src/hg/archaeStuff/data/Genome-info-mods 1.93
1.93 2010/01/20 17:53:30 pchan
changed T. neutrophilus to Pyrobaculum by Todd; add Francisella genomes
Index: src/hg/archaeStuff/data/Genome-info-mods
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-mods,v
retrieving revision 1.92
retrieving revision 1.93
diff -b -B -U 4 -r1.92 -r1.93
--- src/hg/archaeStuff/data/Genome-info-mods 16 Dec 2009 22:12:51 -0000 1.92
+++ src/hg/archaeStuff/data/Genome-info-mods 20 Jan 2010 17:53:30 -0000 1.93
@@ -792,21 +792,44 @@
Seq_src: DOE Joint Genome Institute/UCSC
Trna_abr: Pyro_arse-tRNAs
SP_ID: PYRAE
-Org_abr: Ther_neut_V24Sta
-Menu_name: Thermoproteus neutrophilus
+Org_abr: Pyro_neut_V24Sta
+Menu_name: Pyrobaculum neutrophilus V24Sta
+Org_name: Pyrobaculum neutrophilus V24Sta
DB_name: therNeut1
-SP_ID: PYRAE
+Tax_ID: 444157: Archaea; Crenarchaeota; Thermoprotei; Thermoproteales; Thermoproteaceae; Pyrobaculum.
+SP_ID: THENV PYRAE
+Domain: Archaea
+DB_src: NCBI
+Tax_name: Pyrobaculum neutrophilus 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 neutrophilus</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
@@ -820,9 +843,9 @@
TIGR_ID: 0
JGI_ID: 0
SP_ID: PYRAE
String_ID: 0
-Dom_ct: &Pyro_isla_DSM_4184
+Dom_ct: &Ther_neut_V24Sta
Gen_ID: 0
Gb_acc: None
Seq_acc: Pog-genome-v3 chr ece
Name_chg: chr ece
@@ -1342,11 +1365,34 @@
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