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Prior-Knowledge Description Expectation Prediction Conclusion Leaf Statistics
GenProp0814 urea utilization~This property encompasses two separate urea catabolism pathways, the nickel-dependent urease pathway and the urea carboxylase/allophanate hydrolase pathway. Both - {{t,f}} Both - {{t},{f}} Ambiguous contradictory
Component_241 urease, gamma subunit Both - {{t,f}} True - {{t}} Ambiguous presence
Evidence_75313 TIGR03411 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_51515 urea carboxylase None - {{∅}} False - {{f}} Unconfirmed absence
Component_51516 allophanate hydrolase None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0481 urea carboxylase/allophanate hydrolase pathway~This two-step, ATP-dependent pathway for urea hydrolysis is an alternative to urease. Urease requires a transporter and accessory proteins to produce its nickel metallocenter, while this two-step system uses biotin. Urea carboxylase acts first in this pathway, requiring ATP and bicarbonate as substrates. Allophanate hydrolase acts next, but note that this enzyme may be found in systems that do not contain a urea carboxylase. In yeasts such as Saccaromyces cerevisiae, the two activities of this pathway are encoded in a fusion protein, designated urea amidolyase. This pathway appears to function primarily for the purpose of obtaining nitrogen in the form of ammonia. A pair of uncharacterized, tandem, homologous genes, restricted to organisms with this system and adjacent to the known genes, has been added to this Genome Property. None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_84401 GenProp0481 GENPROP None - {{∅}} False - {{f}} Unconfirmed absence
Component_54339 urea ABC transporter, ATP-binding protein UrtD None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_68289 TIGR02713 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_54337 urea ABC transporter, permease protein UrtB None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_84608 TIGR03669 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_54367 urea carboxylase-associated protein 2 None - {{∅}} False - {{f}} Unconfirmed absence
Component_54366 urea carboxylase-associated protein 1 None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_75310 TIGR03407 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_85071 PF03253 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_75344 TIGR03425 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_215 TIGR01792 HMM Both - {{t,f}} True - {{t}} Ambiguous presence
Component_54338 urea ABC transporter, permease protein UrtC None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_208 TIGR00192 HMM Both - {{t,f}} True - {{t}} Ambiguous presence
Evidence_207 PF00449 HMM Both - {{t,f}} True - {{t}} Ambiguous presence
Component_239 alpha-subunit, N-terminal domain Both - {{t,f}} True - {{t}} Ambiguous presence
Evidence_75314 TIGR03410 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_240 urease, beta subunit Both - {{t,f}} True - {{t}} Ambiguous presence
Evidence_53069 TIGR00802 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_75343 TIGR03424 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_210 PF01774 HMM Both - {{t,f}} False - {{f}} Ambiguous absence
Evidence_75311 TIGR03409 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_209 TIGR00193 HMM Both - {{t,f}} True - {{t}} Ambiguous presence
Evidence_75345 TIGR03427 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_84403 GenProp0743 GENPROP None - {{∅}} False - {{f}} Unconfirmed absence
Component_54340 urea ABC transporter, ATP-binding protein UrtE None - {{∅}} False - {{f}} Unconfirmed absence
Component_244 urease accessory protein UreF Both - {{t,f}} False - {{f}} Ambiguous absence
Component_246 urease, alpha subunit Both - {{t,f}} True - {{t}} Ambiguous presence
GenProp0743 urea ABC transporter UrtABCDE~This property represents a conserved five-gene operon for an ABC transporter with a substrate-binding protein, two permeases, and two ATP-binding cassette proteins. All five genes from this operon are detected in Burkholderia mallei, at very high confidence levels, by means of the partial phylogenetic profiling algorithm (PMID:16930487) vs. a profile for urease, and the operon occurs next to urease genes in B. mallei and most other species. In Cyanobacteria, high-affinity urea transport is shown to be eliminated by mutations to any of several different proteins in this system (PMID:11929526). None - {{∅}} False - {{f}} Unconfirmed absence
Component_242 urease accessory protein UreD Both - {{t,f}} False - {{f}} Ambiguous absence
Component_243 urease accessory protein UreE Both - {{t,f}} False - {{f}} Ambiguous absence
Component_245 urease accessory protein UreG Both - {{t,f}} False - {{f}} Ambiguous absence
Evidence_68288 TIGR02712 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_75312 TIGR03408 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_62827 a urea transporter None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_84607 TIGR03622 HMM None - {{∅}} False - {{f}} Unconfirmed absence
Component_62826 a urea degradation pathway Both - {{t,f}} Both - {{t},{f}} Ambiguous contradictory
Evidence_213 TIGR00101 HMM Both - {{t,f}} False - {{f}} Ambiguous absence
Component_54336 urea ABC transporter, periplasmic binding protein None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_84402 GenProp0051 GENPROP Both - {{t,f}} Both - {{t},{f}} Ambiguous contradictory
Evidence_84609 TIGR03727 HMM None - {{∅}} False - {{f}} Unconfirmed absence
GenProp0051 urease~Urease is a multi-subunit, nickel-containing enzyme required for the hydrolysis of urea to carbon dioxide and ammonia [1]. Its three structural genes are located in an unidirectionally transcribed gene cluster consisting either as separate alpha, beta, and gamma subunits, or as in Helicobacter pylori, a fusion of beta and gamma subunits [2]. Associated with these structural subunits are accessory factors functioning to assemble and incorporate its nickel-containing metallocenter [3]. This property predicts a urease system to be present if both its three structural subunits and four accessory proteins are all found. In Bacillus subtilis, the accessory proteins are not found by homology but urease function has been shown experimentally. This finding raises the question of what alternative mechanism can enable the assembly of functional urease. Both - {{t,f}} Both - {{t},{f}} Ambiguous contradictory
Component_54368 ABC transporter periplasmic binding protein, urea carboxylase region None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_211 PF02814 HMM Both - {{t,f}} False - {{f}} Ambiguous absence
Component_40711 nickel transporter (UreH) None - {{∅}} False - {{f}} Unconfirmed absence
Evidence_212 PF01730 HMM Both - {{t,f}} False - {{f}} Ambiguous absence