GenomeNet

Database: RefSeq
Entry: NC_007515
LinkDB: NC_007515
Original site: NC_007515 
LOCUS       NC_007515              13762 bp    DNA     circular CON 22-FEB-2023
DEFINITION  Geobacter metallireducens GS-15 plasmid unnamed, complete sequence.
ACCESSION   NC_007515
VERSION     NC_007515.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02598399
            Assembly: GCF_000012925.1
KEYWORDS    RefSeq.
SOURCE      Geobacter metallireducens GS-15
  ORGANISM  Geobacter metallireducens GS-15
            Bacteria; Thermodesulfobacteriota; Desulfuromonadia; Geobacterales;
            Geobacteraceae; Geobacter.
REFERENCE   1  (bases 1 to 13762)
  AUTHORS   Aklujkar,M., Krushkal,J., DiBartolo,G., Lapidus,A., Land,M.L. and
            Lovley,D.R.
  TITLE     The genome sequence of Geobacter metallireducens: features of
            metabolism, physiology and regulation common and dissimilar to
            Geobacter sulfurreducens
  JOURNAL   BMC Microbiol 9, 109 (2009)
   PUBMED   19473543
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 13762)
  AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C.,
            Glavina,T., Hammon,N., Israni,S., Pitluck,S., Di Bartolo,G.,
            Chain,P., Schmutz,J., Larimer,F., Land,M., Kyrpides,N., Ivanova,N.
            and Richardson,P.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Complete sequence of plasmid of Geobacter metallireducens GS-15
  JOURNAL   Unpublished
REFERENCE   3  (bases 1 to 13762)
  AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C.,
            Glavina,T., Hammon,N., Israni,S., Pitluck,S., Di Bartolo,G.,
            Chain,P., Schmutz,J., Larimer,F., Land,M., Kyrpides,N., Ivanova,N.
            and Richardson,P.
  CONSRTM   US DOE Joint Genome Institute
  TITLE     Direct Submission
  JOURNAL   Submitted (11-OCT-2005) US DOE Joint Genome Institute, 2400
            Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            CP000149.1.
            URL -- http://www.jgi.doe.gov
            Source DNA and bacteria available from Derek Lovley
            (dlovley@bio.umass.edu)
            Whole genome sequencing and draft assembly at JGI-PGF
            Finishing done by JGI-PGF
            Quality assurance done by JGI-Stanford
            Annotation done by JGI-ORNL and JGI-PGF
            Contacts: Paul Richardson (microbes@cuba.jgi-psf.org)
            Finished microbial genomes have been curated to close all gaps with
            greater than 98% coverage of at least two independent clones. Each
            base pair has a minimum q (quality) value of 30 and the total error
            rate is less than one per 50000.
            Annotation update without protein changes made on September 7, 2012
            by Aklujkar,M., Krushkal,J., DiBartolo,G., Lapidus,A., Land,M.L.
            and Lovley,D.R.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/22/2023 14:01:01
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.4
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,679
            CDSs (total)                      :: 3,619
            Genes (coding)                    :: 3,587
            CDSs (with protein)               :: 3,587
            Genes (RNA)                       :: 60
            rRNAs                             :: 2, 2, 2 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 2, 2 (5S, 16S, 23S)
            tRNAs                             :: 50
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 32
            CDSs (without protein)            :: 32
            Pseudo Genes (ambiguous residues) :: 0 of 32
            Pseudo Genes (frameshifted)       :: 10 of 32
            Pseudo Genes (incomplete)         :: 24 of 32
            Pseudo Genes (internal stop)      :: 2 of 32
            Pseudo Genes (multiple problems)  :: 4 of 32
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..13762
                     /organism="Geobacter metallireducens GS-15"
                     /mol_type="genomic DNA"
                     /strain="GS-15"
                     /type_material="type strain of Geobacter metallireducens"
                     /db_xref="taxon:269799"
                     /plasmid="unnamed"
     gene            complement(join(13670..13762,1..96))
                     /locus_tag="GMET_RS18195"
     CDS             complement(join(13670..13762,1..96))
                     /locus_tag="GMET_RS18195"
                     /inference="COORDINATES: ab initio
                     prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514712.1"
                     /translation="MAKPDELSHHEVLHTAHIIGCIWSDHVLDHAAVQGNPELKAQAE
                     KIAEAIGAFYVAVGGQTP"
     gene            complement(963..2063)
                     /locus_tag="GMET_RS17960"
                     /old_locus_tag="Gmet_A3565"
     CDS             complement(963..2063)
                     /locus_tag="GMET_RS17960"
                     /old_locus_tag="Gmet_A3565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514711.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein RepA"
                     /protein_id="WP_004514711.1"
                     /translation="MLFTEMEIEIPKAVFEELQLYIEYLQEKTGKTIDPMAAIGNILQ
                     TYFENNGLWGVSEEDFKEKAKIAVKKLLTKKAKKDKPLLTKKVEKLLTQAVEIEQVPA
                     KTAGQIAYQAKALVQVTFPHRDPKTPYYRCDSGKYSLIITADPDHGIPYGTYPRLITC
                     WLVTEIVRTNSRRIVLGKCFSDFLRSIGVGLDSRTRKQVEQQIKRLFSADIKLKYNSK
                     ESWQFQRCNVATKAAMWWDTKNPDQFTLDESFVVVGEDFYAMALNAPFPIDLRALAAL
                     KQSPMALDIYMWLTLRMCHLAAPYPLSWPQLKSQFGPETSDLDNFRTKFKDALKKVRV
                     VYPHAKLSVNAKELTLFPSPTHVQKAVKRVAA"
     gene            complement(2067..2378)
                     /locus_tag="GMET_RS17965"
     CDS             complement(2067..2378)
                     /locus_tag="GMET_RS17965"
                     /inference="COORDINATES: ab initio
                     prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_148206096.1"
                     /translation="MEYTINHEEEGPYWNRVMVNSVHDVLYAAGTLDNFKVSLFSPRY
                     QNEDDEMSVSTITEIIEAEEEGHKAYIFKCKNGKTYLETSLGYTEDQLKNKKTLYSIA
                     G"
     gene            complement(2393..3562)
                     /locus_tag="GMET_RS17970"
                     /old_locus_tag="Gmet_A3567"
     CDS             complement(2393..3562)
                     /locus_tag="GMET_RS17970"
                     /old_locus_tag="Gmet_A3567"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011363043.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS4-like element ISGme2 family transposase"
                     /protein_id="WP_011363043.1"
                     /translation="MHTGPTVFKQLLQFLPRYEFNLCVRRHRGEYREKKFSTYDQFLC
                     LAYAQMAGRESLRDIETCLNSHQEKLYHIGFRGDVSRTTLADANERRDWRIFQDFGHV
                     LIGIAQQLYQADAISVELTQPLYAFDSTTIDLCLTLFPWAEFRKTKAAVKMHTLIDLR
                     GPIPTWVTITTGKVHDVRMLDHLPVAKDAIYTMDRGYVDFARLHSIHKQGAFFVVRAK
                     DNLKCQRLYSHPKDKESGVRADQIITLVTQKSKKGYPEKLRRVSYVDKERNKRLVFLT
                     NNFEIPAATVAAIYKQRWQVELFFKWIKQHLRIKSFIGTSVNAVKSQIWVALCIYLLV
                     AITKKKLGVPCSLYTFLQILEVNLFEKKPISSLVAEALKRNADYPERNQLNLFNY"
     gene            complement(3862..4071)
                     /locus_tag="GMET_RS17975"
                     /old_locus_tag="Gmet_A3641"
     CDS             complement(3862..4071)
                     /locus_tag="GMET_RS17975"
                     /old_locus_tag="Gmet_A3641"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514728.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514728.1"
                     /translation="MNGKERQTFITHLTSDHAEARKAYNAATEELRLVTWGKMLGLEA
                     AASCAGMQTLHRDLADLRNRDCENE"
     gene            complement(4068..4409)
                     /locus_tag="GMET_RS17980"
                     /old_locus_tag="Gmet_A3568"
     CDS             complement(4068..4409)
                     /locus_tag="GMET_RS17980"
                     /old_locus_tag="Gmet_A3568"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514727.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514727.1"
                     /translation="MANTETIDYAILQRLIEAGAIRGAEVIGQPGGWSVIFKYGMTER
                     ALGVRGGKVRIFRKIETLVAYLRELGIVQFTVNAANYDPTTTIRPGRPDTSERMKRAF
                     AVAQDIKEGNQ"
     gene            complement(4575..4784)
                     /locus_tag="GMET_RS17985"
                     /old_locus_tag="Gmet_A3642"
     CDS             complement(4575..4784)
                     /locus_tag="GMET_RS17985"
                     /old_locus_tag="Gmet_A3642"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514726.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514726.1"
                     /translation="MSKTPESRTDWPRIEAMKDEEIDLTDSPELDADFIREAIPWGER
                     AKKALDNGFLTEEEGKAWLREKLEE"
     gene            complement(4781..5053)
                     /locus_tag="GMET_RS17990"
                     /old_locus_tag="Gmet_A3569"
     CDS             complement(4781..5053)
                     /locus_tag="GMET_RS17990"
                     /old_locus_tag="Gmet_A3569"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514725.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_004514725.1"
                     /translation="MVWKVEIDPAARRELKKLDPQISGRVLKFLFERVARLDDPRSIG
                     EALKGSRFGDFWKYRVGDYRIITSIEDEALVILVVRVGNRREVYER"
     gene            complement(5037..5261)
                     /locus_tag="GMET_RS17995"
                     /old_locus_tag="Gmet_A3570"
     CDS             complement(5037..5261)
                     /locus_tag="GMET_RS17995"
                     /old_locus_tag="Gmet_A3570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514724.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6290 family protein"
                     /protein_id="WP_004514724.1"
                     /translation="MLAIRLPEEIETRLDSLAKATGRSKSYYVREALVEYLDDLEDIY
                     LAEKRLEDIRAGRTKTIPLEEVMKEYGLES"
     gene            complement(5321..5809)
                     /locus_tag="GMET_RS18000"
                     /old_locus_tag="Gmet_A3571"
     CDS             complement(5321..5809)
                     /locus_tag="GMET_RS18000"
                     /old_locus_tag="Gmet_A3571"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514723.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514723.1"
                     /translation="MANVTITEAARLAGISRQYLYTKYIKPGVLTVKKDENEKPCIDT
                     AELMRVFNGRLPGPKGQSTPDPSSDIHALQNMTRENDIKNAALQAEVEALREAIKAAD
                     KRETWLQGKVDELTGQLATAHRLLEHKAHPSEPPPADPVPVPDPPQEPKRGFFGRLFG
                     RK"
     gene            complement(6011..6196)
                     /locus_tag="GMET_RS18005"
                     /old_locus_tag="Gmet_A3643"
     CDS             complement(6011..6196)
                     /locus_tag="GMET_RS18005"
                     /old_locus_tag="Gmet_A3643"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514722.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514722.1"
                     /translation="MKKQVIMGLVVVVMGAMLVAGCNKAPEGYTADGQPAKALKKGEL
                     PKAGPEKNMLDYYKGKK"
     gene            complement(6237..6956)
                     /gene="trbJ"
                     /locus_tag="GMET_RS18010"
                     /old_locus_tag="Gmet_A3572"
     CDS             complement(6237..6956)
                     /gene="trbJ"
                     /locus_tag="GMET_RS18010"
                     /old_locus_tag="Gmet_A3572"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514721.1"
                     /GO_process="GO:0009291 - unidirectional conjugation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="P-type conjugative transfer protein TrbJ"
                     /protein_id="WP_004514721.1"
                     /translation="MKKALIVTVLILSMSAQAHATIPVLDYTNWAQNLFSYVQQVATA
                     INTAEQLATQYQQLEVAIRQARQLNSDQIRGRIMNGIRQLAEIQQKTRGITYDYGRTE
                     GAFDQYYPDMAAYNGMSGKDYAAQAAKANQQLQNSVRDAMLAQGLISNAATDQDALNA
                     LVAASNSADGQLAAAQAGNQISAMVAQQLIQLQQIMATSAREQSSYMAAQAAEKAKPL
                     KKGDLPKGDDRNMLDYLRKKK"
     gene            complement(7043..8494)
                     /gene="trbL"
                     /locus_tag="GMET_RS18015"
                     /old_locus_tag="Gmet_A3573"
     CDS             complement(7043..8494)
                     /gene="trbL"
                     /locus_tag="GMET_RS18015"
                     /old_locus_tag="Gmet_A3573"
                     /inference="COORDINATES: protein motif:HMM:NF016491.2"
                     /GO_process="GO:0009291 - unidirectional conjugation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="P-type conjugative transfer protein TrbL"
                     /protein_id="WP_011363044.1"
                     /translation="MATATPDVQILTQVLETFNSVFGTGKGALLSWAMYIAGALAVIE
                     MVLLGAFHALKGGEDNIIPPLVKKILTIGFFIFLVQGVARSGLAEIILDGFIAVGLKA
                     GGAGVSFSMKNPSSLISAGFLAADPIYDAIQHMAITAIGDRLMAYGCYLIVILAYVVM
                     ACQIMITFIEFGIVSTLGIILLPFGISKHTAFLSEKAIGAIIAFGIKLMVLSFVVAVI
                     QPVLLALPALGPDPTFNQMMTLGVTVAVIAFVVAQAPGVASAVLSGSPSLSAGAAAGT
                     ALSAAAGAAAPAMAAAGMATGGAAVAGGLAGAKAAAAAGNGSFLGNVARAAAGAMPGA
                     SAFQAAKSGAISAAEAGSAGGIKPASGGSSLKPAADAAAKGAADTGKTEATPTPAPAA
                     DTTATTTDATPPATGSADTTATDAGKTEPAPTTGTGGGTSSLQGSNVGSGGGNGKGQP
                     RRSSLQDAWQQSQRAVPQDASAGGGAGVRLHVD"
     gene            complement(8572..10875)
                     /locus_tag="GMET_RS18020"
                     /old_locus_tag="Gmet_A3574"
     CDS             complement(8572..10875)
                     /locus_tag="GMET_RS18020"
                     /old_locus_tag="Gmet_A3574"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514718.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TraI/MobA(P) family conjugative relaxase"
                     /protein_id="WP_238379090.1"
                     /translation="MPWTKSAGQPWQFSGNLPQKRGPKMISRVWDAPGGRSFSATIKY
                     IRGLGKDFEPHEKVEYELTRNVDDINTAIEEMEFVESTGKSAHAAYHFGFSWREGEKP
                     TREEIEACFDHALKALGMEDLQAVAGFHRDTDNYHLHICINRIDYRTGHVRPIDKDRM
                     KLDKACREMELQHGFERDNGSYMINDKGEIVKKSHDPDRPFSLDQGNRRREIETGEKS
                     FKTWAKERAGKDLTAALADGSWDDLHRAAAKYNLDIRPDPKNQGLVIVDRNDPDQYHA
                     KASEIARQLSRGRLEKALGPYQEPTARVKDLAPVIDYKSDTEKMIAVEPEQKQLYREF
                     KDYQEEWKHHAEERKAITAELTAGRKEIIEWKKEQVKALKESDLPGIEKRAQRAAINL
                     GAARRKAEIEDRAAEKRAALGEFGEAKKGWDKYLVERANKGNEAAIYMLRQKKNRLEV
                     EAPEPGTTGEEEAAKKTPLTTLKDLEIKVSRHGNVSFLDKSGAEAYRDTGRQLLFLGH
                     SKNDPAAIKAGLLLSQEKFGRSFELTGSTAWKRLAAAEAVKLGIEITNKELQPYIAEL
                     KKAQGIGQQIKGRELLPEIRDEIKIITAKIDQGEKWLAEKGQIDGKTDARRVAEQTAT
                     KGISEAIKKERTDLDAEALKLATDMAGGKVSTINREELTARLATNEVNTARLHSYLER
                     PEVQKQVQAEEAKINAVDQETREARAYRADLKKIEKTLAADPKKDRAYKLEPGTDPRD
                     RRQIVKDIQQQINRVQKDIDRGKGMDR"
     gene            complement(10796..11176)
                     /locus_tag="GMET_RS18025"
                     /old_locus_tag="Gmet_A3575"
     CDS             complement(10796..11176)
                     /locus_tag="GMET_RS18025"
                     /old_locus_tag="Gmet_A3575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514717.1"
                     /translation="MKAKSGSERRNKSEMIHIRVTAEDLSRYTAKATASGVSVGELAR
                     RCLDGRATPSKTTIAAVADLRRAVGELRRFGGLQKYLMTRKEITPEEAQKNLGNIDIA
                     LDEIRRAAVAIQRQFAAEEGAEDD"
     gene            11628..12224
                     /locus_tag="GMET_RS18030"
                     /old_locus_tag="Gmet_A3576"
     CDS             11628..12224
                     /locus_tag="GMET_RS18030"
                     /old_locus_tag="Gmet_A3576"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514716.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514716.1"
                     /translation="MGNDKNTAKTLKISKSKSGQSDEKPTYSVDKMRQWLNDNASDTT
                     PDKTPTIWDRLIEIKDDIAAVYPSKMSADKVVKGLKDNGLDITKTTFLTYWQLIKAGH
                     TTRPSTSKKKQPVSEPENSGKNESGFDENPAPVSEEKTGEDLKNSEGEKETYPCPKCK
                     RILTVMRETKPGVHLGQKYISCDADTGGCGYFSYDDGK"
     gene            12335..12967
                     /locus_tag="GMET_RS18035"
                     /old_locus_tag="Gmet_A3577"
     CDS             12335..12967
                     /locus_tag="GMET_RS18035"
                     /old_locus_tag="Gmet_A3577"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004514715.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004514715.1"
                     /translation="MKKESPKHELKSLKDLLDFVRDYPEFMDEITTAMPKATALPGSN
                     QSDFIQPIMPHIVRLKIWGMSDNSIRQLIDFEGPFYFDPRGFGKVLHTAIKKYARSVR
                     YEIAEEVGKIIRESGGDDGHLTETYMDEAIHLFDKWRFPEDQGYENVTDYEFGEAILW
                     AMRGFDPSLYFRRVTAQVLGRKMVKRLKLLYEIDFDSNETHPAEPAHKAA"
CONTIG      join(CP000149.1:1..13762)
//
DBGET integrated database retrieval system