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JOURNAL Unpublished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)
//