A Public Depository of Open Problems and Conjectures Identified by SubSystem analysis

About HOPS database




Summary of Existing Problems and Conjectures
title subsystem type timestamp who conjectures Verification Notes
test other 9-3-2006 19:51:09 Bob Olson 0 0
Catabolic operon for an unknown compound Orphan chromosomal cluster 6-8-2008 12:36:57 SvetaG 0 0
Fuctose-bisphosphate aldolase in Geobacter Missing gene for a role 9-28-2005 9:31:08 SvetaG 0 0
12-31-1969 18:00:00 0 0
Biotin biosynthesis in yeast? Missing input/output 11-4-2005 14:15:43 John_Cronan 0 0
HOPS<> 12-31-1969 18:00:00 0 0
unchangeable unwed 546 Missing gene for a role 12-31-1969 18:00:00 DymnGuinany 0 1
New Staphylococcus serotype in Staphylococcus haemolyticus JCSC1435 Capsular polysaccharide biosynthesis in Staphylococcus other 4-27-2006 11:11:47 JenZ 0 0
Hypothetical glycosyl transferase Carotenoids Functionally coupled hypothetical 10-3-2005 10:57:08 OlgaV 0 0
Lycopene beta cyclase in cyanobacteria Carotenoids Missing gene for a role 9-28-2005 14:51:54 OlgaV 0 0
Missing divinyl protochlorophyllide reductase Chlorophyll Biosynthesis Missing gene for a role 9-28-2005 14:46:16 SvetaG 0 0
Missing Aspartate Decarboxylase Coenzyme A Biosynthesis Missing gene for a role 9-23-2005 18:31:54 AndreiO 0 0
Unknown source of beta-alanine Coenzyme A Biosynthesis Missing input/output 9-23-2005 18:38:42 AndreiO 0 0
A new form of archaeal/eukaryotic DNA primase DNA replication, archaeal 11-16-2006 18:31:52 Isaac Cann 0 0
Di-myo-inositol-1,2-phosphate biosynthesis Di-Inositol-Phosphate biosynthesis Missing gene for a role 9-27-2006 10:45:07 Rodionov 0 0
Missing fructose-1,6-bisphosphatase Embden-Meyerhof and Gluconeogenesis Missing gene for a role 9-28-2005 9:14:29 SvetaG 0 0
Archaeal fructose-bisphosphate aldolase Embden-Meyerhof and Gluconeogenesis Archaeal Missing gene for a role 9-28-2005 9:10:50 SvetaG 0 0
Archaeal glucokinase Embden-Meyerhof and Gluconeogenesis Archaeal 9-28-2005 8:54:32 SvetaG 0 0
Archaeal 6-phosphofructokinase Embden-Meyerhof and Gluconeogenesis Archaeal Missing gene for a role 9-28-2005 8:59:18 SvetaG 0 0
Unsaturated fatty acids? Fatty Acid Biosynthesis FASII Missing gene for a role 11-4-2005 14:21:50 John_Cronan 0 0
RuMP pathway as a sourse of pentose? Formaldehyde assimilation: Ribulose monophosphate pathway other 10-26-2005 14:38:44 SvetaG 0 0
Bacillus licheniformis ATCC 14580 is competent? Gram Positive Competence 1-3-2006 14:33:00 JenZ 0 0
A new form of N-formylglutamate deformylase (EC 3.5.1.68) Histidine Degradation Missing gene for a role 4-29-2006 18:13:10 RossO 0 0
gpOBmORTPT Histidine Degradation Missing gene for a role 9-26-2005 20:59:47 fwjjlwap 2 2
Gene lpxH - mysterious fourth step of Kdo2 – lipid A biosynthesis KDO2-Lipid A biosynthesis Missing gene for a role 9-27-2006 21:34:29 OlgaZ 0 0
Gene lpxH - mysterious fourth step of Kdo2 – lipid A biosynthesis KDO2-Lipid A biosynthesis Missing gene for a role 9-27-2006 21:34:17 OlgaZ 0 0
diAeZcmbEVysWmp L-ascorbate utilization (and related gene clusters) Missing gene for a role 10-23-2005 14:51:19 kvqnem 3 9
L-ascorbate ring hydrolase?? L-ascorbate utilization (and related gene clusters) 10-23-2005 14:29:59 SvetaG 0 0
Lactaldehyde dehydrogenase L-rhamnose utilization Gene in subsystem without clear role 9-27-2006 11:23:52 Rodionov 0 0
L-rhamnose isomerase L-rhamnose utilization 9-27-2006 11:31:43 Rodionov 0 0
Regulatory gene for Leucine degradation/Hmg-CoA Metabolism Leucine Degradation and HMG-CoA Metabolism Missing gene for a role 9-26-2005 20:04:34 RossO 0 0
Lipoate in Bacilli Lipoic acid metabolism Missing gene for a role 11-4-2005 15:44:50 John_Cronan 0 0
Unclear route from 2,3,4,5-Tetrahydrodipicolinate to DAP Lysine Biosynthesis DAP Pathway Missing gene for a role 9-13-2006 13:18:15 AndreiO 0 0
Misssing N-succinyl-L,L-diaminopimelate aminotransferase (EC 2.6.1.17) Lysine Biosynthesis DAP Pathway Missing gene for a role 9-13-2006 13:16:22 AndreiO 0 0
Missing diaminopimelate epimerase (EC 5.1.1.7) Lysine Biosynthesis DAP Pathway Missing gene for a role 9-13-2006 13:20:31 AndreiO 0 0
Missing Glutaminase component of NAD synthase NAD and NADP cofactor biosynthesis global 9-23-2005 18:48:25 AndreiO 0 0
Possible quinolinate salvage in streptococci NAD and NADP cofactor biosynthesis global Missing input/output 10-3-2005 20:33:24 AndreiO 0 0
Missing PPO in Heme biosynthesis Porphyrin, Heme, and Siroheme Biosynthesis Missing gene for a role 9-26-2005 14:55:06 SvetaG 0 0
Why coproporphyrinogen III oxidase homologs are present? Porphyrin, Heme, and Siroheme Biosynthesis Role out of context 9-28-2005 9:47:37 SvetaG 0 0
Missing coproporphyrinogen III oxidase Porphyrin, Heme, and Siroheme Biosynthesis Missing gene for a role 9-28-2005 12:43:19 SvetaG 0 0
aminoimidazolase (EC 3.5.4.8) Purine Utilization Missing gene for a role 1-3-2006 5:02:19 OlgaV 0 0
Anchor protein in Cyanobacterial SDH Succinate dehydrogenase Missing gene for a role 10-3-2005 15:15:29 OlgaV 0 0
Succinyl-CoA lydrolase (EC 3.1.2.3) TCA Cycle Missing gene for a role 10-3-2005 15:28:40 OlgaV 0 0
CydC,CydD missing from cyanobacteria Terminal cytochrome oxidases Missing gene for a role 10-4-2005 4:52:23 OlgaV 0 0
CydC,CydD function in Gram positive bacteria Terminal cytochrome oxidases Gene in subsystem without clear role 10-4-2005 4:46:22 OlgaV 0 0
UbiD - - 3-polyprenyl-4-hydroxybenzoate decarboxylase3-polyprenyl-4-hydroxybenzoate carboxy-lyase (EC 4.1.1.-) is missing Ubiquinone Biosynthesis Missing gene for a role 2-20-2007 17:03:47 OlgaZ 0 0
zNdvTqAQmpeMBTtdFj tRNA modification yeast cytoplasmic Unresolved paralogs 9-11-2008 12:33:44 -12 0 0
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