(data stored in ACNUC7421 zone)

HOGENOMDNA: ACISJ_3

ID   ACISJ_3; SV 1; empty ; DNA; empty ; PRO; 4448856 BP.
XX
AC   NC_008782;
XX
PR   Project: 58427;
XX
DE   Acidovorax sp. JS42, complete genome.
XX
OS   Acidovorax sp. JS42
OC   Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC   Comamonadaceae; Acidovorax.
XX
RN   [1]
RP   1-4448856
RG   US DOE Joint Genome Institute
RA   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina del
RA   Rio,T., Dalin,E., Tice,H., Pitluck,S., Chertkov,O., Brettin,T., Bruce,D.,
RA   Han,C., Tapia,R., Gilna,P., Schmutz,J., Larimer,F., Land,M., Hauser,L.,
RA   Kyrpides,N., Kim,E., Stahl,D. and Richardson,P.;
RT   "Complete sequence of Chromosome1 of Acidovorax sp. JS42";
RL   Unpublished
XX
RN   [2]
RP   1-4448856
RG   NCBI Genome Project
RT   "Direct Submission";
RL   Submitted (10-JAN-2007) National Center for Biotechnology Information,
RL   NIH, Bethesda, MD 20894, USA
XX
RN   [3]
RP   1-4448856
RG   US DOE Joint Genome Institute
RA   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina del
RA   Rio,T., Dalin,E., Tice,H., Pitluck,S., Chertkov,O., Brettin,T., Bruce,D.,
RA   Han,C., Tapia,R., Gilna,P., Schmutz,J., Larimer,F., Land,M., Hauser,L.,
RA   Kyrpides,N., Kim,E., Stahl,D. and Richardson,P.;
RT   "Direct Submission";
RL   Submitted (21-DEC-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 CP000539.
CC   URL -- http://www.jgi.doe.gov
CC   JGI Project ID: 4001426
CC   Source DNA and bacteria available from David Stahl
CC   (dastahl@u.washington.edu)
CC   Contacts: David Stahl (dastahl@u.washington.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-LANL
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..4448856
FT                   /strain="JS42"
FT                   /mol_type="genomic DNA"
FT                   /organism="Acidovorax sp. JS42"
FT                   /db_xref="taxon:232721"
FT   gene            212..694
FT                   /db_xref="GeneID:4672148"
FT                   /locus_tag="Ajs_0001"
FT   CDS_pept        212..694
FT                   /locus_tag="Ajs_0001"
FT                   /gene_family="HOG000229978" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="NLP/P60 protein"
FT                   /transl_table="11"
FT                   /note="PFAM: NLP/P60 protein; KEGG: rfr:Rfer_0741 NLP/P60"
FT                   /db_xref="GI:121592437"
FT                   /db_xref="InterPro:IPR000064"
FT                   /db_xref="InterPro:IPR000437"
FT                   /db_xref="GeneID:4672148"
FT                   /translation="MRAFALPVLTLAASLLVVGCGTTPPTSASRNAAYSRLSPEQSSDI
FT                   AIHALGLVGTPYRYGGNTPDSGFDCSGLIGYVYTSRAGVAPPRTVAQLSGFGQSVDADE
FT                   LRTGDLVVFGRGRPTHAGIYVGEGRFVHAPSSGGTVRLDHLKSRYWSQQFASFRRP"
FT                   /protein_id="YP_984333.1"
FT   sig_peptide     212..298
FT                   /note="Signal predicted by SignalP 2.0 HMM (Signal peptide
FT                   probability 0.994) with cleavage site probability 0.407 at
FT                   residue 29"
FT                   /locus_tag="Ajs_0001"
FT                   /product="hypothetical protein"
FT   misc_feature    371..688
FT                   /note="NlpC/P60 family; Region: NLPC_P60; cl11438"
FT                   /db_xref="CDD:164223"
FT                   /locus_tag="Ajs_0001"
FT   gene            822..1922
FT                   /db_xref="GeneID:4670651"
FT                   /locus_tag="Ajs_0002"
FT   CDS_pept        822..1922
FT                   /locus_tag="Ajs_0002"
FT                   /gene_family="HOG000220501" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="phospho-2-dehydro-3-deoxyheptonate aldolase"
FT                   /EC_number="2.5.1.54"
FT                   /note="catalyzes the formation of
FT                   3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from
FT                   phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine
FT                   sensitive"
FT                   /db_xref="GI:121592438"
FT                   /db_xref="InterPro:IPR006218"
FT                   /db_xref="InterPro:IPR006219"
FT                   /db_xref="GeneID:4670651"
FT                   /translation="MTLTERLASPLTTHDTTRIDDLRIKAVRPLITPALLQEWQPAPEA
FT                   AQTLVESSRVAISRVLHGQDDRLIVVVGPCSIHDHDQAMEYARLLKEQADALAQDLLIV
FT                   MRVYFEKPRTTVGWKGYINDPHLDGSFAINEGLERARALLLDVLALGLPVGTEFLDLLS
FT                   PQFISDLVSWGAIGARTTESQSHRQLASGLSCPVGFKNGTDGGVKVAADAIQAAQAPHA
FT                   FMGMTKMGQAAIFETRGNHDCHVILRGGKTPNYGAADVQAACEMLEKAGQRPQVMIDLS
FT                   HANSSKQHRRQIDVAQDVAQQIAAGDARITGVMIESHLQEGRQDIVDGQPLTPGVSVTD
FT                   ACISFAQTVPVLQQLAAAVRERRTRG"
FT                   /transl_table="11"
FT                   /protein_id="YP_984334.1"
FT   misc_feature    861..1916
FT                   /note="NeuB family; Region: NeuB; cl00496"
FT                   /db_xref="CDD:174244"
FT                   /locus_tag="Ajs_0002"
FT   misc_feature    993..1880
FT                   /note="DAHP synthetase I family; Region: DAHP_synth_1;
FT                   pfam00793"
FT                   /db_xref="CDD:144404"
FT                   /locus_tag="Ajs_0002"
FT   gene            2149..4158
FT                   /db_xref="GeneID:4671061"
FT                   /locus_tag="Ajs_0003"
FT   CDS_pept        2149..4158
FT                   /locus_tag="Ajs_0003"
FT                   /gene_family="HOG000136246" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="diguanylate cyclase/phosphodiesterase with
FT                   PAS/PAC sensor(s)"
FT                   /transl_table="11"
FT                   /note="KEGG: tbd:Tbd_1042 putative diguanylate
FT                   cyclase/phosphodiesterase (GGDEF & EAL domains) with
FT                   PAS/PAC and GAF sensor(s); TIGRFAM: PAS sensor protein;
FT                   diguanylate cyclase; PFAM: GGDEF domain containing protein;
FT                   EAL domain protein; PAS fold-3 domain protein; PAS fold-4
FT                   domain protein; PAS fold domain protein; SMART: PAS domain
FT                   containing protein"
FT                   /db_xref="GI:121592439"
FT                   /db_xref="InterPro:IPR000014"
FT                   /db_xref="InterPro:IPR000160"
FT                   /db_xref="InterPro:IPR001633"
FT                   /db_xref="InterPro:IPR013655"
FT                   /db_xref="InterPro:IPR013656"
FT                   /db_xref="InterPro:IPR013767"
FT                   /db_xref="GeneID:4671061"
FT                   /translation="MVDGVAQPNAEYVLEGTPSERLLTQRSLVIRDRARERFPRAPVLA
FT                   RTGARSYVGQQLTASDGTPIGMIFVVFRQTLERSRFVSNTLQIFAARAAAELQRQTDDQ
FT                   RIRQQASLLDKARDAIIVRDLEHRITFWNEGAERMYGWSREEVLGRSIATLLYQNPEDF
FT                   LRATQQVMQHGVWSGEILQCDRAGRTLEAEGRWTLVRNDRGEPESVLAINADIGTRKHQ
FT                   EREIQRLAFFDPLTHLPNRVQLLDRVDQALAKAQRLEQGGALLFIDLDNFKTLNDTLGH
FT                   DQGDELLQIVAQRLNTCVRSADTVARLGGDEFVVLVEQLSAHSDTLAEQAGAVGEKILA
FT                   VLSAPYALTGYQHRSTPSIGIALFNHAPTTVGELLKQADLAMYQAKTAGRNTLRFFNPS
FT                   MQHAVAERASLEADLRNALAQKEFLLHYQPQINARGAIVGVEALLRWAHPRRGMVSPGQ
FT                   FIPLAEETGLVLPLGHWVLHTACSVLADWQRVPALAPLTMAVNVSSRQFRDAGFVDDVA
FT                   GVLAATGAPASQLKLELTESLLVEDLAATIATMAALRALGVGFSLDDFGTGYSSLAYLK
FT                   RMPLGQLKIDQSFVRDLLTDPNDAAIVRTIIGLAASLGLEVIAEGVETSAQRDWLAHAG
FT                   CAVYQGYFFSRPLPLDLLEQLLHDHIAAARTPSL"
FT                   /protein_id="YP_984335.1"
FT   misc_feature    2479..2826
FT                   /note="PAS domain S-box; Region: sensory_box; TIGR00229"
FT                   /db_xref="CDD:161776"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    2494..2796
FT                   /note="PAS domain; PAS motifs appear in archaea, eubacteria
FT                   and eukarya. Probably the most surprising identification of
FT                   a PAS domain was that in EAG-like K+-channels. PAS domains
FT                   have been found to bind ligands, and to act as sensors for
FT                   light and oxygen in...; Region: PAS; cd00130"
FT                   /db_xref="CDD:29035"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    order(2542..2544,2554..2556,2572..2574,2611..2616,
FT                   2617..2619,2692..2694,2707..2709)
FT                   /note="putative active site; other site"
FT                   /db_xref="CDD:29035"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    order(2602..2604,2614..2616,2635..2637,2644..2649,
FT                   2728..2730,2734..2736)
FT                   /note="heme pocket; other site"
FT                   /db_xref="CDD:29035"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    2839..3330
FT                   /note="Diguanylate-cyclase (DGC) or GGDEF domain; Region:
FT                   GGDEF; cd01949"
FT                   /db_xref="CDD:143635"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    order(2950..2952,3079..3081)
FT                   /note="metal-binding site"
FT                   /db_xref="CDD:143635"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    order(2965..2967,2974..2979,2989..2991,3001..3003,
FT                   3067..3069,3073..3084)
FT                   /note="active site"
FT                   /db_xref="CDD:143635"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    order(3055..3057,3157..3159)
FT                   /note="I-site; other site"
FT                   /db_xref="CDD:143635"
FT                   /locus_tag="Ajs_0003"
FT   misc_feature    3382..4086
FT                   /note="EAL domain. This domain is found in diverse
FT                   bacterial signaling proteins. It is called EAL after its
FT                   conserved residues and is also known as domain of unknown
FT                   function 2 (DUF2).  The EAL domain has been shown to
FT                   stimulate degradation of a second...; Region: EAL; cd01948"
FT                   /db_xref="CDD:30163"
FT                   /locus_tag="Ajs_0003"
FT   gene            complement(4216..5019)
FT                   /db_xref="GeneID:4671169"
FT                   /locus_tag="Ajs_0004"
FT   CDS_pept        complement(4216..5019)
FT                   /locus_tag="Ajs_0004"
FT                   /gene_family="HOG000256786" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="regulatory proteins, IclR"
FT                   /transl_table="11"
FT                   /note="PFAM: regulatory proteins, IclR; KEGG: mag:amb2598
FT                   transcriptional regulator"
FT                   /db_xref="GI:121592440"
FT                   /db_xref="InterPro:IPR005471"
FT                   /db_xref="GeneID:4671169"
FT                   /translation="MARTRNIDFDEGADSRRFVTALARGLDVLACFQVDEKWLTNAEIA
FT                   ARTGLPKPTVVRLAYTLCVLGYLRHSRDSGKYALGDSLAALGITMVSNLRLRRIARPYM
FT                   QDFADRYDISVSLGIRNGLSVLYVENCRSGTPLSLGLDLGARLPVAETAMGHALLAVME
FT                   PRERERLLAEIRQAEGERWPQLRQSIETGCAHWRARGFTVVVRDWQTDIAGVGAAIRQP
FT                   DGRVISFNAGGSASKFPRALLEQEIGPQFARMVKGLEPFVRSEEA"
FT                   /protein_id="YP_984336.1"
FT   misc_feature    complement(4693..4965)
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="Ajs_0004"
FT   misc_feature    complement(4243..4962)
FT                   /note="Transcriptional regulator [Transcription]; Region:
FT                   IclR; COG1414"
FT                   /db_xref="CDD:31604"
FT                   /locus_tag="Ajs_0004"
FT   misc_feature    complement(4270..4614)
FT                   /note="Bacterial transcriptional regulator; Region: IclR;
FT                   pfam01614"
FT                   /db_xref="CDD:144993"
FT                   /locus_tag="Ajs_0004"
FT   gene            5262..6233
FT                   /db_xref="GeneID:4671332"
FT                   /locus_tag="Ajs_0005"
FT   CDS_pept        5262..6233
FT                   /locus_tag="Ajs_0005"
FT                   /gene_family="HOG000126605" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="hypothetical protein"
FT                   /transl_table="11"
FT                   /note="PFAM: Uncharacterized protein UPF0065; KEGG:
FT                   reu:Reut_A1420 twin-arginine translocation pathway signal"
FT                   /db_xref="GI:121592441"
FT                   /db_xref="InterPro:IPR005064"
FT                   /db_xref="GeneID:4671332"
FT                   /translation="MTHALLNRRTLSLLLAAGCVAGPALAQPERFPSRPIKVLIGFTAG
FT                   GSTDVPFRVLAENASKILGQPVIIENKPGAGGVLPAQMMQSTPADGYTLAQVPLPVFRL
FT                   PYTQKINWNPATDLQYVIGLAGYAFGLVVPADSPIKSMQDYIAYAKNNPGKLNYGTPGA
FT                   LTTLHLTMENIALQAGVTLNHIPYKGNSESLQAVLGGHVMSIADTPGWAPYVEQGKLRV
FT                   LSVWGDKRSARFPNVPTLKEVGINLVQTSPFGLVVPKGTDPKITQVLHDAFKKAMEMPN
FT                   YKESLAKFDMDTYYMDSATYKQYALDTMKTEKVIIEKLGLAK"
FT                   /protein_id="YP_984337.1"
FT   sig_peptide     5262..5342
FT                   /note="Signal predicted by SignalP 2.0 HMM (Signal peptide
FT                   probability 1.000) with cleavage site probability 1.000 at
FT                   residue 27"
FT                   /locus_tag="Ajs_0005"
FT                   /product="hypothetical protein"
FT   misc_feature    5412..6224
FT                   /note="The substrate binding domain of LysR-type
FT                   transcriptional regulators (LTTRs), a member of the type 2
FT                   periplasmic binding fold protein superfamily; Region:
FT                   PBP2_LTTR_substrate; cl11398"
FT                   /db_xref="CDD:176835"
FT                   /locus_tag="Ajs_0005"
FT   gene            complement(6572..7177)
FT                   /db_xref="GeneID:4671272"
FT                   /locus_tag="Ajs_0006"
FT   CDS_pept        complement(6572..7177)
FT                   /locus_tag="Ajs_0006"
FT                   /gene_family="HOG000224876" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="hypothetical protein"
FT                   /transl_table="11"
FT                   /note="KEGG: bxe:Bxe_A1159 hypothetical protein"
FT                   /db_xref="GI:121592442"
FT                   /db_xref="InterPro:IPR000437"
FT                   /db_xref="GeneID:4671272"
FT                   /translation="MPTIARRSAFFRRTALLSPVPFLAAAAACLTAPPALAQPSEDRAY
FT                   APSVYVQGEWARRQTDAITIGATLPWGTWRRPLWGGELRGHWDVSLSRWSFDGIGGHNS
FT                   AVVVGVAPTLRLRPDEGRSPWFWEAGIGATVASHRYRVQDHEFSTRFNFASHLGLGRNF
FT                   GAQRQHELMLSVQHVSNAGIKSPNPGENFLQLRYALHF"
FT                   /protein_id="YP_984338.1"
FT   sig_peptide     complement(7064..7177)
FT                   /note="Signal predicted by SignalP 2.0 HMM (Signal peptide
FT                   probability 1.000) with cleavage site probability 1.000 at
FT                   residue 38"
FT                   /locus_tag="Ajs_0006"
FT                   /product="hypothetical protein"
FT   misc_feature    complement(6575..7012)
FT                   /note="Lipid A 3-O-deacylase (PagL); Region: PagL;
FT                   pfam09411"
FT                   /db_xref="CDD:150172"
FT                   /locus_tag="Ajs_0006"
FT   gene            complement(7318..7947)
FT                   /db_xref="GeneID:4671717"
FT                   /locus_tag="Ajs_0007"
FT   CDS_pept        complement(7318..7947)
FT                   /locus_tag="Ajs_0007"
FT                   /gene_family="HOG000220307" [ FAMILY / ALN / TREE ]
FT                   /codon_start="1"
FT                   /product="hypothetical protein"
FT                   /transl_table="11"
FT                   /note="KEGG: pol:Bpro_0029 hypothetical protein"
FT                   /db_xref="GI:121592443"
FT                   /db_xref="GeneID:4671717"
FT                   /translation="MARFKITQRLAATAVAAAVLAGMAVPTLAQPGPGPAATEQGASQA
FT                   QQRPRQRALTPEQREQYMAQRAEAFKRKLQLTPEQEPAWNSFLQSMKPDADARKARLDW
FT                   QGMDQLTTPERIDRMRALRSQRAAEMDRRGDAVKAFYGTLTPAQQKTFDAEGKRMYRHW
FT                   GGDHPMGKRWGKDGARGDFRGDGRGMRHQGPGPGAGAAPGAPLTPQ"
FT                   /protein_id="YP_984339.1"
FT   sig_peptide     complement(7858..7947)
FT                   /note="Signal predicted by SignalP 2.0 HMM (Signal peptide
FT                   probability 1.000) with cleavage site probability 0.998 at
FT                   residue 30"
FT                   /locus_tag="Ajs_0007"
FT                   /product="hypothetical protein"
FT   misc_feature    complement(7483..7758)
FT                   /note="Domain of Unknown Function (DUF1520); Region:
FT                   DUF1520; pfam07480"
FT                   /db_xref="CDD:148852"
FT                   /locus_tag="Ajs_0007"
FT   gene            8260..9237
FT                   /db_xref="GeneID:4671890"
FT                   /locus_tag="Ajs_0008"