(data stored in ACNUC8465 zone)

HOGENOMDNA: NITHX_1

ID   NITHX_1; SV 1; empty ; DNA; empty ; PRO; 294829 BP.
XX
AC   NC_007959;
XX
PR   Project: 58293;
XX
DE   Nitrobacter hamburgensis X14 plasmid 1, complete sequence.
XX
OS   Nitrobacter hamburgensis X14
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales;
OC   Bradyrhizobiaceae; Nitrobacter.
XX
RN   [1]
RP   1-294829
RX   PUBMED; 18326675.
RA   Starkenburg,S.R., Larimer,F.W., Stein,L.Y., Klotz,M.G., Chain,P.S.,
RA   Sayavedra-Soto,L.A., Poret-Peterson,A.T., Gentry,M.E., Arp,D.J., Ward,B.
RA   and Bottomley,P.J.;
RT   "Complete genome sequence of Nitrobacter hamburgensis X14 and comparative
RT   genomic analysis of species within the genus Nitrobacter";
RL   Appl. Environ. Microbiol. 74 (9), 2852-2863 (2008)
XX
RN   [2]
RP   1-294829
RG   US DOE Joint Genome Institute
RA   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina del
RA   Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S., Chain,P.,
RA   Malfatti,S., Shin,M., Vergez,L., Schmutz,J., Larimer,F., Land,M.,
RA   Hauser,L., Kyrpides,N., Ivanova,N., Ward,B., Arp,D., Klotz,M., Stein,L.,
RA   O'Mullan,G., Starkenburg,S., Sayavedra,L., Poret-Peterson,A.T.,
RA   Gentry,M.E., Bruce,D. and Richardson,P.;
RT   "Complete sequence of Plasmid1 of Nitrobacter hamburgensis X14";
RL   Unpublished
XX
RN   [3]
RP   1-294829
RG   NCBI Genome Project
RT   "Direct Submission";
RL   Submitted (15-APR-2006) National Center for Biotechnology Information,
RL   NIH, Bethesda, MD 20894, USA
XX
RN   [4]
RP   1-294829
RG   US DOE Joint Genome Institute
RA   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina del
RA   Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S., Chain,P.,
RA   Malfatti,S., Shin,M., Vergez,L., Schmutz,J., Larimer,F., Land,M.,
RA   Kyrpides,N., Ivanova,N., Ward,B., Arp,D., Klotz,M., Stein,L., O'Mullan,G.,
RA   Starkenburg,S., Sayavedra,L., Poret-Peterson,A.T., Gentry,M.E. and
RA   Richardson,P.;
RT   "Direct Submission";
RL   Submitted (28-MAR-2006) US DOE Joint Genome Institute, 2800 Mitchell Drive
RL   B100, Walnut Creek, CA 94598-1698, USA
XX
CC   PROVISIONAL REFSEQ: This record has not yet been subject to final
CC   NCBI review. The reference sequence was derived from CP000320.
CC   URL -- http://www.jgi.doe.gov
CC   JGI Project ID: 3634489
CC   Source DNA and bacteria available from Dan Arp (arpd@bcc.orst.edu)
CC   Contacts: Dan Arp (arpd@bcc.orst.edu)
CC   Paul Richardson (microbes@cuba.jgi-psf.org)
CC   Quality assurance done by JGI-Stanford
CC   Annotation done by JGI-ORNL and JGI-PGF
CC   Finishing done by JGI-LLNL
CC   Finished microbial genomes have been curated to close all gaps with
CC   greater than 98% coverage of at least two independent clones. Each
CC   base pair has a minimum q (quality) value of 30 and the total error
CC   rate is less than one per 50000.
CC   The JGI and collaborators endorse the principles for the
CC   distribution and use of large scale sequencing data adopted by the
CC   larger genome sequencing community and urge users of this data to
CC   follow them. it is our intention to publish the work of this
CC   project in a timely fashion and we welcome collaborative
CC   interaction on the project and analysis.
CC   (http://www.genome.gov/page.cfm?pageID=10506376).
CC   COMPLETENESS: full length.
XX
FH   Key             Location/Qualifiers
FT   source          1..294829
FT                   /strain="X14"
FT                   /mol_type="genomic DNA"
FT                   /organism="Nitrobacter hamburgensis X14"
FT                   /plasmid="1"
FT                   /db_xref="taxon:323097"
FT   gene            99..1436
FT                   /db_xref="GeneID:4025394"
FT                   /locus_tag="Nham_4041"
FT   CDS_pept        99..1436
FT                   /locus_tag="Nham_4041"
FT                   /gene_family="HOG000002547" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="transposase, IS4"
FT                   /transl_table="11"
FT                   /db_xref="GI:92109251"
FT                   /db_xref="InterPro:IPR002559"
FT                   /db_xref="GeneID:4025394"
FT                   /translation="MAQLSFASLDYAAKKKRTKRDAFLAEMAAVVPWVALEALIEPHYP
FT                   KAGPSGGRRPFPLAVMLRIYCLQQWYNLSDPGAEEVLYDICSMRTFAGLELGRDTIPDE
FT                   TTILNFRHLLERHELTKAIFVAIAEFLETRGALLRGGTIIDATLIAASPSTKNKAQKRD
FT                   PEMRSSKKGNQWYFGMKAHIGVDATSGLVHTAGVTTGSVHDAKVMDNLIREDDRAVYGD
FT                   KGYANDRKQRQAEAAGVLWAVKAKAKPGRPLSISQRRRNRRFGKIRAKVEHVFRVMKCQ
FT                   FGYRKGSLSRHRQKRRTGLRVARSRKPIPCPQDTCVRLTKSPDDCRPRQVQTKNPSPPA
FT                   QTCCDCFRKSDVAQRFPNSAYLSGTRGPLQYGVKLRRRLTTAGGQTREALLRRDPRAAF
FT                   KQLSPTAEERVRGRSHLRTRPAVTSPQRRLRLVLCAKRVRVHTTPF"
FT                   /protein_id="YP_571539.1"
FT   misc_feature    252..479
FT                   /note="Transposase domain (DUF772); Region: DUF772;
FT                   cl12084"
FT                   /db_xref="CDD:159744"
FT                   /locus_tag="Nham_4041"
FT   misc_feature    288..1040
FT                   /note="Transposase and inactivated derivatives, IS5 family
FT                   [DNA replication, recombination, and repair]; Region:
FT                   COG3039"
FT                   /db_xref="CDD:32853"
FT                   /locus_tag="Nham_4041"
FT   gene            complement(1510..2088)
FT                   /db_xref="GeneID:4025395"
FT                   /locus_tag="Nham_4042"
FT                   /pseudo
FT   gene            2346..2672
FT                   /db_xref="GeneID:4025396"
FT                   /locus_tag="Nham_4043"
FT   CDS_pept        2346..2672
FT                   /locus_tag="Nham_4043"
FT                   /gene_family="HOG000277970" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="nitrogen regulatory protein P-II (GlnB, GlnK)"
FT                   /transl_table="11"
FT                   /db_xref="GI:92109252"
FT                   /db_xref="InterPro:IPR002187"
FT                   /db_xref="GeneID:4025396"
FT                   /translation="MNAIKLHPLKKLEIILAGEHKEFATDLLDRAGVKGYTIVGNLSGK
FT                   GSHGLYGGHLMFNEDDVLIMIIAAVPQSLVDPLLDGFQPFFDAHSGVIFVSDIQVGRLA
FT                   KFMA"
FT                   /protein_id="YP_571540.1"
FT   misc_feature    2370..2639
FT                   /note="Nitrogen regulatory protein P-II; Region: P-II;
FT                   cl00412"
FT                   /db_xref="CDD:174186"
FT                   /locus_tag="Nham_4043"
FT   gene            complement(2613..3593)
FT                   /db_xref="GeneID:4025397"
FT                   /locus_tag="Nham_4044"
FT   CDS_pept        complement(2613..3593)
FT                   /locus_tag="Nham_4044"
FT                   /gene_family="HOG000233518" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="LysR family transcriptional regulator"
FT                   /transl_table="11"
FT                   /db_xref="GI:92109253"
FT                   /db_xref="InterPro:IPR000847"
FT                   /db_xref="InterPro:IPR005119"
FT                   /db_xref="GeneID:4025397"
FT                   /translation="MHLTLRQLQIFDAVVRQQSFTRAADALHLTQPAVSMQMRHLEEQI
FT                   GVPLFDHVGKQIQPTDAGRELHRHATLISAKMRDLKSAMEEFRGIHRGELDLTVASTAN
FT                   YFMPKLIAAFCACHAKVQVRLQVSNQTHILEMLSASNQDLAIMGQPREDAELVARGFLD
FT                   NPLVVIASPAHPLAKSRQIPLEQLGRQRFITREPGSGTRNAAERHFSRHGVEFHSVMEM
FT                   SSNEAIKQAVDAGLGLGILSLHTLELELAMRRLVILDVESFPLVRQWFVVHRKGKRLSA
FT                   VAQSFLAFLTQQARPLTSPKHPQPTPLRHELGQAADLDVADENHP"
FT                   /protein_id="YP_571541.1"
FT   misc_feature    complement(2715..3593)
FT                   /note="putative DNA-binding transcriptional regulator;
FT                   Provisional; Region: PRK10837"
FT                   /db_xref="CDD:170754"
FT                   /locus_tag="Nham_4044"
FT   misc_feature    complement(3402..3581)
FT                   /note="Winged helix-turn-helix (WHTH) DNA-binding domain of
FT                   the GntR family of transcriptional regulators; Region:
FT                   WHTH_GntR; cl00088"
FT                   /db_xref="CDD:173998"
FT                   /locus_tag="Nham_4044"
FT   misc_feature    complement(2724..3314)
FT                   /note="The C-terminal substrate binding of LysR-type
FT                   transcriptional regulator (CbbR) of RubisCO operon, which
FT                   is involved in the carbon dioxide fixation, contains the
FT                   type 2 periplasmic binding fold; Region:
FT                   PBP2_CbbR_RubisCO_like; cd08419"
FT                   /db_xref="CDD:176111"
FT                   /locus_tag="Nham_4044"
FT   misc_feature    complement(order(2892..2897,2901..2906,2922..2939,
FT                   3213..3233,3237..3239,3249..3251,3258..3263,3267..3272))
FT                   /note="putative dimerization interface; other site"
FT                   /db_xref="CDD:176111"
FT                   /locus_tag="Nham_4044"
FT   gene            complement(3655..3944)
FT                   /db_xref="GeneID:4025398"
FT                   /locus_tag="Nham_4045"
FT                   /pseudo
FT   gene            4067..5104
FT                   /db_xref="GeneID:4025399"
FT                   /locus_tag="Nham_4046"
FT   CDS_pept        4067..5104
FT                   /locus_tag="Nham_4046"
FT                   /gene_family="HOG000191264" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="fructose-1,6-bisphosphatase"
FT                   /EC_number="3.1.3.11"
FT                   /note="catalyzes the formation of D-fructose 6-phosphate
FT                   from fructose-1,6-bisphosphate"
FT                   /db_xref="GI:92109254"
FT                   /db_xref="InterPro:IPR000146"
FT                   /db_xref="GeneID:4025399"
FT                   /translation="MSHELTLQQRLEVQAGPDPLHRAVKEAVAALAQAAIDISDLTCRG
FT                   ALAGITGEAQGRNTDGDIQKDLDVRADQIIRDALSALPIAVLASEEMAELDILNPGAPI
FT                   SVAFDPLDGSSNINTNISVGTIFSIMPTPPDASAAFTQPGSAQLAAGFVVYGPQTSLIL
FT                   TLGQGVDIFTLDRVERVFKLTGSMMQIPADATEFAINTSNRRHWDLPVRAYIDECLMGA
FT                   DGPSGKNFNMRWIGSLVAEAFRILVRGGIFLYPGDARDGYEDGRLRLVYEAHPMAFIIE
FT                   QAGGGASTGRKRILDIVPGSLHQRVPLIMGSIKNVRRLEDMHTGPNVALEANAPLFGHR
FT                   GLFRV"
FT                   /transl_table="11"
FT                   /protein_id="YP_571542.1"
FT   misc_feature    4175..5035
FT                   /note="Fructose-1,6-bisphosphatase, an enzyme that
FT                   catalyzes the hydrolysis of fructose-1,6-biphosphate  into
FT                   fructose-6-phosphate and is critical in gluconeogenesis
FT                   pathway. The alignment model also includes chloroplastic
FT                   FBPases and sedoheptulose-1,7...; Region: FBPase; cd00354"
FT                   /db_xref="CDD:30130"
FT                   /locus_tag="Nham_4046"
FT   misc_feature    order(4268..4270,4334..4339,4391..4393,4397..4399,
FT                   4880..4882)
FT                   /note="metal-binding site"
FT                   /db_xref="CDD:30130"
FT                   /locus_tag="Nham_4046"
FT   misc_feature    order(4400..4402,4406..4411,4673..4675,4763..4768,
FT                   4778..4780,4826..4828,4862..4864)
FT                   /note="active site"
FT                   /db_xref="CDD:30130"
FT                   /locus_tag="Nham_4046"
FT   gene            5125..5997
FT                   /db_xref="GeneID:4025400"
FT                   /locus_tag="Nham_4047"
FT   CDS_pept        5125..5997
FT                   /locus_tag="Nham_4047"
FT                   /gene_family="HOG000272991" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="phosphoribulokinase/uridine kinase"
FT                   /transl_table="11"
FT                   /db_xref="GI:92109255"
FT                   /db_xref="InterPro:IPR006083"
FT                   /db_xref="GeneID:4025400"
FT                   /translation="MSRKYPIISITGSSGAGTTSVKRTFEQIFRRENVVAAYIEGDAFH
FT                   RYNRADMRTRMAEESDRGNKHFSHFSPETNLFDELEAVFRSYSESGTGNTRYYVHDDVE
FT                   SAKHGVPPGTFTDWQALPENSDLLFYEGLHGAVVTDKVNVAQYADLKIGVVPVINLEWI
FT                   QKLHRDRSARGYSTEAVTDTILRRMPDYVNYICPQFAETDINFQRVPTVDTSNPFIARW
FT                   IPTPDESMVVIRLKNPRGIDFPYLLSMIPNSFMSRANSIVIHGSKMDLAMQLILTPLIL
FT                   QLIDRKRRA"
FT                   /protein_id="YP_571543.1"
FT   misc_feature    5185..5940
FT                   /note="Nucleoside/nucleotide kinase (NK) is a protein
FT                   superfamily consisting of multiple families of enzymes that
FT                   share structural similarity and are functionally related to
FT                   the catalysis of the reversible phosphate group transfer
FT                   from nucleoside...; Region: NK; cl11962"
FT                   /db_xref="CDD:175376"
FT                   /locus_tag="Nham_4047"
FT   gene            6119..7204
FT                   /db_xref="GeneID:4025401"
FT                   /locus_tag="Nham_4048"
FT   CDS_pept        6119..7204
FT                   /locus_tag="Nham_4048"
FT                   /gene_family="HOG000227792" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="fructose-1,6-bisphosphate aldolase"
FT                   /EC_number="4.1.2.13"
FT                   /note="class II aldolase; catalyzes the reversible aldol
FT                   condensation of dihydroxyacetonephosphate and
FT                   glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis
FT                   and gluconeogenesis"
FT                   /db_xref="GI:92109256"
FT                   /db_xref="InterPro:IPR000771"
FT                   /db_xref="InterPro:IPR006412"
FT                   /db_xref="GeneID:4025401"
FT                   /translation="MARITLRQLLDHAAEHGYGVPAFNINNMEQGLAIMEAAAAVDAPV
FT                   ILQASRGARSYANDIMLAKMIDALEQMYPQIPLCMHQDHGNEEATCATAIKYGFTSVMM
FT                   DGSLKADAKSAADYEYNVDITRRVVDMAHWVGASVEGELGVLGSLEHGGGEQEDGHGIE
FT                   GPVSHDQLLTDPDQAVDFVRATKVDALAIAMGTSHGAYKFSRKPDGDILAMKVVEEIHR
FT                   RLPNTHLVMHGSSSVPQHLQDEFNKFGGEMPQTWGVPVEEIVRGIKHGVRKVNIDTDCR
FT                   LAMTAVFRKIATSNRSEFDPRKFLKPAMDAMRDLCRERFEQFGTAGNAAKIRVIPLSEM
FT                   AKLYRAGKLDPRIGETAVAAE"
FT                   /transl_table="11"
FT                   /protein_id="YP_571544.1"
FT   misc_feature    6134..7111
FT                   /note="hypothetical protein; Provisional; Region: PRK08185"
FT                   /db_xref="CDD:169264"
FT                   /locus_tag="Nham_4048"
FT   misc_feature    6134..7099
FT                   /note="Tagatose-1,6-bisphosphate (TBP) aldolase and related
FT                   Type B Class II aldolases. TBP aldolase is a tetrameric
FT                   class II aldolase that catalyzes the reversible
FT                   condensation of dihydroxyacetone phosphate with
FT                   glyceraldehyde 3-phsophate to produce tagatose...; Region:
FT                   TBP_aldolase_IIB; cd00947"
FT                   /db_xref="CDD:29573"
FT                   /locus_tag="Nham_4048"
FT   misc_feature    order(6197..6205,6212..6214,6272..6274,6281..6289,
FT                   6299..6301,6311..6313,6320..6325,6602..6604,6950..6955,
FT                   6959..6964,6971..6973,6983..6985,6992..6994)
FT                   /note="intersubunit interface; other site"
FT                   /db_xref="CDD:29573"
FT                   /locus_tag="Nham_4048"
FT   misc_feature    order(6365..6370,6707..6715,6719..6721,6812..6817,
FT                   6821..6823,6941..6943,6947..6952)
FT                   /note="active site"
FT                   /db_xref="CDD:29573"
FT                   /locus_tag="Nham_4048"
FT   misc_feature    order(6368..6370,6710..6712,6812..6814)
FT                   /note="zinc binding site; other site"
FT                   /db_xref="CDD:29573"
FT                   /locus_tag="Nham_4048"
FT   misc_feature    order(6707..6709,6713..6715,6719..6721,6815..6817,
FT                   6821..6823)
FT                   /note="Na+ binding site; other site"
FT                   /db_xref="CDD:29573"
FT                   /locus_tag="Nham_4048"
FT   gene            7266..8732
FT                   /db_xref="GeneID:4025375"
FT                   /locus_tag="Nham_4049"