GapMind for catabolism of small carbon sources

 

Protein 15361 in Escherichia coli BW25113

Annotation: b1241 fused acetaldehyde-CoA dehydrogenase/iron-dependent alcohol dehydrogenase/pyruvate-formate lyase deactivase (NCBI)

Length: 891 amino acids

Source: Keio in FitnessBrowser

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
2'-deoxyinosine catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
2-deoxy-D-ribose catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
ethanol catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
ethanol catabolism etoh-dh-nad hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6 aldehyde dehydrogenase/alcohol dehydrogenase (EC 1.2.1.57) 59% 1046.2
L-threonine catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
thymidine catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
L-tryptophan catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 100% 100% 1749.6
4-hydroxybenzoate catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
2'-deoxyinosine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
2-deoxy-D-ribose catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
ethanol catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
L-threonine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
thymidine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
L-tryptophan catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 56% 100% 988.8 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
L-fucose catabolism fucO lo Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized) 32% 97% 212.2 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6
L-rhamnose catabolism fucO lo Lactaldehyde reductase; Propanediol oxidoreductase; EC 1.1.1.77 (characterized) 32% 97% 212.2 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 100% 1749.6

Sequence Analysis Tools

View 15361 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG
IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA
IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA
LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF
DNGVICASEQSVVVVDSVYDAVRERFATHGGYLLQGKELKAVQDVILKNGALNAAIVGQP
AYKIAELAGFSVPENTKILIGEVTVVDESEPFAHEKLSPTLAMYRAKDFEDAVEKAEKLV
AMGGIGHTSCLYTDQDNQPARVSYFGQKMKTARILINTPASQGGIGDLYNFKLAPSLTLG
CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK
RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLSIVRKGAELANSFKPDVI
IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMIAVTTTSG
TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMDMPKSLCAFGGLDAVTHAME
AYVSVLASEFSDGQALQALKLLKEYLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG
VCHSMAHKLGSQFHIPHGLANALLICNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD
HLGLSAPGDRTAAKIEKLLAWLETLKAELGIPKSIREAGVQEADFLANVDKLSEDAFDDQ
CTGANPRYPLISELKQILLDTYYGRDYVEGETAAKKEAAPAKAEKKAKKSA

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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