Get results CSV file
Prior-Knowledge Description Expectation Prediction Conclusion Leaf Statistics
Evidence_63637 TIGR01469 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63664 TIGR02469 HMM None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0269 coenzyme B12 biosynthesis from cob(II)yrinate diamide~This property covers the main branch of the latter part of the Coenzyme B12 (5-deoxyadenosyl cobalamin) biosynthesis pathway from cob(II)yrinate diamide which is the product of cobalt chelatase. Additionally, in order to have a complete pathway, an organism must have the capability to synthesize (or otherwise obtain) 1-amino-2-propanol and alpha-ribazole. None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_63585 PF03186 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63682 PF01923 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63670 TIGR00379 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51054 cobyrinic acid diamide biosynthesis, aerobic pathway: GenProp0113 None - {{∅}} None - {{∅}} Unexplained
Component_48846 porphobilinogen deaminase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63662 PF01888 HMM None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0275 cobyrinic acid diamide biosynthesis, anaerobic pathway~This property covers that part of the Vitamin B12 (cobalamin) biosynthesis pathway in which uroporphyrinogen III is converted to cobyrinic acid diamide under anaerobic conditions. This process differs from the aerobic version in several key respects. The most striking is the fact that here the cobalt atom is inserted early in the process (after the formation of the branchpoint compound precorrin-2 by CbiK or CbiX) in an ATP-independent manner, as opposed to the aerobic pathway in which the cobalt is inserted at the end by a multimeric ATP-hydrolyzing system. Another distinctive feature is the nature of the enzyme catalyzing the oxidative ring contraction. In the aerobic pathway, this is carried out by an oxygenase (CobG), while the as-of-yet uncharacterized anaerobic enzyme clearly must utilize some other mechanism. Finally, the methylation at position C-1 at the point of the ring contraction is carried out by CobF in the aerobic pathway, and by an as-of-yet uncharacterized enzyme in the anaerobic pathway (presumably because the proximity of this carbon to the cobalt changes the chemistry somewhat). Two genes (CbiD and CbiG) are found in most anaerobic B12 biosynthetic clusters and have been shown to be essential to the pathway. CbiD is homologous to methylases and is likely to catalyze the C-1 methylation. CbiG then, by process of elimination and (coupled with unique nature of the chemical transformation) its lack of homology to other known classes of enzyme is likely to catalyze the ring contraction. CbiJ, the analog of precorrin-6x reductase (CobK), is not found in deltaproteobacteria, a number of archaea and a scattering of other species, oftentimes this is the only component missing. Most likely, an unknown reductase replaces CbiJ/CobK in these species. For this reason, the detection of this component is not a requirement for the assertion of YES for this property. The majority of genomes for which some evidence has been asserted are missing evidence of the CbiK or CbiX chelatase. This step is still required for assertion of the YES state since it is part of the suite of components which are diagnostic for the anaerobic pathway. The evidence for the anaerobic pathway is nonetheless quite strong when this is the only component missing, especially when the aerobic pathway is not supported. None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_63587 PF02654 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_74950 TIGR03161 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51053 Uroporphyrinogen III from 5-aminolevulinate: GenProp0220 None - {{∅}} True - {{t}} Unconfirmed presence
Component_48845 Delta-aminolevulinic acid dehydratase None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63667 TIGR00715 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_74951 TIGR03162 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63660 TIGR01466 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51095 C-20 methylase (CbiL) None - {{∅}} False - {{f}} Unconfirmed absence
Component_48847 uroporphyrinogen-III synthase None - {{∅}} True - {{t}} Unconfirmed presence
Component_51057 alpha-ribazole from nicotinate mononucleotide and dimethylbenzimidazole: GenProp0270 None - {{∅}} None - {{∅}} Unexplained
Evidence_63668 PF02571 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51067 uroporphyrinogen methyltransferase (2.1.1.107) None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_63669 PF02570 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63626 GenProp0220 GENPROP None - {{∅}} True - {{t}} Unconfirmed presence
Component_51107 cobalamin-utilizing enzymes: GenProp0284 None - {{∅}} None - {{∅}} Unexplained
Evidence_63665 TIGR01467 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63631 PF06180 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63590 TIGR00708 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51028 cobyric acid synthase (CobQ/CbiP) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_74956 TIGR01140 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_54064 threonine-phosphate decarboxylase None - {{∅}} False - {{f}} Unconfirmed absence
Component_51031 bifunctional cobinamide kinase, cobinamide phosphate guanylyltransferase (CobP) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63632 GenProp0275 GENPROP None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
GenProp0220 uroporhyrinogen III biosynthesis from 5-aminolevulinate~This property describes the three step pathway that takes 5-aminolevulinate and converts it into uroporhyrinogen III, a compund which is used in the biosynthesis of siroheme, coenzyme B12, protoporphyrin IX and heme. Protoporphyrin IX is used in the creation of chlorophyll. None - {{∅}} True - {{t}} Unconfirmed presence
Component_51096 C-11 methylase (CbiF) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_74949 TIGR03160 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63586 TIGR00313 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63584 PF02283 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63659 PF01890 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51030 adenosylcobinamide synthase (CobD) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63661 TIGR00312 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51097 Co-precorrin 6 reductase (CbiJ) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63627 GenProp0113 GENPROP None - {{∅}} None - {{∅}} Unexplained
GenProp0274 coenzyme B12 biosynthesis - overview~This property summarizes and contains the various pathways and systems required for the complete biosynthesis of vitamin B12, 5-deoxyadenosyl cobalamin, from 5-aminolevulinate, S-adenosyl methionine, glutamine, cobalt, ATP, 1-amino-2-propanol, GDP, nicotinate mononucleotide and dimethylbenzimidazole. None - {{∅}} Both - {{∅},{t},{f}} Unconfirmed contradictory
Component_51034 alpha-ribazole-5`-phosphate phosphatase None - {{∅}} False - {{f}} Unconfirmed absence
Component_51027 cobyrinate adenosyltransferases (BtuR, PduO, EutT) None - {{∅}} True - {{t}} Unconfirmed presence
Component_51032 cobalamine 5-phosphate synthase (alpha ribazole transferase) (CobV) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63588 TIGR00317 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63663 TIGR02467 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51091 C-17 methylase (CbiH) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63645 PF01903 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_51056 B12 from cob(II)yrinate diamide and alpha-ribazole: GenProp0269 None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Evidence_63666 TIGR01465 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63658 GenProp0279 GENPROP None - {{∅}} None - {{∅}} Unexplained
Evidence_61345 TIGR00212 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_61346 PF02602 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_51093 C-5,15 methylase/C-12 decarboxylase (CbiE) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_74957 TIGR00380 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51033 nicotinate nucleotide-DBI P-ribosyltransferase None - {{∅}} False - {{f}} Unconfirmed absence
Component_51092 CbiD None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63630 GenProp0270 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_51089 CbiG None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63681 TIGR00636 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Evidence_61344 PF00490 HMM None - {{∅}} True - {{t}} Unconfirmed presence
Component_51094 C-5,15 methylase/C-12 decarboxylase (CbiT) None - {{∅}} False - {{f}} Unconfirmed absence
Component_54065 adenosylcobinamide-phosphate synthase None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_63680 GenProp0284 GENPROP None - {{∅}} None - {{∅}} Unexplained
Component_51088 Cobalt import systems: GenProp0279 None - {{∅}} None - {{∅}} Unexplained
Evidence_63629 GenProp0269 GENPROP None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Component_51098 C-11, C-12 mutase (CbiC) None - {{∅}} False - {{f}} Unconfirmed absence
Component_51059 cobyrinic acid diamide biosynthesis, anaerobic pathway None - {{∅}} Both - {{t},{f}} Unconfirmed contradictory
Component_51099 cobyrinate diamide synthase (CbiA) None - {{∅}} False - {{f}} Unconfirmed absence
Component_51058 cobaltochelatase, monomeric None - {{∅}} True - {{t}} Unconfirmed presence