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
12-31-1969 18:00:00 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
Catabolic operon for an unknown compound Bacterial Caspases Orphan chromosomal cluster 6-8-2008 12:36:57 -12 1 1
Biotin biosynthesis in yeast? Biotin biosynthesis Missing input/output 11-4-2005 14:15:43 John_Cronan 1 1
New Staphylococcus serotype in Staphylococcus haemolyticus JCSC1435 Capsular polysaccharide biosynthesis in Staphylococcus other 4-27-2006 11:11:47 JenZ 1 1
Lycopene beta cyclase in cyanobacteria Carotenoids Missing gene for a role 9-28-2005 14:51:54 OlgaV 1 1
Hypothetical glycosyl transferase Carotenoids Functionally coupled hypothetical 10-3-2005 10:57:08 OlgaV 1 1
Missing divinyl protochlorophyllide reductase Chlorophyll Biosynthesis Missing gene for a role 9-28-2005 14:46:16 SvetaG 1 1
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 1 1
A new form of archaeal/eukaryotic DNA primase DNA replication, archaeal other 11-16-2006 18:31:52 Isaac Cann 1 1
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 1 1
Jackson Embden-Meyerhof and Gluconeogenesis Functionally coupled hypothetical 9-28-2005 9:31:08 Peyton 1 1
Archaeal glucokinase Embden-Meyerhof and Gluconeogenesis Archaeal Missing gene for a role 9-28-2005 8:54:32 SvetaG 1 1
Archaeal 6-phosphofructokinase Embden-Meyerhof and Gluconeogenesis Archaeal Missing gene for a role 9-28-2005 8:59:18 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
Unsaturated fatty acids? Fatty Acid Biosynthesis FASII Missing gene for a role 11-4-2005 14:21:50 John_Cronan 1 1
RuMP pathway as a sourse of pentose? Formaldehyde assimilation: Ribulose monophosphate pathway other 10-26-2005 14:38:44 SvetaG 1 1
Bacillus licheniformis ATCC 14580 is competent? Gram Positive Competence Gene in subsystem without clear role 1-3-2006 14:33:00 JenZ 1 1
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 1 1
newwm2092 Histidine Degradation Missing gene for a role 9-26-2005 20:59:47 TattMitte 0 33
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 1 1
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
L-ascorbate ring hydrolase?? L-ascorbate utilization (and related gene clusters) Missing gene for a role 10-23-2005 14:29:59 SvetaG 1 1
ndzurquhhu L-ascorbate utilization (and related gene clusters) Orphan chromosomal cluster 10-23-2005 14:51:19 SvetaG 2 2
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 Functionally coupled hypothetical 9-27-2006 11:31:43 Rodionov 1 1
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 1 1
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
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
Missing diaminopimelate epimerase (EC 5.1.1.7) Lysine Biosynthesis DAP Pathway Missing gene for a role 9-13-2006 13:20:31 AndreiO 8 4
Possible quinolinate salvage in streptococci NAD and NADP cofactor biosynthesis global Missing input/output 10-3-2005 20:33:24 AndreiO 1 1
Missing Glutaminase component of NAD synthase NAD and NADP cofactor biosynthesis global Missing gene for a role 9-23-2005 18:48:54 AndreiO 1 1
test PA0057 cluster other 9-3-2006 19:51:09 -12 1 1
Jason Porphyrin, Heme, and Siroheme Biosynthesis Role out of context 9-28-2005 9:47:37 Jarrett 5 3
Missing coproporphyrinogen III oxidase Porphyrin, Heme, and Siroheme Biosynthesis Missing gene for a role 9-28-2005 12:43:19 SvetaG 1 1
Missing PPO in Heme biosynthesis Porphyrin, Heme, and Siroheme Biosynthesis Missing gene for a role 9-26-2005 20:48:21 SvetaG 1 1
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 hydrolase (EC 3.1.2.3) TCA Cycle Missing gene for a role 10-3-2005 15:28:40 OlgaV 1 1
CydC,CydD function in Gram positive bacteria Terminal cytochrome oxidases Gene in subsystem without clear role 10-4-2005 4:46:22 OlgaV 1 1
CydC,CydD missing from cyanobacteria Terminal cytochrome oxidases Missing gene for a role 10-4-2005 4:52:23 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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