src/hg/archaeStuff/data/Genome-info-mods 1.100
1.100 2010/05/22 03:25:20 pchan
add therAggr1
Index: src/hg/archaeStuff/data/Genome-info-mods
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-mods,v
retrieving revision 1.99
retrieving revision 1.100
diff -b -B -U 1000000 -r1.99 -r1.100
--- src/hg/archaeStuff/data/Genome-info-mods 18 Apr 2010 20:54:19 -0000 1.99
+++ src/hg/archaeStuff/data/Genome-info-mods 22 May 2010 03:25:20 -0000 1.100
@@ -1,1959 +1,1972 @@
## Genome-info-mods - only add fields which you wish to over-ride in Genome-info-db (automatically
## generated using "make-genome-info" perl script).
#
# Description of Fields for each genome entry:
#
# Org_abr: first four letters of genus & species, plus strain identifier (if any)
# NOTE: Org_abr *must* occur prior to any of the fields given below to be associated
# with the right genome!
# Org_name: Species name (no length restriction -- taken from NCBI directory name;
# should NOT be changed)
# Menu_name: Species name preferred in pull-down menu (usually a shortenned version
# of Org_name -- i.e. without strain; should still be unique)
# Domain: Domain (Bacteria, Archaea, or Eukarya)
# DB_name: name used for species database in mysql
# Cent_DB: Production central database which must be set to same value as variable
# "central.db" in hg.conf in cgi-bin directory; will use a default value if not set explicitly
# DB_src: Source of information for genome DB which determines the format of information
# input into genome browser; defalt value "NCBI"; alt vals: "JGI", etc.;
# will use default if not set explicitly
# Tax_name: Full name of species (including strain) (normally taken from NCBI Genbank files)
# Tax_ID: NCBI's unique species identifier used in its taxonomy classification
# Dom_ct: Domain count -- priority order in which you want it displayed in the browser;
# can put an integer, or assign same priority as another organism (allows floating to stay
in correct place for unpublished genomes) using notation '&Org_abbr' i.e. (Dom_ct: &Heli_pylo_J99)
# Gen_ID: Genome unique ID number used to access organim's genome page at NCBI
# Pub_id: Pubmed identifier for publication describing genome sequence
# Seq_acc: List of accession numbers for all refseq (NC*) genome files
# Name_chg: Name mapping for each genome sequence file in pairs (i.e. NC2001 chr1 NC2002 chr2 ..etc)
# Seq_size: Size of sequences, in same order as names in Seq_acc:
# Gene_ct: Gene count list, separated by spaces, in order of seqs in Seq_acc field
# Multiz: track abbreviation, followed by list of organisms (db names) to be aligned in multiz or blastz track
# Public_multiz: track abbreviation, followed by list of organisms (db names) to be aligned in multiz or blastz track (used in public browser)
# Phylo: phylogenetic tree string used to construct phylohmm track i.e. (org1,(org2,org3))
# Rel_date: Release date for current sequence version of genome, read from NCBI's microbial genomes page
# Sp_info: Optional sentences about species included in description.html front page (no length
# restriction, but no newlines allowed)
# Seq_src: Sequencing center that submitted the genome sequence (also from NCBI's microbial genomes page)
# Web_seq: web/ftp address for fasta/genbank sequence files
# Web_db: NCBI web address for this organism's genome
# Trna_opt: tRNAscan-SE options to use in auto-runs
# Trna_abr: tRNAscan-SE output files prefix
# Gen_seq: location of local FASTA genome sequence file
# Prot_seq: location of local copy of protein sequences
# Feat_seq: All features in genome file (including protein genes, ncRNA genes, intergenic
# regions), separated into individual fasta seqs
Org_abr: Arch_fulg
DB_name: archFulg1
Iso_pub: 17777850
Rel_date: Dec 1997
Sp_info: <I>A. fulgidus</I> is a sulfur-metabolizing anaerobe that grows optimally around 83C. High-temperature sulfate reduction by Archaeoglobus species contributes to deep subsurface oil-well 'souring' by iron sulfide, which causes corrosion of iron and steel in oil-and gas-processing systems.
Multiz: Archaeoglobaceae ferrPlac1 archProf1 archFulg1
Phylo: ((archFulg1,archProf1),ferrPlac1)
Org_abr: Aero_pern
DB_name: aerPer1
Iso_pub: 8863437
Rel_date: April 1999
Sp_info: <I>A. pernix</I> is an aerobic hyperthermophilic crenarchaeon that grows optimally at 95C.
# This is a draft genome, so most info needed to added manually
Org_abr: Ferr_acid_Fer1
Menu_name: Ferroplasma acidarmanus
Domain: Archaea
#Put incomplete genomes at the end of the list
DB_name: ferrAcid1
Iso_pub: 10710303
Tax_name: Ferroplasma acidarmanus Fer1
Gen_ID: 5000
Name_chg: Contig90 Contig109 Contig112 Contig116 Contig102 Contig45 Contig114 Contig111 Contig115 Contig103 Contig106 Contig107 Contig117 Contig121 Contig125 Contig118 Contig123 Contig119 Contig124 Contig120 Contig126 Contig132 Contig134 Contig130 Contig133 Contig129 Contig128 Contig135 Contig140 Contig137 Contig139 Contig138 Contig136 Contig142 Contig141 Contig144 Contig148 Contig143 Contig145 Contig146 Contig147 Contig149 Contig150 Contig151 Contig155 Contig152 Contig156 Contig159 Contig157 Contig160 Contig158 Contig154 Contig161 Contig162 Contig163 Contig165 Contig164 Contig166 Contig167 Contig168 Contig169
Rel_date: June 2005 Draft
Seq_src: US DOE Joint Genome Institute
Web_seq: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Ferroplasma_acidarmanus/
Web_db: http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=Genome&gi=5000
Sp_info: <I>F. acidarmanus</I> is an acidophilic iron-oxidizing euryarchaeon that is native to metal-rich environments (including those rich in arsenic). It grows optimally at 42C and pH 1.2. The genome is still in draft form.
Prot_seq: /projects/lowelab/db/genomes/Bacteria/Ferroplasma_acidarmanus_Fer1/Ferr_acid_Fer1-prot.fa
Multiz: Thermoplasmas picrTorr1 therVolc1 therAcid1
Phylo: (((therVolc1,therAcid1),ferrAcid1),picrTorr1)
Org_abr: Halo_mari_ATCC_43049
Menu_name: Haloarcula marismortui
DB_name: halMar1
Iso_pub: 11536469
Rel_date: Nov. 2004
Sp_info: <I>H. marismortui</I> is a halophilic archaeon found in the Dead Sea, where it optimally grows at around 4.5 molar salt.
Multiz: HalophilesPriv natrPhar1 haloWals1 haloUtah1 haloVolc1_1 natrMaga1 haloHalo1 haloSali1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: (((((haloHalo1,haloSali1),haloUtah1),natrPhar1),halMar1),(haloWals1,haloVolc1))
Org_abr: Halo_sp
DB_name: haloHalo1
Rel_date: Oct 2000
Sp_info: <I>Halobacterium</I> is a halophilic aerobic euryarchaeon found under conditions of extremely high salinity, at an optimum of 4.3M salt. It is a mesophile which grows optimally at 42C. A well-developed genetic system is available for this species.
Multiz: HalophilesPriv haloSali1 natrMaga1 haloVolc1_1 natrPhar1 haloWals1 halMar1 haloUtah1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
SP_ID: HALSA
Org_abr: Halo_sali_R1
Menu_name: Halobacterium salinarum R1
DB_name: haloSali1
Rel_date: Feb 2008
Seq_src: Max Planck Institute
Name_chg: chr plasmid_PHS1 plasmid_PHS4 plasmid_PHS3 plasmid_PHS2
SP_ID: HALSA
Iso_pub:
Multiz: HalophilesPriv haloHalo1 natrMaga1 haloVolc1_1 natrPhar1 haloWals1 halMar1 haloUtah1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Halo_wals
Rel_date: 07/25/06
Seq_src: Max-Planck-Institute of Biochemistry and the University of Groningen
Pub_id: 16820047
DB_name: haloWals1
#Iso_pub: 15560825
SP_ID: HALWD HALMA HALSP NATPD
Multiz: HalophilesPriv haloVolc1_1 halMar1 haloUtah1 natrPhar1 natrMaga1 haloHalo1 haloSali1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Halo_volc_DS2
Org_name: Haloferax volcanii DS2
Menu_name: Haloferax volcanii
Domain: Archaea
DB_name: haloVolc1
Iso_pub: 1190944
DB_src: TIGR
#DB_src: NCBI
Tax_name: Haloferax volcanii DS2
BLAT_IDs: 61000 61001
Tax_ID: 309800: Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloferax.
TIGR_ID: 0
Dom_ct: &Halo_sp
Gen_ID: 0
SP_ID: HALVO HALSQ HALSA HALWD HALMA HALSP NATPD
Seq_acc: Hvo-genome TG_gha_455 TG_gha_452 TG_gha_453 TG_gha_454 TG_gha_450
Name_chg: chr pHV4 pHV3 pHV1 pHV2
Seq_size: 2847757 635786 437906 85092 6359
Seq_GC: 66.64 61.67 65.56 55.5 56.06
Gene_ct: 4209
Gb_acc: None
Multiz: HalophilesPriv haloWals1 natrPhar1 natrMaga1 haloHalo1 haloSali1 halMar1 haloUtah1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1))
Public_phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Pub_id:
Rel_date: April 2007
Seq_src: Institute for Genomic Research
Sp_info: The genome is complete and being publicly released by Jonathan Eisen before journal publication while genome annotation is in progress. <I>H. volcanii</I> is a chemoorganotroph requiring complex nutrient medium and 1.5-2.5 M NaCl for growth. Cultures will grow at 37C, but optimal growth is at 42C.
Web_seq:
Web_db:
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Halo_volc-tRNAs
Prot_seq: /projects/lowelab/db/genomes/Other-genomes/Haloferax_volcanii_DS2/Hvol-genome-prot.fa
Org_abr: Halo_volc_DS2_1_1
Org_name: Haloferax volcanii DS2
Menu_name: Haloferax volcanii
Domain: Archaea
DB_name: haloVolc1_1
Iso_pub: 1190944
DB_src: TIGR
Tax_name: Haloferax volcanii DS2
BLAT_IDs: 61024 61025
Tax_ID: 309800: Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloferax.
TIGR_ID: 0
Dom_ct: &Halo_volc_DS2
Gen_ID: 0
SP_ID: HALVO HALSQ HALSA HALWD HALMA HALSP NATPD
Seq_acc: Hvo-genome chr pHV4 pHV3 pHV1 pHV2
Name_chg: chr pHV4 pHV3 pHV1 pHV2
Seq_size: 2847757 635786 437906 85092 6359
Seq_GC: 66.64 61.67 65.56 55.5 56.06
Gene_ct: 4135
Gb_acc: None
Multiz: HalophilesPriv haloWals1 natrPhar1 natrMaga1 haloHalo1 haloSali1 halMar1 haloUtah1
Public_multiz: Halophiles haloWals1 natrPhar1 haloHalo1 haloSali1 halMar1 haloUtah1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: (((((haloHalo1,haloSali1),haloUtah1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Pub_id:
Rel_date: 1 Oct 2009
Seq_src: Halolex
Sp_info: The genome is complete and being publicly released by Jonathan Eisen before journal publication while genome annotation is provided through Halolex. <I>H. volcanii</I> is a chemoorganotroph requiring complex nutrient medium and 1.5-2.5 M NaCl for growth. Cultures will grow at 37C, but optimal growth is at 42C.
Web_seq:
Web_db:
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Halo_volc-tRNAs
Prot_seq: /projects/lowelab/db/genomes/Other-genomes/Haloferax_volcanii_DS2/Hvol-genome-prot.fa
Org_abr: Halo_utah_DSM_12940
DB_name: haloUtah1
Name_chg: chr
Iso_pub: 10826803
Rel_date: April 2009
Multiz: HalophilesPriv haloWals1 natrPhar1 natrMaga1 haloHalo1 haloSali1 haloVolc1_1 halMar1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Natr_phar
DB_name: natrPhar1
Iso_pub:
Rel_date: Oct 2005
Sp_info: <I>N. pharaonis</I> grows at high salt and pH and has multiple systems for nitrogen assimilation.
Multiz: HalophilesPriv haloWals1 haloHalo1 natrMaga1 haloSali1 haloVolc1_1 halMar1 haloUtah1
Public_multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((((haloHalo1,haloSali1),haloUtah1),natrMaga1),natrPhar1),halMar1),(haloWals1,haloVolc1_1))
Public_phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Meth_jann
DB_name: methJann1
Iso_pub: http://www.springerlink.com/content/u8774k126821777x/
Name_chg: chr lg_extrachr sm_extrachr
TIGR_ID: 57
Rel_date: August 1996
Sp_info: The organism's genus was formerly <I>Methanococcus</I>, but it has been reclassified as <I>Methanocaldococcus</I>. <I>M. jannaschii</I> is a methanogen which grows optimally at 85C, and has the distinction of being the first archaeon and first hyperthermophile sequenced.
Multiz: Methanococcus methFerv1 methVulc1 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1 methSp_FS406_1
Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc1),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_mari_S2
Menu_name: Methanococcus maripaludis S2
DB_name: metMar1
Rel_date: May 2004
Iso_pub: http://www.springerlink.com/content/nv3wj86641n40147/
Sp_info: <I>M. maripaludis S2</I> is a mesophilic methanogen which was isolated from salt marsh sediment in South Carolina. It grows on carbon dioxide and hydrogen, producing methane.
Multiz: Methanococcus methMari_C5_1 methMari_C7 methVann1 methAeol1 methJann1 methSp_FS406_1
Phylo: (methKand1,(methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1))))))))
Org_abr: Meth_mari_C5
DB_name: methMari_C5_1
Iso_pub:
Multiz: Methanococcus metMar1 methMari_C6 methMari_C7 methVann1 methAeol1 methJann1 methSp_FS406_1
Phylo: (methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1)))))))
Org_abr: Meth_mari_C6
DB_name: methMari_C6
Iso_pub:
Multiz: Methanococcus metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methJann1 methSp_FS406_1
Phylo: (methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1)))))))
Rel_date: Nov 2007
Org_abr: Meth_mari_C7
DB_name: methMari_C7
Iso_pub:
Multiz: Methanococcus metMar1 methMari_C5_1 methMari_C6 methVann1 methAeol1 methJann1 methSp_FS406_1
Phylo: (methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1)))))))
Org_abr: Meth_aeol_Nankai-3
Menu_name: Methanococcus aeolicus
Iso_pub: 16825624
DB_name: methAeol1
SP_ID: METAO METMP
Multiz: Methanococcus metMar1 methMari_C5_1 methMari_C6 methMari_C7 methVann1 methJann1 methSp_FS406_1
Phylo: (methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1)))))))
Org_abr: Meth_vann_SB
Menu_name: Methanococcus vannielii SB
Iso_pub: 14888644
DB_name: methVann1
SP_ID: METVA METMP
Multiz: Methanococcus metMar1 methMari_C5_1 methMari_C6 methMari_C7 methAeol1 methJann1 methSp_FS406_1
Phylo: (methTher1,(methJann1,(methAeol1,(methVann1,(methMari_C7,(methMari_C6,(metMar1,methMari_C5_1)))))))
Org_abr: Meth_ferv_AG86
Menu_name: Methanocaldococcus fervens
DB_name: methFerv1
Iso_pub: 10319479
Tax_name: Methanocaldococcus fervens AG86
SP_ID: METJA
Rel_date: July 2009
Name_chg: chr pMEFER01
Seq_src: Joint Genome Institute
Multiz: Methanococcus methJann1 methVulc1 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1 methSp_FS406_1
Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc1),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_infe_ME
Menu_name: Methanocaldococcus infernus
DB_name: methInfe0
Iso_pub: 9734046
Tax_name: Methanocaldococcus infernus ME
SP_ID: METJA
Rel_date: July 2009
Name_chg: ctg00065 ctg00004 ctg00020 ctg00072 ctg00034 ctg00022 ctg00031 ctg00044 ctg00045 ctg00063 ctg00039 ctg00103 ctg00043 ctg00019 ctg00040 ctg00051 ctg00026 ctg00037 ctg00018 ctg00010 ctg00085 ctg00032 ctg00028 ctg00021 ctg00049 ctg00052 ctg00042 ctg00095 ctg00038 ctg00033 ctg00081 ctg00070 ctg00113 ctg00016 ctg00002 ctg00069 ctg00024 ctg00027 ctg00108 ctg00017 ctg00107 ctg00062 ctg00036 ctg00029 ctg00035 ctg00041 ctg00023 ctg00009 ctg00047 ctg00082 ctg00025 ctg00046 ctg00030 ctg00059
Seq_src: Joint Genome Institute
Multiz: Methanococcus methJann1 methFerv1 methVulc1 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1 methSp_FS406_1
Phylo: (methKand1,(methTher1,(((methJann1,methFerv1),methVulc1),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_acet
DB_name: metAce1
Rel_date: April 2002
Iso_pub: 16346552
Sp_info: <I>M. acetivorans</I> is the largest known archaeal genome. Only Methanosarcina species possess all three known pathways for methanogenesis and are capable of utilizing no less than nine methanogenic substrates, including acetate. In contrast, all other orders of methanogens possess a single pathway for methanogenesis, and many utilize no more than two substrates.
Multiz: MethanosarcinaMethanomicrobiales methMaze1 methBark1 methBurt2 methTherPT1 methHung1 methLabrZ_1 mculMari1
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_bark_fusaro
Menu_name: Methanosarcina barkeri
DB_name: methBark1
Iso_pub: 889387
Name_chg: plasmid1 chr
Rel_date: Oct 2005
Sp_info: <I>M. barkeri</I> is a mesophilic methanogen isolated from mud at a freshwater lake near Naples, Italy.
Multiz: MethanosarcinaMethanomicrobiales methMaze1 metAce1 methBurt2 methTherPT1 methHung1 methLabrZ_1 mculMari1
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_maze
DB_name: methMaze1
Iso_pub:
Rel_date: July 2002
TIGR_ID: 45681
Multiz: MethanosarcinaMethanomicrobiales methMaze1 metAce1 methBurt2 methTherPT1 methHung1 methLabrZ_1 mculMari1
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_maze
DB_name: methMaze1
Rel_date: July 2002
TIGR_ID: 45681
Multiz: MethanosarcinaMethanomicrobiales methBark1 metAce1 methBurt2 methTherPT1 methHung1 methLabrZ_1 mculMari1
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_burt_DSM_6242
Org_name: Methanococcoides burtonii DSM 6242
Menu_name: Methanococcoides burtonii
Domain: Archaea
DB_name: methBurt2
Iso_pub:
Rel_date: 4/10/2006
Multiz: MethanosarcinaMethanomicrobiales methBark1 methMaze1 metAce1 methTherPT1 methHung1 methLabrZ_1 mculMari1
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_ther_PT
Org_name: Methanosaeta thermophila PT
Menu_name: Methanosaeta thermophila
DB_name: methTherPT1
SP_ID: METTP METAC METHJ METBU
Iso_pub: 1380291
Rel_date: 10/28/06
Seq_src: DOE/JGI
Multiz: Methanosarcinales methBark1 methMaze1 metAce1 methBurt2 methHung1
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_hung_JF-1
Org_name: Methanospirillum hungatei JF-1
Menu_name: Methanospirillum hungatei
DB_name: methHung1
SP_ID: METLZ METHJ METMJ METAC METBU
Iso_pub: http://www.bmb.psu.edu/faculty/ferry/lab/publications/publications/INT%20J%20SYST%20BACT%20v24%20p465.pdf
Pub_id: 0
Multiz: Methanomicrobiales mculMari1 methLabrZ_1 methTherPT1 metAce1 methMaze1 methBark1 methBurt2
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_labr_Z
DB_name: methLabrZ_1
Iso_pub:
SP_ID: METLZ METHJ METMJ METAC METBU
Multiz: Methanomicrobiales mculMari1 methHung1 methTherPT1 metAce1 methMaze1 methBark1 methBurt2
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_mari_JR1
DB_name: mculMari1
Iso_pub: http://www.springerlink.com/content/q37783t3001327u5/
SP_ID: METLZ METHJ METMJ METAC METBU
Multiz: Methanomicrobiales methLabrZ_1 methHung1 methTherPT1 metAce1 methMaze1 methBark1 methBurt2
Phylo: (mculMari1,(methLabrZ_1,(methHung1,(methTherPT1,(methBurt2,(metAce1,(methMaze1,methBark1)))))))
Org_abr: Meth_stad
DB_name: methStad1
Iso_pub: 3994486
Multiz: Methanogens methSmit1 methTher1 metMar1 methMari_C5_1 methJann1
Phylo: ((((methStad1,methSmit1),methTher1),(metMar1,methMari_C5_1)),methJann1)
Org_abr: Meth_ther
DB_name: methTher1
Iso_pub: 4550816
TIGR_ID: 87
Rel_date: Aug 1997
Sp_info: <I>M. thermoautotrophicus</I> is anaerobic and thermophilic. It grows at pH 7.2-7.6, and produces methane by reducing carbon dioxide.
Multiz: Methanogens methStad1 methSmit1 metMar1 methMari_C5_1 methJann1
Phylo: ((((methStad1,methSmit1),methTher1),(metMar1,methMari_C5_1)),methJann1)
Org_abr: Meth_smit_ATCC_35061
Menu_name: Methanobrevibacter smithii
Iso_pub: 6798932
DB_name: methSmit1
Multiz: Methanogens methStad1 methTher1 metMar1 methMari_C5_1 methJann1
Phylo: ((((methStad1,methSmit1),methTher1),(metMar1,methMari_C5_1)),methJann1)
SP_ID: METSM METTH
Org_abr: Meth_kand
DB_name: methKand1
Iso_pub: http://www.springerlink.com/content/m133vw1544m5k8u9/
Rel_date: April 2002
Phylo: (methKand1,((methStad1,methTher1),(methJann1,metMar1)))
Org_abr: Nano_equi
DB_name: nanEqu1
Iso_pub: 11986665
Rel_date: Oct. 2003
Sp_info: <I>N. equitans</I> is a hyperthermophilic archaeon found as a parasite to Ignicoccus.
Org_abr: Pyro_aero
DB_name: pyrAer1
Iso_pub: 7692819
#Cent_DB: centraldb_pbac
Multiz: PbacCmaTtxTpe pyroOgun03 pyroArse1 pyroCali1 pyroIsla1 therNeut1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroArse1 pyroCali1 pyroIsla1 therNeut1 vulcDist0 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: Dec 2001
Sp_info: <I>P. aerophilum</I> is a hyperthermophilic crenarchaeon which was isolated from a boiling marine hole at Martoni Beach, Italy. It grows optimally at 100 C, either in the presence of low amounts of oxygen or anaerobically. It is remarkable for being able to utilize five different oxidants in respiration: oxygen, nitrate, arsenate, selenate, iron (III), and thiosulfate. The genome was sequenced and annotated as the PhD project of Sorel Fitz-Gibbon, a student in Jeffrey Miller's lab.
Org_abr: Pyro_abys
DB_name: pyrAby1
Iso_pub: http://www.springerlink.com/content/f516281626601h12/
Rel_date: June 2001
Sp_info: <I>P. abyssi</I> is a hyperthermophilic archaeon isolated from samples taken close to a hot spring situated 3500 meters deep in the south-east Pacific. The optimal growth conditions are reported as 103C at 200 atmospheres pressure.
Pub_id: 12622808
Multiz: Thermococcales pyrHor1 pyrFur2 therKoda1 therOnnu1 therGamm1 therBaro0 therSibi1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Org_abr: Pyro_furi
DB_name: pyrFur2
Rel_date: Feb. 2002
Iso_pub: http://www.springerlink.com/content/p50m447v02t436wp/
Sp_info: <I>P. furiosus</I> was isolated from a shallow marine solfatara at Vulcano Island off southern Italy. The ceils are fermentative, sulfur-reducing, flagellated cocci with a maximal growth temperature of 103C and optimal growth at 100C. Generation times of 35 min and cell densities of more than 10^10 cells/ml have been reported. Because it is able to grow to high cell densities, and in the absence of elemental sulfur, it has become a favored source of highly thermostable enzymes (<I>partially excerpted from Robb et al. reference below</I>).
Multiz: Thermococcales pyrHor1 pyrAby1 therKoda1 therOnnu1 therGamm1 therBaro0 therSibi1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Org_abr: Pyro_hori
DB_name: pyrHor1
Iso_pub: 9672687
Rel_date: April 1998
Sp_info: <I>P. horikoshii</I> is a hyperthermophilic archaeon isolated from a hydrothermal vent at a depth of 1395 meters in the Okinawa Trough in the Pacific Ocean. It grows optimally at 98C.
Multiz: Thermococcales pyrAby1 pyrFur2 therKoda1 therOnnu1 therGamm1 therBaro0 therSibi1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Org_abr: Ther_koda_KOD1
Menu_name: Thermococcus kodakaraensis
Iso_pub: 7811092
DB_name: therKoda1
TIGR_ID: 50445
JGI_ID: 638154520
Rel_date: May 2004
Sp_info: <I>T. kodakaraensis</I> (also spelled <I>kodakarensis</I>) is a hyperthermophile that grows at 60-100C (optimally at 85C) and in a pH range of 5-9 (optimally at 6.5). It was isolated from a solfatara on the shore of Kodakara Island, Japan. It can use elemental sulfur in respiration, or grow by fermentation on starch, maltose, or pyruvate.
Pub_id: 15710748
Multiz: Thermococcales therOnnu1 therGamm1 therBaro0 therSibi1 pyrFur2 pyrAby1 pyrHor1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Org_abr: Ther_baro_MP
Menu_name: Thermococcus barophilus
DB_name: therBaro0
SP_ID: PYRKO
Rel_date: July 2008
Seq_src: J. Craig Venter Institute
Gene_ct: NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Seq_acc: NZ_ABSF01000015 NZ_ABSF01000018 NZ_ABSF01000016 NZ_ABSF01000005 NZ_ABSF01000011 NZ_ABSF01000007 NZ_ABSF01000003 NZ_ABSF01000010 NZ_ABSF01000004 NZ_ABSF01000009 NZ_ABSF01000013 NZ_ABSF01000008 NZ_ABSF01000002 NZ_ABSF01000021 NZ_ABSF01000014 NZ_ABSF01000001 NZ_ABSF01000019 NZ_ABSF01000012 NZ_ABSF01000017 NZ_ABSF01000020 NZ_ABSF01000006
Name_chg: ctg_330 ctg_231 ctg_321 ctg_287 ctg_326 ctg_293 ctg_323 ctg_325 ctg_324 ctg_307 ctg_328 ctg_320 ctg_322 ctg_303 ctg_329 ctg_285 ctg_259 ctg_327 ctg_331 ctg_265 ctg_290
Multiz: Thermococcales therKoda1 therOnnu1 pyrFur2 pyrAby1 pyrHor1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
Org_abr: Ther_onnu_NA1
Menu_name: Thermococcus onnurineus
DB_name: therOnnu1
SP_ID: PYRKO
Rel_date: Nov 2008
Seq_src: Korea Ocean Research & Development Institute
Multiz: Thermococcales therKoda1 therGamm1 therBaro0 therSibi1 pyrFur2 pyrAby1 pyrHor1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Org_abr: Ther_gamm_EJ3
Menu_name: Thermococcus gammatolerans
DB_name: therGamm1
Seq_acc: NC_012804
Name_chg: chr
Pub_id: 0
#Pub_id: 12807211
Rel_date: June 2009
SP_ID: PYRKO
#Multiz: Thermococcales therKoda1 therOnnu1 therBaro0 therSibi1 pyrFur2 pyrHor1 pyrAby1
#Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Multiz: Thermococcales therKoda1 therOnnu1 therSibi1 pyrFur2 pyrHor1 pyrAby1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),therSibi1))
Org_abr: Ther_sibi_MM_739
Menu_name: Thermococcus sibiricus
DB_name: therSibi1
SP_ID: PYRKO
Seq_acc: NC_012883
Name_chg: chr
Pub_id: 11354459
Rel_date: July 2009
Multiz: Thermococcales therBaro0 therOnnu1 therKoda1 therGamm1 pyrFur2 pyrHor1 pyrAby1
Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therGamm1,(therKoda1,therOnnu1)),(therBaro0,therSibi1)))
Org_abr: Sulf_acid_DSM_639
Menu_name: Sulfolobus acidocaldarius
Iso_pub: 4559703
DB_name: sulfAcid1
Rel_date: July 2005
Sp_info: <I>S. acidocaldarius</I> is a thermophilic acidophile. It grows optimally at pH 2-3, and between 70-75C.
Multiz: Sulfolobes sulSol1 sulfToko1 metaSedu
Phylo: (metaSedu,(sulSol1,(sulfAcid1,sulfToko1)))
Org_abr: Sulf_solf
DB_name: sulSol1
Iso_pub: http://www.springerlink.com/content/q425w03846155604/
Rel_date: June 2001
Sp_info: <I>S. solfataricus</i> is a thermophilic acidophile growing optimally at a pH 2-4 at 80C.
Multiz: Sulfolobes sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,(sulSol1,(sulfAcid1,sulfToko1)))
Org_abr: Sulf_toko
DB_name: sulfToko1
Iso_pub: 11878560
Rel_date: August 2001
Sp_info: <I>S. tokodaii</I> is a hyperthermophilic acidophile. It grows optimally at pH 2.5-3 at approximately 80C. <I>S. tokodaii</I> is an obligate aerobe and metabolizes sulfur.
Multiz: Sulfolobes sulfAcid1 sulSol1 metaSedu
Phylo: (metaSedu,(sulSol1,(sulfAcid1,sulfToko1)))
Org_abr: Sulf_isla_L_S_2_15
Pub_id: 19435847
Iso_pub: 12881573
Rel_date: April 2009
Name_chg: chr
SP_ID: SULIL
Multiz: Sulfolobes sulfIsla_Y_N_15_51 sulfIsla_Y_G_57_14 sulfIsla_M_16_27 sulfIsla_M_14_25 sulfIsla_M_16_4 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),sulfIsla_L_S_2_15))),(sulfAcid1,sulfToko1)))
Org_abr: Sulf_isla_M_14_25
Pub_id: 19435847
Iso_pub: 12881573
Rel_date: April 2009
Name_chg: chr
SP_ID: SULIM
Multiz: Sulfolobes sulfIsla_M_16_27 sulfIsla_M_16_4 sulfIsla_Y_G_57_14 sulfIsla_Y_N_15_51 sulfIsla_L_S_2_15 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),sulfIsla_L_S_2_15))),(sulfAcid1,sulfToko1)))
Org_abr: Sulf_isla_M_16_27
Pub_id: 19435847
Iso_pub: 12881573
Rel_date: April 2009
SP_ID: SULIA
Multiz: Sulfolobes sulfIsla_M_14_25 sulfIsla_M_16_4 sulfIsla_Y_G_57_14 sulfIsla_Y_N_15_51 sulfIsla_L_S_2_15 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),sulfIsla_L_S_2_15))),(sulfAcid1,sulfToko1)))
Org_abr: Sulf_isla_M_16_4
Pub_id: 19435847
Iso_pub: 12881573
Rel_date: May 2009
SP_ID: SULIK
Multiz: Sulfolobes sulfIsla_M_14_25 sulfIsla_M_16_27 sulfIsla_Y_G_57_14 sulfIsla_Y_N_15_51 sulfIsla_L_S_2_15 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),sulfIsla_L_S_2_15))),(sulfAcid1,sulfToko1)))
Org_abr: Sulf_isla_Y_G_57_14
Pub_id: 19435847
Iso_pub: 12881573
Rel_date: April 2009
SP_ID: SULIY
Multiz: Sulfolobes sulfIsla_Y_N_15_51 sulfIsla_L_S_2_15 sulfIsla_M_16_27 sulfIsla_M_14_25 sulfIsla_M_16_4 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),sulfIsla_L_S_2_15))),(sulfAcid1,sulfToko1)))
Org_abr: Sulf_isla_Y_N_15_51
Pub_id: 19435847
Iso_pub: 12881573
Rel_date: April 2009
SP_ID: SULIN
Multiz: Sulfolobes sulfIsla_Y_G_57_14 sulfIsla_L_S_2_15 sulfIsla_M_16_27 sulfIsla_M_14_25 sulfIsla_M_16_4 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),sulfIsla_L_S_2_15))),(sulfAcid1,sulfToko1)))
Org_abr: Meta_sedu_DSM_5348
Org_name: Metallosphaera sedula DSM 5348
Menu_name: Metallosphaera sedula
Iso_pub:
DB_name: metaSedu
SP_ID: SULAC SULSO SULTO
Multiz: Sulfolobes sulfAcid1 sulfToko1 sulSol1
Phylo: (metaSedu,(sulSol1,(sulfAcid1,sulfToko1)))
Org_abr: Ther_acid
DB_name: therAcid1
Iso_pub: 5481857
Rel_date: Sep 2000
Sp_info: <I>T. acidophilum</I> is a thermophilic, acidophilic mycoplasma that grows optimally at 59C and pH 2.0. This species is a facultative aerobe. The thermoplasamas are euryarchaea, distantly related to sulfolobes which are crenarchaea, yet both inhabit similar thermal acidic environments.
Multiz: Thermoplasmas therVolc1 picrTorr1 ferrAcid1
Phylo: (((therVolc1,therAcid1),ferrAcid1),picrTorr1)
Org_abr: Ther_volc
Rel_date: Dec 2004
Iso_pub:
Sp_info: <I>T. volcanium</I> is a thermophilic, acidophilic mycoplasma that grows optimally at 60C and pH 2.0. This species is a facultative aerobe. The thermoplasamas are euryarchaea, distantly related to sulfolobes which are crenarchaea, yet both inhabit similar thermal acidic environments.
DB_name: therVolc1
Multiz: Thermoplasmas therAcid1 picrTorr1 ferrAcid1
Phylo: (((therVolc1,therAcid1),ferrAcid1),picrTorr1)
Org_abr: Picr_torr_DSM_9790
DB_name: picrTorr1
Iso_pub: 7541113
Menu_name: Picrophilus torridus
Rel_date: June 2004
Sp_info: <I>P. torridus</I> is a thermoacidophile that can grow at temperatures around 60C. A membrane that is very impermiable to protons allows this euryarchaeon to live at pH as low as 0, while maintaining a pH of 4.6 internally.
Multiz: Thermoplasmas therVolc1 therAcid1 ferrAcid1
Phylo: (((therVolc1,therAcid1),ferrAcid1),picrTorr1)
Org_abr: Vibr_chol
DB_name: vibrChol1
Name_chg: chrI chrII
Multiz: Vibrio vibrChol_O395_1 vibrChol_MO10_1 vibrVuln_CMCP6_1 vibrVuln_YJ016_1 vibrPara1 vibrFisc_ES114_1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Menu_name: Vibrio cholerae O1 El Tor
Org_abr: Vibr_fisc_ES114
DB_name: vibrFisc_ES114_1
Multiz: Vibrio vibrChol1 vibrChol_O395_1 vibrChol_MO10_1 vibrVuln_CMCP6_1 vibrVuln_YJ016_1 vibrPara1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Org_abr: Vibr_para
DB_name: vibrPara1
Multiz: Vibrio vibrChol1 vibrChol_O395_1 vibrChol_MO10_1 vibrVuln_CMCP6_1 vibrVuln_YJ016_1 vibrFisc_ES114_1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Org_abr: Vibr_vuln_CMCP6
DB_name: vibrVuln_CMCP6_1
Multiz: Vibrio vibrChol1 vibrChol_O395_1 vibrChol_MO10_1 vibrVuln_YJ016_1 vibrPara1 vibrFisc_ES114_1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Org_abr: Vibr_vuln_YJ016
DB_name: vibrVuln_YJ016_1
Multiz: Vibrio vibrChol1 vibrChol_O395_1 vibrChol_MO10_1 vibrVuln_CMCP6_1 vibrPara1 vibrFisc_ES114_1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Org_abr: Vibr_chol_MO10
Tax_name: Vibrio cholerae MO10
DB_name: vibrChol_MO10_1
Tax_ID: 345072: Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae; Vibrio.
Rel_date: 09/17/2005
Seq_src: TIGR
Web_seq: None
Multiz: Vibrio vibrChol1 vibrChol_O395_1 vibrVuln_CMCP6_1 vibrVuln_YJ016_1 vibrPara1 vibrFisc_ES114_1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Org_abr: Vibr_chol_O395
Tax_name: Vibrio cholerae O395
DB_name: vibrChol_O395_1
Rel_date: 09/17/2005
Multiz: Vibrio vibrChol1 vibrChol_MO10_1 vibrVuln_CMCP6_1 vibrVuln_YJ016_1 vibrPara1 vibrFisc_ES114_1
Phylo: (((((vibrChol1,vibrChol_O395_1),vibrChol_MO10_1),(vibrVuln_CMCP6_1,vibrVuln_YJ016_1)),vibrPara1),vibrFisc_ES114_1)
Org_abr: Geob_meta_GS-15
Org_name: Geobacter metallireducens GS-15
Menu_name: Geobacter metallireducens
Seq_acc: NC_007515 NC_007517
Name_chg: plasmid chr
DB_name: geobMeta_GS15
Multiz: Geobacters geobSulf geobUran_RF4 geobFRC_32 geobBemi_BEM geobLovl_SZ peloProp_DSM2379 peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Geob_sulf
DB_name: geobSulf
Multiz: Geobacters geobMeta_GS15 geobUran_RF4 geobFRC_32 geobBemi_BEM geobLovl_SZ peloProp_DSM2379 peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Geob_uran_Rf4
Menu_name: Geobacter uraniumreducens
DB_name: geobUran_RF4
Rel_date: 12/11/2007
Multiz: Geobacters geobFRC_32 geobMeta_GS15 geobSulf geobBemi_BEM geobLovl_SZ peloProp_DSM2379 peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Geob_lovl_SZ
SP_ID: GEOMG GEOSL GEOUR
Rel_date: Dec 2006
Seq_src: US DOE Joint Genome Institute
Multiz: Geobacters geobMeta_GS15 geobSulf geobUran_RF4 geobFRC_32 geobBemi_BEM peloProp_DSM2379 peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Geob_bemi_Bem
SP_ID: GEOMG GEOSL GEOUR
Rel_date: Aug 2008
Seq_src: US DOE Joint Genome Institute
Multiz: Geobacters geobMeta_GS15 geobSulf geobUran_RF4 geobFRC_32 geobLovl_SZ peloProp_DSM2379 peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Geob_FRC_32
SP_ID: GEOMG GEOSL GEOUR
Rel_date: Jan 2009
Seq_src: US DOE Joint Genome Institute
Multiz: Geobacters geobUran_RF4 geobMeta_GS15 geobSulf geobBemi_BEM geobLovl_SZ peloProp_DSM2379 peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Pelo_carb
Multiz: Geobacters geobUran_RF4 geobMeta_GS15 geobSulf geobFRC_32 geobBemi_BEM geobLovl_SZ peloProp_DSM2379
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Pelo_prop_DSM_2379
Menu_name: Pelobacter propionicus
DB_name: peloProp_DSM2379
Multiz: Geobacters geobMeta_GS15 geobSulf geobUran_RF4 geobFRC_32 geobBemi_BEM geobLovl_SZ peloCarb
Phylo: ((((((geobMeta_GS15,geobSulf), (geobUran_RF4, geobFRC_32)),geobBemi_BEM),peloProp_DSM2379),geobLovl_SZ),peloCarb)
Org_abr: Croc_wats_WH8501
DB_name: crocWats_WH8501_0
Tax_name: Crocosphaera watsonii WH 8501
Rel_date: Mar 2004
Seq_src: US DOE Joint Genome Institute
Org_abr: Yers_pseu_IP32953
TIGR_ID: 50404
Org_abr: Azor_caul_ORS_571
DB_name: azorCaul2
Org_abr: Pyro_isla_DSM_4184
Menu_name: Pyrobaculum islandicum
DB_name: pyroIsla1
Iso_pub: http://www.springerlink.com/content/j7016363n25h5221/
SP_ID: PYRAE
Multiz: PbacTtxCmaTpe therNeut1 pyrAer1 pyroOgun03 pyroArse1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe therNeut1 pyrAer1 pyroArse1 pyroCali1 vulcDist0 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: 12/20/06
Seq_src: DOE Joint Genome Institute/UCSC
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Pyro_isla-tRNAs
Prot_seq: /projects/lowelab/db/genomes/Other-genomes/Pyrobaculum_islandicum/Pis-genome-prot.fa
Org_abr: Pyro_cali_JCM_11548
Org_name: Pyrobaculum calidifontis JCM 11548
Menu_name: Pyrobaculum calidifontis
Domain: Archaea
Iso_pub: 15803649
DB_name: pyroCali1
Tax_name: Pyrobaculum calidifontis JCM 11548
TIGR_ID: 0
SP_ID: PYRAE
Multiz: PbacTtxCmaTpe pyrAer1 pyroOgun03 pyroArse1 pyroIsla1 therNeut1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 vulcDist0 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: 02/27/07
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Pyro_cali-tRNA
Org_abr: Pyro_arse_DSM_13514
Menu_name: Pyrobaculum arsenaticum
DB_name: pyroArse1
Iso_pub: 11108007
Multiz: PbacTtxCmaTpe pyroOgun03 pyrAer1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyrAer1 pyroIsla1 therNeut1 pyroCali1 vulcDist0 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: April 2006
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Pyro_arse-tRNAs
SP_ID: PYRAE
Org_abr: Pyro_neut_V24Sta
Menu_name: Pyrobaculum neutrophilum V24Sta
Org_name: Pyrobaculum neutrophilum V24Sta
DB_name: therNeut1
Tax_ID: 444157: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum.
SP_ID: THENV PYRAE
Domain: Archaea
DB_src: NCBI
Tax_name: Pyrobaculum neutrophilum V24Sta
BLAT_IDs: 20526 20527
TIGR_ID: 0
JGI_ID: 641380436
String_ID: 0
Gen_ID: 0
Seq_acc: NC_010525
Name_chg: chr
Gb_acc: CP001014
Seq_size: 1769823
Gene_ct: 2053
Seq_GC: 59.91
Pub_id: 0
Web_seq: ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Thermoproteus_neutrophilus_V24Sta/
Web_db: http://www.ncbi.nlm.nih.gov/genomes/framik.cgi?db=Genome&gi=0
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Ther_neut_V24Sta-tRNAs
Gen_ID: 15645
Dom_ct: &Pyro_isla_DSM_4184
Pub_id: 0
Iso_pub:
Rel_date: Mar 2008
Seq_src: DOE Joint Genome Institute / UCSC
Trna_abr: Ther_neut-tRNAs
Multiz: PbacTtxCmaTpe pyroIsla1 pyrAer1 pyroOgun03 pyroArse1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroIsla1 pyrAer1 pyroArse1 pyroCali1 vulcDist0 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Sp_info: Initially placed in the genus <I>Thermoproteus</I>, this species is in the process of formally being reclassified into the <I>Pyrobaculum</I> genus. It was originally classified in 1983 (<a href="http://www.nature.com/nature/journal/v301/n5900/abs/301511a0.html">Fischer et al., Nature 30:511-513</a>) when few Thermoproteales organisms were described and the classification decision did not utilize ribosomal RNA sequence information. Now, it clearly falls within <I>Pyrobaculum</I> in both rRNA-based trees (see analyses presented for the <I>P. oguniense</I> isolation <a href="http://ijs.sgmjournals.org/cgi/content/abstract/51/2/303">Sako, et al., 2001</a>) and protein-based trees now possible with the complete genome sequence (Lowe et al., in preparation). <I>Pyrobaculum neutrophilum</I> and <I>Pyrobaculum islandicum</I> are the two most-closely related species among the five <I>Pyrobaculum</I> species sequenced to date -- both were isolated from hot springs in Iceland.
Org_abr: Pyro_ogun
Org_name: Pyrobaculum oguniense
Menu_name: Pyrobaculum oguniense
Domain: Archaea
DB_name: pyroOgun03
DB_src: LOWELAB
Tax_name: Pyrobaculum oguniense
Tax_ID: 99007: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum.
Iso_pub: 11321074
BLAT_IDs: 61015 61016
TIGR_ID: 0
JGI_ID: 0
SP_ID: PYRAE
String_ID: 0
Dom_ct: &Pyro_neut_V24Sta
Gen_ID: 0
Gb_acc: None
Seq_acc: Pog-genome-v3 chr ece
Name_chg: chr ece
Seq_size: 2436064 16887
Seq_GC: 55.08 50.58
Gene_ct: 3214
Multiz: PbacTtxCmaTpe pyroArse1 pyrAer1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroArse1 pyrAer1 pyroIsla1 therNeut1 pyroCali1 vulcDist0 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: 09/13/09
Seq_src: UC Santa Cruz
Trna_abr: Pyro_ogun-tRNAs
Org_abr: Cald_maqu_IC-167
Menu_name: Caldivirga maquilingensis
Domain: Archaea
Iso_pub: 10425774
DB_name: caldMaqu1
SP_ID: PYRAE
Multiz: PbacTtxCmaTpe pyrAer1 pyroOgun03 pyroArse1 pyroIsla1 therNeut1 pyroCali1 therTena1 vulcDist0
Public_multiz: PbacCmaTpe pyrAer1 pyroArse1 pyroIsla1 therNeut1 pyroCali1 vulcDist0
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: Nov 2007
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Cald_maqu-tRNAs
Org_abr: Ther_pend_Hrk_5
DB_name: therPend1
Menu_name: Thermofilum pendens
Iso_pub: Zillig, W., A. Gierl, G. Schreiber, S. Wunderl, D. Janekovic, K. O. Stetter, and H. P. Klenk. (1983) "The archaebacterium <I>Thermofilum pendens</I> represents a novel genus of the thermophilic, anaerobic sulfur respiring Thermoproteales." <I>Syst. Appl. Microbiol.</I> <B>4</B>:79-87.
Seq_acc: NC_008696 NC_008698
Name_chg: pTPEN01 chr
Multiz: PbacTtxCmaTpe caldMaqu1 vulcDist0 pyroCali1 pyrAer1 pyroOgun03 pyroArse1 pyroIsla1 therNeut1
Public_multiz: PbacCmaTpe caldMaqu1 vulcDist0 pyroCali1 pyrAer1 pyroArse1 pyroIsla1 therNeut1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Rel_date: 03/01/06
Seq_src: DOE Joint Genome Institute
Trna_abr: Ther_pend-tRNAs
Org_abr: Cena_symb
Org_name: Cenarchaeum symbiosum
Menu_name: Cenarchaeum symbiosum
Iso_pub: 8692799
Domain: Archaea
DB_name: cenaSymb1
DB_src: JGI
Tax_name: Cenarchaeum symbiosum
Tax_ID: 414004: Archaea; Thaumarchaeota; Cenarchaea; Cenarchaeales; Cenarchaeaceae; Cenarchaeum.
TIGR_ID: 0
Gen_ID: 0
Seq_acc: CENSYa
Name_chg: chr
Seq_size: 2023713
Seq_GC: 57.46
Gene_ct: 2011
Pub_id: 16533068
Rel_date: 03/01/06
Seq_src: MIT Sequencing Center
Web_seq:
Web_db:
Prot_seq: /projects/lowelab/db/genomes/JGI-genomes/Cenarchaeum_symbiosum/Cysm-genome-prot.fa
Multiz: MarineCrens nitrMari1
Phylo: (nitrMari1, cenaSymb1)
Org_abr: Nitr_mari_SCM1
Iso_pub: 16177789
DB_name: nitrMari1
SP_ID: NITMS CENSY
Name_chg: chr
Rel_date: Nov 2007
Seq_src: Joint Genome Institute / Univ. of Washington
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Nitr_mari-tRNAs
Multiz: MarineCrens cenaSymb1
Phylo: (cenaSymb1,nitrMari1)
Org_abr: Ther_tena
Org_name: Thermoproteus tenax
Menu_name: Thermoproteus tenax
Iso_pub:
Domain: Archaea
DB_name: therTena1
#Cent_DB: centraldb_pbac
DB_src: ORNL
Tax_name: Thermoproteus tenax
BLAT_IDs: 61004 61005
Tax_ID: 2271: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Thermoproteus.
TIGR_ID: 0
Dom_ct: &Ther_pend_Hrk_5
Gen_ID: 0
Seq_acc: Ttenax-genome chr
Name_chg: chr
Gb_acc: None
Seq_size: 1841542
Seq_GC: 55.13
Gene_ct: 1800
Multiz: PbacTtxCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
Public_multiz: PbacCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
Phylo: (((((((pyroArse1,pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: Private
Seq_src: University Duisburg-Essen
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Ther_tena-tRNAs
Org_abr: Vulc_dist
Org_name: Vulcanisaeta distributa
Menu_name: Vulcanisaeta distributa
Iso_pub: 12148613
Domain: Archaea
DB_name: vulcDist0
DB_src: ORNL
Tax_name: Vulcanisaeta distributa IC-017
BLAT_IDs: 61006 61007
Tax_ID: 572478: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Vulcanisaeta.
TIGR_ID: 0
Dom_ct: &Ther_tena
Gen_ID: 0
Seq_acc: Vdistributa-genome Contig00003 Contig00014 Contig00022 Contig00023 Contig00024 Contig00025 Contig00026 Contig00027 Contig00028 Contig00029 Contig00030 Contig00031 Contig00032 Contig00033 Contig00034 Contig00035 Contig00036
Name_chg: Contig00003 Contig00014 Contig00022 Contig00023 Contig00024 Contig00025 Contig00026 Contig00027 Contig00028 Contig00029 Contig00030 Contig00031 Contig00032 Contig00033 Contig00034 Contig00035 Contig00036
Gb_acc: None
Seq_size: 534 515 264733 65541 174207 139013 122896 196801 158953 39744 100608 15899 178459 562434 78852 109394 157801
Seq_GC: 42.7 42.33 44.63 44.66 45.67 44.93 46.6 47.02 46.38 50.39 50.63 48.37 43.6 44.3 45.13 44.15 45.72
Gene_ct: 2634
Multiz: PbacTtxVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroOgun03 pyroArse1 caldMaqu1 therPend1
Public_multiz: PbacVdiCmaTpe pyroIsla1 therNeut1 pyroCali1 pyrAer1 pyroArse1 caldMaqu1 therPend1
Phylo: ((((((((pyroArse1,pyroOgun03),pyrAer1),(pyroIsla1,therNeut1)),pyroCali1),therTena1),vulcDist0),caldMaqu1),therPend1)
Pub_id:
Rel_date: 03/2009
Seq_src: JGI
Trna_opt: -o# -f# -m# -F# -HyA
Trna_abr: Vulc_dist-tRNAs
Org_abr: Carb_hydr_Z-2901
Org_name: Carboxydothermus hydrogenoformans Z-2901
Menu_name: Carboxydothermus hydrogenoformans
Domain: Bacteria
DB_name: carbHydrZ2901
Org_abr: Baci_halo
Pub_id: 11058132
Org_abr: Baci_subt
DB_name: baciSubt2
Rel_date: 11/09/2009
Org_abr: Brad_japo
Org_abr: Myco_smeg_MC2_155
Multiz: Mycobacterium mycoTube_H37RV
Phylo: (mycoSmeg_MC2_155,mycoTube_H37RV)
Org_abr: Myco_tube_H37Rv
Pub_id: 9634230
Multiz: Mycobacterium mycoSmeg_MC2_155
Phylo: (mycoSmeg_MC2_155,mycoTube_H37RV)
Org_abr: Shew_ANA3
DB_name: shewANA3
SP_ID: SHESA SHEON
Multiz: Shewanella shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
#Phylo: (((((((shewMR4,shewMR7),shewANA3),shewOnei),(shewPutrCN32,shewW318)),shewLoihPV4),shewFrig),(shewAmaz,shewBalt))
Org_abr: Shew_MR4
DB_name: shewMR4
SP_ID: SHESM SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_MR7
DB_name: shewMR7
SP_ID: SHESR SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR4 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_W318
DB_name: shewW318
SP_ID: SHESW SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_amaz_SB2B
DB_name: shewAmaz
SP_ID: SHEAM SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_deni_OS217
DB_name: shewDeni
SP_ID: SHEDO SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_frig_NCIMB_400
DB_name: shewFrig
SP_ID: SHEFN SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_onei
DB_name: shewOnei
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_balt_OS155
DB_name: shewBalt
SP_ID: SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_loih_PV-4
DB_name: shewLoihPV4
SP_ID: SHELP SHEON
Multiz: Shewanella shewANA3 shewPutrCN32 shewW318 shewOnei shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_putr_CN-32
DB_name: shewPutrCN32
SP_ID: SHEPU SHEON
Multiz: Shewanella shewANA3 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_putr_CN-32
DB_name: shewPutrCN32
SP_ID: SHEPU SHEON
Multiz: Shewanella shewANA3 shewW318 shewOnei shewLoihPV4 shewMR4 shewMR7 shewAmaz shewFrig shewBalt shewDeni
Phylo: (((((((shewPutrCN32,shewW318),(shewOnei,shewMR7)),(shewANA3,shewMR4)),shewBalt),(shewFrig,shewDeni)),shewAmaz),shewLoihPV4)
Org_abr: Shew_wood_ATCC_51908
Menu_name: Shewanella woodyi ATCC 51908
DB_name: shewWood
SP_ID: SHEPU SHEON
Org_abr: Shew_hali_HAW_EB4
Menu_name: Shewanella halifaxensis HAW EB4
DB_name: shewHali
SP_ID: SHEPU SHEON
Org_abr: Shew_peal_ATCC_700345
Menu_name: Shewanella pealeana ATCC 700345
DB_name: shewPeal
SP_ID: SHEPU SHEON
Org_abr: Shew_sedi_HAW-EB3
Menu_name: Shewanella sediminis HAW-EB3
DB_name: shewSedi_HAW_EB3
SP_ID: SHEPU SHEON
Org_abr: Heli_pylo_G27
BLAT_IDs: 61010 61011
Rel_date: Oct 2008
Seq_src: Washington University in St. Louis
Multiz: HeliCampMultiZ heliPylo_SHI470 heliPylo_J99 heliPylo_26695 heliPylo_HPAG1 heliAcin_SHEEBA heliHepa campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Heli_pylo_J99
SP_ID: HELPJ
Multiz: HeliCampMultiZ heliPylo_26695 heliPylo_HPAG1 heliPylo_G27 heliPylo_SHI470 heliAcin_SHEEBA heliHepa campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Camp_jeju
Multiz: HeliCampMultiZ heliPylo_J99 heliPylo_26695 heliPylo_HPAG1 heliPylo_G27 heliPylo_SHI470 heliAcin_SHEEBA heliHepa
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Heli_acin_Sheeba
Multiz: HeliCampMultiZ heliPylo_J99 heliPylo_26695 heliPylo_HPAG1 heliPylo_G27 heliPylo_SHI470 heliHepa campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Heli_hepa
Multiz: HeliCampMultiZ heliPylo_J99 heliPylo_26695 heliPylo_HPAG1 heliPylo_G27 heliPylo_SHI470 heliAcin_SHEEBA campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Heli_pylo_26695
Multiz: HeliCampMultiZ heliPylo_J99 heliPylo_HPAG1 heliPylo_G27 heliPylo_SHI470 heliAcin_SHEEBA heliHepa campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Heli_pylo_HPAG1
Multiz: HeliCampMultiZ heliPylo_J99 heliPylo_26695 heliPylo_G27 heliPylo_SHI470 heliAcin_SHEEBA heliHepa campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Heli_pylo_Shi470
Rel_date: July 2008
Seq_src: Washington University Medical School
Multiz: HeliCampMultiZ heliPylo_J99 heliPylo_26695 heliPylo_G27 heliAcin_SHEEBA heliHepa campJeju
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,(heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695)))))
Phylo: (campJeju,(heliHepa,(heliAcin_SHEEBA,((heliPylo_G27,heliPylo_SHI470),(heliPylo_HPAG1,(heliPylo_J99,heliPylo_26695))))))
Org_abr: Aero_pern
Multiz: Desulfurococcales hypeButy1 stapMari1 desuKamc1 igniHosp1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
Org_abr: Stap_hell
Org_name: Staphylothermus hellenicus
Menu_name: Staphylothermus hellenicus
Domain: Archaea
DB_name: stapHell0
Iso_pub: 11155985
Rel_date: January 2009
DB_src: ORNL
Tax_name: Staphylothermus hellenicus
BLAT_IDs: 61021 61022
Tax_ID: 591019: Archaea; Crenarchaeota; Thermoprotei; Desulfurococcales; Desulfurococcaceae; Staphylothermus.
TIGR_ID: 0
SP_ID: 0
Dom_ct: &Pyro_hori
Gen_ID: 0
Seq_acc: Stap_hell-draft0109 Contig4 Contig1 Contig3 Contig2 Contig5 Contig6 Contig7
Name_chg: Contig4 Contig1 Contig3 Contig2 Contig5 Contig6 Contig7
Seq_size: 645254 269689 255976 218769 177705 11137 636
Seq_GC: 36.87 36.6 36.72 37.3 36.55 38.23 40.72
Seq_src: Joint Genome Institute
Multiz: Desulfurococcales stapMari1 desuKamc1 hypeButy1 aerPer1 igniHosp1
Phylo: (((((stapHell0,stapMari1),desuKamc1),hypeButy1),aerPer1),igniHosp1)
Org_abr: Stap_mari_F1
DB_name: stapMari1
Iso_pub: Fiala G, Stetter KO, Jannasch HW, Langworthy TA, and Madon J (1986) "<I>Staphylothermus marinus sp.</I> nov. represents a novel genus of extremely thermophilic submarine heterotrophic archaebacteria growing up to 98 degree C" (1986) <I>Systematic and Applied Microbiology</I> <B>8</B>: 106.
Multiz: Desulfurococcales desuKamc1 hypeButy1 aerPer1 igniHosp1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
Org_abr: Hype_buty
DB_name: hypeButy1
Iso_pub: 2113915
Multiz: Desulfurococcales stapMari1 aerPer1 desuKamc1 igniHosp1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
Org_abr: Igni_hosp_KIN4_I
DB_name: igniHosp1
Org_name: Ignicoccus hospitalis KIN4 I
Menu_name: Ignicoccus hospitalis
# Iso_pub: 17392210
SP_ID: HYPBU STAMF
Multiz: Desulfurococcales stapMari1 hypeButy1 aerPer1 desuKamc1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
Sp_info: <I>I. hospitalis</I> is a chemolithoautotrophic, hyperthermophilic crenarchaeon that was isolated from a submarine hydrothermal system at the Kolbeinsey Ridge, to the north of Iceland (<a href="http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&dopt=AbstractPlus&list_uids=17392210">Paper <I>et al.</I>, <I>Int J Syst Evol Microbiol.</I> 2007, 57:803-808</a>). It is the only organism known so far which is able to serve as a host for 'Nanoarchaeum equitans', the only cultivated member of the Nanoarchaeota. The genome sequencing was a collaboration between Diversa and the Joint Genome Institute, publicly available <a href="http://genome.jgi-psf.org/draft_microbes/ign_k/ign_k.home.html">here</a>. Draft annotation within the genome browser is available from <a href="http://genome.ornl.gov/microbial/igni/">Oak Ridge National Labs</a>.
Org_abr: Desu_kamc_1221n
Menu_name: Desulfurococcus kamchatkensis
DB_name: desuKamc1
Name_chg: chr
SP_ID: STAMF HYPBU AERPE
Pub_id: 19114480
Iso_pub:
Rel_date: Dec 2008
Seq_src: Institute of Microbiology of the Russian Academy of Sciences
Multiz: Desulfurococcales stapMari1 hypeButy1 aerPer1 igniHosp1
Phylo: ((((stapMari1,desuKamc1),hypeButy1),aerPer1),igniHosp1)
+Org_abr: Ther_aggr_DSM_11486_uid48993
+Menu_name: Thermosphaera aggregans DSM 11486
+DB_name: therAggr1
+SP_ID: STAMF HYPBU AERPE
+Pub_id:
+Iso_pub: 9542073
+Name_chg: chr
+GB_acc: CP001939
+Rel_date: May 17, 2010
+Seq_src: Joint Genome Institute
+Multiz: Desulfurococcales desuKamc1 stapMari1 hypeButy1 aerPer1 igniHosp1
+Phylo: ((((desuKamc1,therAggr1),stapMari1),hypeButy1),aerPer1),igniHosp1)
+
Org_abr: uncu_meth_archaeon_RC-I
Org_name: uncultured methanogenic archaeon RC-I
Menu_name: Uncultured methanogenic archaeon RC-I
Domain: Archaea
DB_name: uncuMeth_RCI
Tax_name: Uncultured methanogenic archaeon RC-I
Iso_pub:
Tax_ID: 351160: Archaea; Euryarchaeota; environmental samples.
TIGR_ID: 0
JGI_ID: 0
SP_ID: UNCMA
Gen_ID: 020979
Seq_acc: NC_009464
Name_chg: chr
Org_abr: Cand_Meth_boonei_6A8
Org_name: Candidatus Methanoregula boonei 6A8
Menu_name: Methanoregula boonei
Domain: Archaea
Iso_pub: 16699521
DB_name: methBoon1
DB_src: NCBI
Tax_name: Candidatus Methanoregula boonei 6A8
SP_ID: METLZ METHJ METMJ METAC METBU
Multiz: Methanomicrobiales mculMari1 methLabrZ_1 methHung1
Phylo: (((mculMari1,methBoon1),methLabrZ_1),methHung1)
Dom_ct: &Meth_kand
Org_abr: Cand_Kora_cryptofilum_OPF8
Org_name: Candidatus Korarchaeum cryptofilum OPF8
Menu_name: Korarchaeum cryptofilum OPF8
Domain: Archaea
Iso_pub: 18535141
DB_name: koraCryp1
DB_src: NCBI
Tax_name: Candidatus Korarchaeum cryptofilum OPF8
BLAT_IDs: 20482 20483
Tax_ID: 374847: Archaea; Korarchaeota; Candidatus Korarchaeum.
TIGR_ID: 0
Pub_id: 18535141
JGI_ID: 0
SP_ID:
String_ID: 0
Dom_ct: &Igni_hosp_KIN4_I
Rel_date: Mar 2008
Seq_src: DOE Joint Genome Institute
Org_abr: Pseu_halo_TAC125
Domain: Bacteria
Org_abr: Neis_gono_FA_1090
DB_name: neisGono_FA1090_1
Multiz: Neisseria neisMeni_MC58_1 neisMeni_FAM18_1 neisMeni_Z2491_1
Phylo: (((neisMeni_FAM18_1, neisMeni_MC58_1), neisMeni_Z2491_1), neisGono_FA1090_1)
Org_abr: Neis_meni_MC58
DB_name: neisMeni_MC58_1
SP_ID: NEIMB
Multiz: Neisseria neisMeni_FAM18_1 neisMeni_Z2491_1 neisGono_FA1090_1
Phylo: (((neisMeni_FAM18_1, neisMeni_MC58_1), neisMeni_Z2491_1), neisGono_FA1090_1)
Org_abr: Neis_meni_FAM18
DB_name: neisMeni_FAM18_1
SP_ID: NEIMF
Multiz: Neisseria neisMeni_MC58_1 neisMeni_Z2491_1 neisGono_FA1090_1
Phylo: (((neisMeni_FAM18_1, neisMeni_MC58_1), neisMeni_Z2491_1), neisGono_FA1090_1)
Org_abr: Neis_meni_Z2491
DB_name: neisMeni_Z2491_1
SP_ID: NEIMA
Multiz: Neisseria neisMeni_MC58_1 neisMeni_FAM18_1 neisGono_FA1090_1
Phylo: (((neisMeni_FAM18_1, neisMeni_MC58_1), neisMeni_Z2491_1), neisGono_FA1090_1)
Org_abr: Syne_elon_PCC_7942
Multiz: Synechococcus syneSp_WH8102
Phylo: (syneSp_WH8102, syneElon_PCC_7942)
Org_abr: Syne_sp_WH8102
Multiz: Synechococcus syneElon_PCC_7942
Phylo: (syneSp_WH8102, syneElon_PCC_7942)
# Fixing bad (non-unique) database naming
Org_abr: Cyan_bact_Yellowstone_A-Prime
DB_name: cyanBact_YELLOWSTONE_A
Org_abr: Cyan_bact_Yellowstone_B-Prime
DB_name: cyanBact_YELLOWSTONE_B
Org_abr: Lept_borg_serovar_Hardjo-bovis_JB197
DB_name: leptBorg_JB197
Org_abr: Lept_borg_serovar_Hardjo-bovis_L550
DB_name: leptBorg_L550
# Fixing incorrect chromosome naming
Org_abr: Buch_aphi
Seq_acc: NC_004545 NC_004555
Name_chg: chr plasmid_pBBp1
Org_abr: Buch_sp
Seq_acc: NC_002252 NC_002253 NC_002528
Name_chg: plasmid_pTrp plasmid_pLeu chr
Org_abr: Esch_coli_CFT073
SP_ID: ECOLI
Org_abr: Esch_coli_536
SP_ID: ECOL5 ECOLI
Org_abr: Esch_coli_O157H7_EDL933
SP_ID: ECO57 ECOLI
Org_abr: Esch_coli_K12
SP_ID: ECOLI ECO57
Multiz: Enterobacteria eschColi_O157H7 eschColi_APEC_O1 ente638 shigFlex_2A salmTyph salmEnte_PARATYPI_ATC yersPest_CO92 blocFlor buchSp
Phylo: ((((((((eschColi_K12,eschColi_0157H7),eschColi_APEC_O1),ente638),shigFlex_2A),(salmTyph,salmEnte_PARATYPI_ATC)),yersPest_CO92),blocFlor),buchSp)
Org_abr: Esch_coli_O157H7
JGI_ID: 637000108
Seq_acc: NC_002127 NC_002128 NC_002695
Name_chg: plasmid_pOSAK1 plasmid_pO157 chr
SP_ID: ECO57 ECOLI
Org_abr: Esch_coli_APEC_O1
SP_ID: ECOLI ECOK1
Org_abr: Esch_coli_W3110
Seq_acc: AC_000091
Name_chg: chr
Gb_acc: AP009048
SP_ID: ECO57 ECOLI
Org_abr: Salm_ente_Paratypi_ATCC_9150
Tax_ID: 295319: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella; Salmonella enterica subsp. enterica
Org_abr: Salm_ente_Choleraesuis
Tax_ID: 321314: Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella; Salmonella enterica subsp. enterica
Org_abr: Fran_phil_ATCC_25017
Seq_acc: NC_010336 NC_010331
Name_chg: chr plasmid_pFPHI01
Rel_date: 05/17/2006
Multiz: Francisella franTula_HOLARCTICA_OSU18 franTula_HOLARCTICA_1 franTula_FSC_198 franTula_TULARENSIS
Phylo: (((franTula_HOLARCTICA_OSU18,franTula_HOLARCTICA_1),(franTula_FSC_198,franTula_TULARENSIS)),franPhil_ATCC25017)
Org_abr: Fran_tula_FSC_198
Multiz: Francisella franTula_HOLARCTICA_OSU18 franTula_HOLARCTICA_1 franTula_TULARENSIS franPhil_ATCC25017
Phylo: (((franTula_HOLARCTICA_OSU18,franTula_HOLARCTICA_1),(franTula_FSC_198,franTula_TULARENSIS)),franPhil_ATCC25017)
Org_abr: Fran_tula_tularensis
Seq_acc: NC_006570
Name_chg: chr
Multiz: Francisella franTula_HOLARCTICA_OSU18 franTula_HOLARCTICA_1 franTula_FSC_198 franPhil_ATCC25017
Phylo: (((franTula_HOLARCTICA_OSU18,franTula_HOLARCTICA_1),(franTula_FSC_198,franTula_TULARENSIS)),franPhil_ATCC25017)
Org_abr: Fran_tula_holarctica
DB_name: franTula_HOLARCTICA_1
Multiz: Francisella franTula_HOLARCTICA_OSU18 franTula_FSC_198 franTula_TULARENSIS franPhil_ATCC25017
Phylo: (((franTula_HOLARCTICA_OSU18,franTula_HOLARCTICA_1),(franTula_FSC_198,franTula_TULARENSIS)),franPhil_ATCC25017)
Org_abr: Fran_tula_holarctica_OSU18
DB_name: franTula_HOLARCTICA_OSU18
Multiz: Francisella franTula_HOLARCTICA_1 franTula_FSC_198 franTula_TULARENSIS franPhil_ATCC25017
Phylo: (((franTula_HOLARCTICA_OSU18,franTula_HOLARCTICA_1),(franTula_FSC_198,franTula_TULARENSIS)),franPhil_ATCC25017)
Org_abr: Haem_infl
DB_name: haemInfl_KW20
Org_name: Haemophilus influenzae
Menu_name: Haemophilus influenzae Rd KW20
Seq_acc: NC_000907
Name_chg: chr
Tax_ID: 71421: Bacteria; Proteobacteria; Gammaproteobacteria; Pasteurellales; Pasteurellaceae; Haemophilus.
Tax_name: Haemophilus influenzae Rd KW20
Seq_size: 1830138
Gene_ct: 1788
Seq_GC: 38.15
Seq_src: TIGR
Pub_id: 7542800
Rel_date: 1995
Gen_ID: 025
Org_abr: Stap_sapr
Seq_acc: NC_007350 NC_007351 NC_007352
Name_chg: chr plasmid_pSSP1 plasmid_PSSP2
Org_abr: Stre_coel
Seq_acc: NC_003888 NC_003903 NC_003904
Name_chg: chr plasmid_SCP1 plasmid_SCP2
Org_abr: Clos_diff_QCD-32g58
Seq_acc: NC_007774
Name_chg: chr
Org_abr: Buch_aphi_Sg
Seq_acc: NC_004061
Name_chg: chr
Org_abr: Rhiz_legu_bv_viciae_3841
Seq_acc: NC_008378 NC_008379 NC_008380 NC_008381 NC_008382 NC_008383 NC_008384
Name_chg: plasmid_pRL12 plasmid_pRL9 chr plasmid_pRL10 plasmid_pRL7 plasmid_pRL8 plasmid_pRL11
Org_abr: Borr_burg
Seq_acc: NC_000948 NC_000949 NC_000950 NC_000951 NC_000952 NC_000953 NC_000954 NC_000955 NC_000956 NC_000957 NC_001318 NC_001849 NC_001850 NC_001851 NC_001852 NC_001853 NC_001854 NC_001855 NC_001856 NC_001857 NC_001903 NC_001904
Name_chg: plasmid_cp32-1 plasmid_cp32-3 plasmid_cp32-4 plasmid_cp32-6 plasmid_cp32-7 plasmid_cp32-8 plasmid_cp32-9 plasmid_lp21 plasmid_lp56 plasmid_lp5 chr plasmid_lp17 plasmid_lp25 plasmid_lp28-1 plasmid_lp28-2 plasmid_lp28-3 plasmid_lp28-4 plasmid_lp36 plasmid_lp38 plasmid_lp54 plasmid_cp26 plasmid_cp9
Org_abr: Lact_sali_UCC118
Tax_name: Lactobacillus salivarius subsp. salivarius UCC118
Tax_ID: 362948: Bacteria; Firmicutes; Lactobacillales; Lactobacillaceae; Lactobacillus.
Seq_acc: NC_006529 NC_006530 NC_007929 NC_007930
Name_chg: plasmid_pSF118-20 plasmid_pSF118-44 chr plasmid_pMP118
Org_abr: Baci_halo
Pub_id: 11058132
Org_abr: Flav_psyc_JIP02_86
DB_name: flavPsyc
Org_abr: Burk_383
Multiz: Burkholderia burkCeno_HI2424 burkXeno_LB400 burkCeno_AU_1054 burkCepa_AMMD burkViet_G4 burkThai_E264 burkPseu_1106A burkMall_ATCC23344
Phylo: (burkMall_ATCC23344,burkMall_NCTC_10247),((((burkPseu_K96243,((((((burk383,burkCeno_HI2424),burkXeno_LB400),burkCeno_AU_1054),burkCepa_AMMD),burkViet_G4),burkThai_E264)),burkPseu_668),burkPseu_1710B),burkPseu_1106A)),burkMall_SAVP1,burkMall_NCTC_10229)
Org_abr: Burk_ceno_AU_1054
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Multiz: Burkholderia burkCeno_HI2424 burkXeno_LB400 burk383 burkCepa_AMMD burkViet_G4 burkThai_E264 burkPseu_1106A burkMall_ATCC23344
Phylo: (burkMall_ATCC23344,burkMall_NCTC_10247),((((burkPseu_K96243,((((((burk383,burkCeno_HI2424),burkXeno_LB400),burkCeno_AU_1054),burkCepa_AMMD),burkViet_G4),burkThai_E264)),burkPseu_668),burkPseu_1710B),burkPseu_1106A)),burkMall_SAVP1,burkMall_NCTC_10229)
Org_abr: Burk_ceno_HI2424
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Multiz: Burkholderia bburkCeno_AU_1054 burk383 burkXeno_LB400 burkCepa_AMMD burkViet_G4 burkThai_E264 burkPseu_1106A burkMall_ATCC23344
Phylo: (burkMall_ATCC23344,burkMall_NCTC_10247),((((burkPseu_K96243,((((((burk383,burkCeno_HI2424),burkXeno_LB400),burkCeno_AU_1054),burkCepa_AMMD),burkViet_G4),burkThai_E264)),burkPseu_668),burkPseu_1710B),burkPseu_1106A)),burkMall_SAVP1,burkMall_NCTC_10229)
Org_abr: Burk_cepa_AMMD
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Org_abr: Burk_mall_ATCC_23344
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Org_abr: Burk_pseu_1106a
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Org_abr: Burk_thai_E264
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Org_abr: Burk_viet_G4
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Org_abr: Burk_xeno_LB400
SP_ID: BURS3 BURCA BURCH BURCM BURP0 BURP1 BURP6 BURTA BURVI BURXL
Org_abr: Yers_pseu_IP_31758
Org_name: Yersinia pseudotuberculosis IP 31758
Menu_name: Yersinia pseudotuberculosis IP31758
Domain: Bacteria
DB_name: yersPseu_IP31758
Org_abr: Acid_bott_virus
Org_name: Acidianus bottle-shaped virus
Menu_name: Acidianus bottle-shaped virus
Domain: Viruses
Rel_date: 5/11/2007
Pub_id: 17412384
Org_abr: Acid_fila_virus_1
Org_name: Acidianus filamentous virus 1
Menu_name: Acidianus filamentous virus 1
Domain: Viruses
Rel_date: 2/23/2004
Pub_id: 14592760
Org_abr: Acid_fila_virus_2
Org_name: Acidianus filamentous virus 2
Menu_name: Acidianus filamentous virus 2
Domain: Viruses
DB_name: acidFila_VIRUS_2
DB_src: VIRUS
Rel_date: 4/01/2005
Pub_id: 15901711
Org_abr: Acid_fila_virus_3
Org_name: Acidianus filamentous virus 3
Menu_name: Acidianus filamentous virus 3
Domain: Vi15994761ruses
DB_name: acidFila_VIRUS_3
DB_src: VIRUS
Rel_date: 9/16/2007
Pub_id: 17942536
Org_abr: Acid_fila_virus_6
Org_name: Acidianus filamentous virus 6
Menu_name: Acidianus filamentous virus 6
Domain: Viruses
DB_name: acidFila_VIRUS_6
DB_src: VIRUS
Rel_date: 9/16/2007
Pub_id: 17942536
Org_abr: Acid_fila_virus_7
Org_name: Acidianus filamentous virus 7
Menu_name: Acidianus filamentous virus 7
Domain: Viruses
DB_name: acidFila_VIRUS_7
Rel_date: 9/16/2007
Pub_id: 17942536
Org_abr: Acid_fila_virus_8
Org_name: Acidianus filamentous virus 8
Menu_name: Acidianus filamentous virus 8
Domain: Viruses
DB_name: acidFila_VIRUS_8
DB_src: VIRUS
Rel_date: 9/16/2007
Pub_id: 17942536
Org_abr: Acid_fila_virus_9
Org_name: Acidianus filamentous virus 9
Menu_name: Acidianus filamentous virus 9
Domain: Viruses
DB_name: acidFila_VIRUS_9
DB_src: VIRUS
Rel_date: 3/31/2009
Pub_id: 18565736
Org_abr: Acid_rods_virus_1
Org_name: Acidianus rod-shaped virus 1
Menu_name: Acidianus rod-shaped virus 1
Domain: Viruses
DB_name: acidRods_VIRUS_1
DB_src: VIRUS
Rel_date: 9/12/2005
Pub_id: 15866073
Org_abr: Acid_twot_virus
Org_name: Acidianus two-tailed virus
Menu_name: Acidianus two-tailed virus
Domain: Viruses
DB_name: acidTwot_VIRUS
DB_src: VIRUS
Rel_date: 9/12/2005
Pub_id: 16677670
Org_abr: Arch_BJ1_virus
Org_name: Archaeal BJ1 virus
Menu_name: Archaeal BJ1 virus
Domain: Viruses
DB_name: archBJ1_VIRUS
DB_src: VIRUS
Rel_date: 12/15/2006
Pub_id: 17996081
Org_abr: Halo_phag_SH1
Org_name: Haloarcula phage SH1
Menu_name: Haloarcula phage SH1
Domain: Viruses
DB_name: haloPhag_SH1
DB_src: VIRUS
Rel_date: 8/02/2005
Pub_id: 15994804
Org_abr: Halo_phag_HF2
Org_name: Halorubrum phage HF2
Menu_name: Halorubrum phage HF2
Rel_date: 11/20/2002
Domain: Viruses
DB_name: haloPhag_HF2
DB_src: VIRUS
Org_abr: Halo_HF1
Org_name: Halovirus HF1
Menu_name: Halovirus HF1
Domain: Viruses
DB_name: haloHF1
DB_src: VIRUS
Tax_name: Halovirus HF1
Rel_date: 07/07/2003
Pub_id: 15090523
Org_abr: His1_viru
Org_name: His1 virus
Menu_name: His1 virus
Domain: Viruses
DB_name: his1Viru
DB_src: VIRUS
Rel_date: 3/24/2006
Pub_id: 9765495
Org_abr: His2_viru
Org_name: His2 virus
Menu_name: His2 virus
Domain: Viruses
DB_name: his2Viru
DB_src: VIRUS
Rel_date: 3/24/2006
Pub_id: 16530800
Org_abr: Meth_phag_psiM2
Org_name: Methanobacterium phage psiM2
Menu_name: Methanobacterium phage psiM2
Domain: Viruses
DB_name: methPhag_PSIM2
DB_src: VIRUS
Rel_date: 6/24/1998
Pub_id: 9791169
Org_abr: Meth_phag_psiM100
Org_name: Methanothermobacter phage psiM100
Menu_name: Methanothermobacter phage psiM100
Domain: Viruses
DB_name: methPhag_PSIM100
DB_src: VIRUS
Rel_date: 12/13/2000
Pub_id: 11544247
Org_abr: Natr_phag_PhiCh1
Rel_date: 07/30/2002
Org_abr: Pyro_sphe_virus
Org_name: Pyrobaculum spherical virus
Menu_name: Pyrobaculum spherical virus
Domain: Viruses
DB_name: pyroSphe_VIRUS
DB_src: VIRUS
Rel_date: 05/01/2004
Pub_id: 15193919
Org_abr: Pyro_abys_virus_1
Org_name: Pyrococcus abyssi virus 1
Menu_name: Pyrococcus abyssi virus 1
Domain: Viruses
DB_name: pyroAbys_VIRUS_1
DB_src: VIRUS
Rel_date: 06/21/2007
Org_abr: Sulf_isla_filamentous_virus
Org_name: Sulfolobus islandicus filamentous virus
Menu_name: Sulfolobus islandicus filamentous virus
Domain: Viruses
DB_name: sulfIsla_FILAMENTOUS
DB_src: VIRUS
Rel_date: 11/06/2001
Pub_id: 10662621
Org_abr: Sulf_isla_rod-shaped_virus_1
Org_name: Sulfolobus islandicus rod-shaped virus 1
Menu_name: Sulfolobus islandicus rod-shaped virus 1
Domain: Viruses
DB_name: sulfIsla_ROD_SHAPED_V
DB_src: VIRUS
Rel_date: 03/05/2002
Pub_id: 11878892
Org_abr: Sulf_isla_rod-shaped_virus_2
Org_name: Sulfolobus islandicus rod-shaped virus 2
Menu_name: Sulfolobus islandicus rod-shaped virus 2
Domain: Viruses
DB_name: sulfIsla_ROD_SHAPED_VIRUS_2
DB_src: VIRUS
Rel_date: 11/29/2001
Pub_id: 11878892
Org_abr: Sulf_spin_virus_4
Org_name: Sulfolobus spindle-shaped virus 4
Menu_name: Sulfolobus spindle-shaped virus 4
Domain: Viruses
DB_name: sulfSpin_VIRUS_4
DB_src: VIRUS
Rel_date: 11/20/2007
Org_abr: Sulf_turr_icosahedral_virus
Org_name: Sulfolobus turreted icosahedral virus
Menu_name: Sulfolobus turreted icosahedral virus
Domain: Viruses
DB_name: sulfTurr_ICOSAHEDRAL
DB_src: VIRUS
Rel_date: 06/04/2004
Org_abr: Sulf_viru_1
Org_name: Sulfolobus virus 1
Menu_name: Sulfolobus virus 1
Domain: Viruses
DB_name: sulfViru_1
DB_src: VIRUS
Rel_date: 07/16/1988
Org_abr: Sulf_viru_2
Org_name: Sulfolobus virus 2
Menu_name: Sulfolobus virus 2
Domain: Viruses
DB_name: sulfViru_2
DB_src: VIRUS
Org_abr: Sulf_viru_Kamchatka_1
Org_name: Sulfolobus virus Kamchatka 1
Menu_name: Sulfolobus virus Kamchatka 1
Domain: Viruses
DB_name: sulfViru_KAMCHATKA_1
DB_src: VIRUS
Rel_date: 02/10/2004
Pub_id: 14747560
Org_abr: Sulf_viru_Ragged_Hills
Org_name: Sulfolobus virus Ragged Hills
Menu_name: Sulfolobus virus Ragged Hills
Domain: Viruses
DB_name: sulfViru_RAGGED_HILLS
DB_src: VIRUS
Rel_date: 02/10/2004
Pub_id: 14747560
Org_abr: Sulf_viru_STSV1
Org_name: Sulfolobus virus STSV1
Menu_name: Sulfolobus virus STSV1
Domain: Viruses
DB_name: sulfViru_STSV1
DB_src: VIRUS
Rel_date: 09/05/2004
Pub_id: 15994761
Org_abr: Ther_tena_spherical_virus_1
Org_name: Thermoproteus tenax spherical virus 1
Menu_name: Thermoproteus tenax spherical virus 1
Domain: Viruses
DB_name: therTena_SPHERICAL_VI
DB_src: VIRUS
Rel_date: 12/17/2004
Pub_id: 16682063
Org_abr: Clos_perf_SM101
Domain: Viruses
Org_abr: Schi_pomb
DB_name: schiPomb1
Seq_acc: NC_003424 NC_003423 NC_003421 NC_001326
Name_chg: chrI chrII chrIII chrM
Seq_size: 5579133 4539804 2452883 19431
Gene_ct: 2486 2020 1016 38
Seq_GC: 36.09 35.92 36.24 30.09
Rel_date: Jan 2008
Seq_src: Sanger Center, Schizosaccharomyces pombe European Sequencing Consortium (EUPOM), and Cold Spring Harbor
Sprinzl: 764
Org_abr: Sacc_cere
DB_name: sacCer1
Seq_acc: NC_001133 NC_001134 NC_001135 NC_001136 NC_001137 NC_001138 NC_001139 NC_001140 NC_001141 NC_001142 NC_001143 NC_001144 NC_001145 NC_001146 NC_001147 NC_001148 NC_001224
Name_chg: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chrM
Sprinzl: 763
Org_abr: Aspe_fumi
DB_name: aspeFumi1
Seq_acc: NC_007194 NC_007195 NC_007196 NC_007197 NC_007198 NC_007199 NC_007200 NC_007201 NZ_AAHF00000000
Name_chg: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chrUn
Org_abr: Cand_glab_CBS138
Seq_acc: NC_004691 NC_005967 NC_005968 NC_006026 NC_006027 NC_006028 NC_006029 NC_006030 NC_006031 NC_006032 NC_006033 NC_006034 NC_006035 NC_006036
Name_chg: chrMT chrA chrB chrC chrD chrE chrF chrG chrH chrI chrJ chrK chrL chrM
Org_abr: Deba_hans_CBS767
Seq_acc: NC_006043 NC_006044 NC_006045 NC_006046 NC_006047 NC_006048 NC_006049 NC_010166
Name_chg: chrA chrB chrC chrD chrE chrF chrG chrMT
Org_abr: Erem_goss
Seq_acc: NC_005782 NC_005783 NC_005784 NC_005785 NC_005786 NC_005787 NC_005788 NC_005789
Name_chg: chrI chrII chrIII chrIV chrV chrVI chrVII chrMT
Org_abr: Kluy_lact_NRRL_Y-1140
Seq_acc: NC_006037 NC_006038 NC_006039 NC_006040 NC_006041 NC_006042 NC_006077
Name_chg: chrA chrB chrC chrD chrE chrF chrMT
Org_abr: Aqui_aeol
Multiz: Aquificales hydrSp_128_5R1 hydrY04A sulfYO3A
Phylo: (((aquiAeol, hydrSp_128_5R1), hydrY04A), sulfYO3A)
Org_abr: Hydr_Y04A
SP_ID: AQUAE
Multiz: Aquificales aquiAeol hydrSp_128_5R1 ospSpri14_050609_1 sulfYO3A
Phylo: ((((aquiAeol, hydrSp_128_5R1), hydrY04A), ospSpri14_050609_1), sulfYO3A)
Org_abr: Sulf_YO3A
SP_ID: AQUAE
Multiz: Aquificales aquiAeol hydrSp_128_5R1 hydrY04A
Phylo: (((aquiAeol, hydrSp_128_5R1), hydrY04A), sulfYO3A)
Org_abr: Hydr_sp_128-5-R1-1
Menu_name: Hydrogenivirga sp. 128-5-R1-1
DB_name: hydrSp_128_5R1
JGI_ID: 641380441
SP_ID: AQUAE
Rel_date: Dec 2007
Seq_src: J. Craig Venter Institute
Multiz: Aquificales aquiAeol hydrY04A ospSpri14_050609_1 sulfYO3A
Phylo: ((((aquiAeol, hydrSp_128_5R1), hydrY04A), ospSpri14_050609_1), sulfYO3A)
Org_abr: Cand_Desu_audaxviator_MP104C
DB_name: desuAuda
Rel_date: July 2008
Multiz: Peptococcaceae peloTher_SI carbHydrZ2901 desuRedu_MI_1
Phylo: ((desuAuda,(peloTher_SI,carbHydrZ2901)), desuRedu_MI_1)
Org_abr: Acid_boon_T469_uid43333
DB_name: acidBoon1
Menu_name: Aciduliprofundum boonei T469
Name_chg: chr
Seq_src: DOE/JGI
Rel_date: Feb 2010
Iso_pub: 16871216
SP_ID: 9EURY
Org_abr: Meth_FS40_22_uid42499
Menu_name: Methanocaldococcus FS406 22
DB_name: methSp_FS406_1
Seq_src: DOE/JGI
Name_chg: chr plasmid_pFS01
Seq_acc: NC_013887 NC_013888
Rel_date: Feb 2010
Multiz: Methanococcus methFerv1 methVulc1 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1
Phylo: (methKand1,(methTher1,((((methJann1, methSp_FS406_1),methFerv1),methVulc1),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Meth_vulc_M7
Menu_name: Methanocaldococcus vulcanius M7
DB_name: methVulc1
Seq_acc: NC_013407 NC_013408 NC_013409
Name_chg: chr plasmid_pMETVU01 plasmid_pMETVU02
Seq_src: DOE/JGI
Rel_date: Dec 2009
SP_ID: METVM
Iso_pub: 10319479
Multiz: Methanococcus methJann1 methFerv1 methInfe0 metMar1 methMari_C5_1 methMari_C7 methVann1 methAeol1 methTher1 methKand1 methSp_FS406_1
Phylo: (methKand1,(methTher1,((((methJann1, methSp_FS406_1),methFerv1),methVulc1),methInfe0)),(methAeol1,(methVann1,(methMari_C7,(metMar1,methMari_C5_1)))))
Org_abr: Natr_maga_ATCC_43099_uid46245
DB_name: natrMaga1
Menu_name: Natrialba magadii ATCC 43099
Seq_acc: NC_013922 NC_013923 NC_013924 NC_013925
Name_chg: chr plasmid_pNMAG01 plasmid_pNMAG02 plasmid_pNMAG03
Seq_src: DOE/JGI
Rel_date: Feb 2010
Iso_pub: 9226918
SP_ID: NATMA
Multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Ferr_plac_DSM_10642_uid40863
Menu_name: Ferroglobus placidus DSM 10642
DB_name: ferrPlac1
Seq_acc: NC_013849
Name_chg: chr
Seq_src: DOE/JGI
Rel_date: Feb 2010
SP_ID: FERPL
Iso_pub: 8929276
Multiz: Archaeoglobaceae archProf1 archFulg1
Phylo: ((archFulg1,archProf1),ferrPlac1)
Org_abr: Meth_rumi_M1_uid45857
Menu_name: Methanobrevibacter ruminantium M1
DB_name: methRumi1
Seq_acc: NC_013790
Name_chg: chr
Seq_src: Pastoral Greenhouse Gas Research Consortium
Rel_date: Feb 2010
Iso_pub: 13549377
Pub_id: 20126622
Multiz: Methanogens methSmit1 methTher1 metMar1 methMari_C5_1 methJann1 methRumi1
Phylo: ((((methStad1,(methSmit1,methRumi1)),methTher1),(metMar1,methMari_C5_1)),methJann1)
Org_abr: Sulf_isla_L_D_8_5_uid43679
Menu_name: Sulfolobus islandicus L D 8 5
DB_name: sulfIsla_L_D_8_5
Seq_acc: NC_013769 NC_013770
Name_chg: chr plasmid_pLD8501
Seq_src: DOE/JGI
Rel_date: Feb 2010
SP_ID SULIS
Multiz: Sulfolobes sulfIsla_Y_N_15_51 sulfIsla_Y_G_57_14 sulfIsla_M_16_27 sulfIsla_M_14_25 sulfIsla_M_16_4 sulfIsla_L_D_8_5 sulSol1 sulfAcid1 sulfToko1 metaSedu
Phylo: (metaSedu,((sulSol1,((sulfIsla_M_16_4,(sulfIsla_M_14_25,sulfIsla_M_16_27)),((sulfIsla_Y_G_57_14,sulfIsla_Y_N_15_51),(sulfIsla_L_S_2_15,sulfIsla_L_D_8_5)))),(sulfAcid1,sulfToko1)))
Org_abr: Arch_prof_DSM_5631_uid43493
Menu_name: Archaeoglobus profundus DSM 5631
DB_name: archProf1
SP_ID: ARCPR
Seq_acc: NC_013741 NC_013742
Name_chg: chr plasmid_pArcpr01
Seq_src: DOE/JGI
Rel_date: Jan 2010
Multiz: Archaeoglobaceae ferrPlac1 archProf1 archFulg1
Phylo: ((archFulg1,archProf1),ferrPlac1)
SP_ID: ARCPR
Org_abr: Halo_turk_DSM_5511_uid43501
Menu_name: Haloterrigena turkmenica DSM 5511
DB_name: haloTurk1
Seq_acc: NC_013743 NC_013744 NC_013745 NC_013746 NC_013747 NC_013748 NC_013749
Name_chg: chr plasmid_pHTUR01 plasmid_pHTUR02 plasmid_pHTUR03 plasmid_pHTUR04 plasmid_pHTUR05 plasmid_pHTUR06
Seq_src: DOE/JGI
Rel_date: Jan 2010
Multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Meth_palu_SANAE
Menu_name: Methanocella paludicola SANAE
DB_name: methPalud1
Seq_acc: NC_013665
Name_chg: chr
Seq_src: NITE
Rel_date: Dec 2009
SP_ID: METPS
Iso_pub: 18398197
Org_abr: Halo_muko_DSM_12286
Menu_name: Halomicrobium mukohataei DSM 12286
DB_name: haloMuko1
Seq_acc: NC_013202 NC_013201
Name_chg: chr plasmid_pHmuk01
Gb_acc: CP001688 CP001689
Seq_size: 3110487 221862
Gene_ct: 3277 198
Seq_GC: 65.63 64.15
Seq_src: DOE/JGI
Rel_date: Sept 2009
SP_ID: HALMD
Iso_pub: 8995805
Multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Halo_lacu_ATCC_49239
Menu_name: Halorubrum lacusprofundi ATCC 49239
DB_name: haloLacu1
Seq_acc: NC_012029 NC_012028 NC_012030
Name_chg: chr1 chr2 plasmid_pHLAC01
Gb_acc: CP001365 CP001366 CP001367
Seq_size: 2735295 525943 431338
Gene_ct: 2802 522 402
Seq_GC: 66.72 57.14 54.86
Seq_src: DOE/JGI
Rel_date: Feb 2009
SP_ID: HALLT
Multiz: Halophiles haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
Phylo: ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
Org_abr: Cand_Meth_palustris_E1_9c
Menu_name: Methanosphaerula palustris E1 9c
DB_name: methPalus1
Seq_acc: NC_011832
Name_chg: chr
Seq_src: DOE/JGI
Rel_date: Sept 2009
SP_ID: METPE
Iso_pub: 19406770
# haloHalo1 haloSali1 natrPhar1 halMar1 haloUtah1 haloWals1 haloVolc1 natrMaga1 haloTurk1 haloLacu1 haloMuko1
# ((((natrPhar1,((haloUtah1,(haloSali1,haloHalo1)),(haloMuko1,halMar1))),(haloTurk1,natrMaga1)),haloLacu1),haloWals1,haloVolc1)
\ No newline at end of file