :: 4,891\nGenes (coding) :: 4,827\nCDSs (with protein) :: 4,827\nGenes (RNA) :: 108\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 76\nncRNAs :: 10\nPseudo Genes (total) :: 64\nCDSs (without protein) :: 64\nPseudo Genes (ambiguous residues) :: 0 of 64\nPseudo Genes (frameshifted) :: 28 of 64\nPseudo Genes (incomplete) :: 44 of 64\nPseudo Genes (internal stop) :: 6 of 64\nPseudo Genes (multiple problems) :: 14 of 64\nCRISPR Arrays :: 2\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+.
COORDINATES: similar to AA sequence:RefSeq:WP_001561257.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
type IV toxin-antitoxin system AbiEi family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_004966265.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006710053.1
COORDINATES: similar to AA sequence:RefSeq:WP_013965819.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
nuclear transport factor 2 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_017709209.1
COORDINATES: similar to AA sequence:RefSeq:WP_010671956.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: similar to AA sequence:RefSeq:WP_013575581.1
COORDINATES: similar to AA sequence:RefSeq:WP_015344209.1
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_004853905.1
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:YP_005228627.1
COORDINATES: similar to AA sequence:RefSeq:YP_005228626.1
COORDINATES: similar to AA sequence:RefSeq:YP_005228625.1
COORDINATES: similar to AA sequence:RefSeq:WP_012147136.1
GO:0016407 - acetyltransferase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF025663.2
ATP-grasp fold amidoligase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013574942.1
COORDINATES: similar to AA sequence:RefSeq:WP_013574944.1
GO:0005215 - transporter activity [Evidence IEA]
efflux RND transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_019105504.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333835.1
COORDINATES: similar to AA sequence:RefSeq:WP_006118265.1
COORDINATES: similar to AA sequence:RefSeq:WP_013790730.1
COORDINATES: similar to AA sequence:RefSeq:WP_007781216.1
COORDINATES: protein motif:HMM:NF017970.2
COORDINATES: similar to AA sequence:RefSeq:WP_007374801.1
COORDINATES: protein motif:HMM:NF005495.0
COORDINATES: protein motif:HMM:NF012334.2
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_002435233.1
COORDINATES: similar to AA sequence:RefSeq:WP_004157545.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014333844.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_019083005.1
COORDINATES: similar to AA sequence:RefSeq:WP_017799584.1
COORDINATES: similar to AA sequence:RefSeq:WP_017799583.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014542702.1
COORDINATES: similar to AA sequence:RefSeq:WP_013510874.1
COORDINATES: similar to AA sequence:RefSeq:WP_004160913.1
COORDINATES: protein motif:HMM:TIGR01594.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333851.1
COORDINATES: similar to AA sequence:RefSeq:WP_005161896.1
ogr/Delta-like zinc finger family protein
COORDINATES: similar to AA sequence:RefSeq:WP_018436732.1
COORDINATES: similar to AA sequence:RefSeq:WP_019092232.1
COORDINATES: similar to AA sequence:RefSeq:WP_013935126.1
COORDINATES: similar to AA sequence:RefSeq:WP_013578364.1
sensor domain-containing diguanylate cyclase
COORDINATES: similar to AA sequence:RefSeq:WP_008813541.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001303459.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611429.1
COORDINATES: similar to AA sequence:RefSeq:WP_013578402.1
thioredoxin fold domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_076611470.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016495728.1
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: similar to AA sequence:RefSeq:WP_015584228.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495726.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014683046.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014683045.1
COORDINATES: similar to AA sequence:RefSeq:WP_013578408.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333871.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013201208.1
TetR/AcrR family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_017491543.1
COORDINATES: similar to AA sequence:RefSeq:WP_014263850.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333870.1
COORDINATES: similar to AA sequence:RefSeq:WP_000156610.1
NAD-dependent succinate-semialdehyde dehydrogenase
COORDINATES: similar to AA sequence:RefSeq:WP_006051110.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011544423.1
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_020065046.1
COORDINATES: similar to AA sequence:RefSeq:WP_020065047.1
glutathione S-transferase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_011846847.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000091962.1
COORDINATES: similar to AA sequence:RefSeq:WP_003403410.1
COORDINATES: similar to AA sequence:RefSeq:WP_003403407.1
enoyl-CoA hydratase/isomerase family protein
COORDINATES: similar to AA sequence:RefSeq:NP_460228.1
four-helix bundle copper-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_004386807.1
GO:0009326 - formate dehydrogenase complex [Evidence IEA]
GO:0008863 - formate dehydrogenase (NAD+) activity [Evidence IEA]
GO:0015942 - formate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_003855172.1
COORDINATES: similar to AA sequence:RefSeq:WP_009091556.1
COORDINATES: protein motif:HMM:NF014386.2
cytochrome d ubiquinol oxidase subunit II
COORDINATES: similar to AA sequence:RefSeq:WP_004946180.1
COORDINATES: similar to AA sequence:RefSeq:WP_004946181.1
COORDINATES: similar to AA sequence:RefSeq:WP_016162043.1
COORDINATES: similar to AA sequence:RefSeq:WP_008957830.1
COORDINATES: similar to AA sequence:RefSeq:WP_008957831.1
COORDINATES: similar to AA sequence:RefSeq:WP_016495764.1
COORDINATES: similar to AA sequence:RefSeq:WP_005131818.1
PLP-dependent aminotransferase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_005131815.1
carboxymuconolactone decarboxylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_009128354.1
COORDINATES: similar to AA sequence:RefSeq:WP_008109407.1
COORDINATES: similar to AA sequence:RefSeq:WP_008109409.1
COORDINATES: similar to AA sequence:RefSeq:WP_013574963.1
pyridoxamine 5'-phosphate oxidase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013574946.1
COORDINATES: similar to AA sequence:RefSeq:WP_014683040.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors [Evidence IEA]; GO:0030976 - thiamine pyrophosphate binding [Evidence IEA]
GO:0022900 - electron transport chain [Evidence IEA]
pyruvate:ferredoxin (flavodoxin) oxidoreductase
COORDINATES: similar to AA sequence:RefSeq:WP_047611511.1
GO:0009055 - electron transfer activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014683038.1
COORDINATES: similar to AA sequence:RefSeq:WP_012541104.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:1904047 - S-adenosyl-L-methionine binding [Evidence IEA]
GO:0009399 - nitrogen fixation [Evidence IEA]
nitrogenase cofactor biosynthesis protein NifB
COORDINATES: similar to AA sequence:RefSeq:WP_014333905.1
GO:0009399 - nitrogen fixation [Evidence IEA]; GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
nif-specific transcriptional activator NifA
COORDINATES: similar to AA sequence:RefSeq:WP_004122419.1
nitrogen fixation negative regulator NifL
COORDINATES: similar to AA sequence:RefSeq:WP_014683034.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333908.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333909.1
nitrogenase-stabilizing/protective protein NifW
COORDINATES: similar to AA sequence:RefSeq:WP_014683031.1
GO:0004410 - homocitrate synthase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004122403.1
GO:0031071 - cysteine desulfurase activity [Evidence IEA]
GO:0006520 - amino acid metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014683029.1
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]; GO:0009399 - nitrogen fixation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014683028.1
COORDINATES: similar to AA sequence:RefSeq:WP_014683027.1
NifB/NifX family molybdenum-iron cluster-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_014683026.1
nitrogenase iron-molybdenum cofactor biosynthesis protein NifN
COORDINATES: similar to AA sequence:RefSeq:WP_017456746.1
nitrogenase iron-molybdenum cofactor biosynthesis protein NifE
COORDINATES: similar to AA sequence:RefSeq:WP_014683024.1
COORDINATES: similar to AA sequence:RefSeq:WP_014333918.1
COORDINATES: similar to AA sequence:RefSeq:WP_016161448.1
GO:0016612 - molybdenum-iron nitrogenase complex [Evidence IEA]
GO:0016163 - nitrogenase activity [Evidence IEA]
nitrogenase molybdenum-iron protein subunit beta
COORDINATES: similar to AA sequence:RefSeq:WP_004138788.1
nitrogenase molybdenum-iron protein alpha chain
COORDINATES: similar to AA sequence:RefSeq:WP_014333921.1
GO:0016611 - iron-iron nitrogenase complex [Evidence IEA]; GO:0016612 - molybdenum-iron nitrogenase complex [Evidence IEA]; GO:0016613 - vanadium-iron nitrogenase complex [Evidence IEA]