src/hg/archaeStuff/data/Genome-info-mods 1.91

Index: src/hg/archaeStuff/data/Genome-info-mods
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/archaeStuff/data/Genome-info-mods,v
retrieving revision 1.90
retrieving revision 1.91
diff -b -B -U 4 -r1.90 -r1.91
--- src/hg/archaeStuff/data/Genome-info-mods	15 Oct 2009 17:15:29 -0000	1.90
+++ src/hg/archaeStuff/data/Genome-info-mods	20 Oct 2009 23:33:34 -0000	1.91
@@ -101,8 +101,9 @@
 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 natrMaga0 haloVolc1_1 natrPhar1 haloWals1 halMar1 haloUtah1  
 Public_multiz:	Halophiles haloHalo1 haloVolc1 natrPhar1 haloWals1 halMar1 haloUtah1  
@@ -440,26 +441,26 @@
 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 therBaro0
-Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
+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 therBaro0
-Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
+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 therBaro0
-Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
+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
@@ -468,10 +469,10 @@
 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 therBaro0 pyrFur2 pyrAby1 pyrHor1
-Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
+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
@@ -489,10 +490,10 @@
 DB_name:  therOnnu1
 SP_ID: PYRKO
 Rel_date: Nov 2008
 Seq_src: Korea Ocean Research & Development Institute 
-Multiz: Thermococcales therKoda1 therBaro0 pyrFur2 pyrAby1 pyrHor1  
-Phylo: ((pyrFur2,(pyrHor1,pyrAby1)),((therKoda1,therOnnu1),therBaro0))
+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
@@ -501,10 +502,13 @@
 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 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