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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This site was inspired by the events surrounding the Scottish book and the impact that it made upon mathematics. If you wish to know more about that topic, ask Rick or Ross over beers.