As text, or see rules and steps
# Thymidine degradation in GapMind is based on thymidine phoshorylase (EC:2.4.2.4), # which yields 2-deoxyribose-1-phosphate and thymine. The catabolism of thymine is # not represented, as it may be excreted. nupG thymidine permease NupG/XapB curated:CharProtDB::CH_088596 curated:SwissProt::P45562 # Transporters were identified using # query: transporter:thymidine:deoxythymidine thymidine-transport: nupG Slc29a1 thymidine transporter Slc29a1 curated:SwissProt::O54698 thymidine-transport: Slc29a1 # A nupC-like protein from Shewanella sp. ANA-3 (Shewana3_1039, A0KU05) # is important for utilization of thymidine and other nucleosides. # A similar protein from V. cholerae (uniprot:Q9KPL5) binds uridine and 2'-deoxyuridine and # is likely to be a thymidine transporter as well, but this is not proven. # The nupC protein from B. subtilis (P39141) was shown to be a uridine transporter (PMID:8550462) # and is suspected to be a thymidine transporter as well, so it is ignored. # The specificity of E. coli nupX (P33021, also known as yeiJ) seems to be unknown. nupC thymidine permease NupC curated:SwissProt::P0AFF2 ignore:SwissProt::P39141 uniprot:A0KU05 ignore:TCDB::Q9KPL5 ignore:SwissProt::P33021 thymidine-transport: nupC Slc28a3 thymidine:Na+ symporter SLC28A3 curated:TCDB::Q9UA35 thymidine-transport: Slc28a3 # A non-specific lysosomal transporter (TC 2.A.74.1.1 / Q60961) was ignored # P19663 is ignored because it is a sequence fragment. # Many uridine phosphorylases (EC:2.4.2.3) are also deoxyuridine phosphorylases and thymidine phosphyrylases, so # hits to these are ignored. deoA thymidine phosphorylase DeoA EC:2.4.2.2 EC:2.4.2.4 ignore:SwissProt::P19663 ignore_other:2.4.2.3 import deoxyinosine.steps:deoB # phosphopentomutase import deoxyribose.steps:deoC # deoxyribose-5-phosphate aldolase import ethanol.steps:acetaldehyde-degradation # After the phosphorylase deoA forms deoxyribose 1-phosphate, a # phosphopentomutase forms deoxyribose-5-phosphate, and an aldolase # yields glyceraldehyde 3-phosphate (an intermediate in glycolysis) # and acetaldehyde. all: thymidine-transport deoA deoB deoC acetaldehyde-degradation
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory