GapMind for catabolism of small carbon sources

 

Protein BWI76_RS17250 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS17250

Length: 891 amino acids

Source: Koxy in FitnessBrowser

Candidate for 15 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) 96% 100% 1691.8
2'-deoxyinosine catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8
2-deoxy-D-ribose catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8
ethanol catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8
ethanol catabolism etoh-dh-nad hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8 aldehyde dehydrogenase/alcohol dehydrogenase (EC 1.2.1.57) 59% 1039.3
L-threonine catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8
thymidine catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8
L-tryptophan catabolism ald-dh-CoA hi aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 96% 100% 1691.8
4-hydroxybenzoate catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8
2'-deoxyinosine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8
2-deoxy-D-ribose catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8
ethanol catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8
L-threonine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8
thymidine catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8
L-tryptophan catabolism adh med aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 (characterized) 57% 100% 989.9 aldehyde-alcohol dehydrogenase; EC 1.1.1.1; EC 1.2.1.10 96% 1691.8

Sequence Analysis Tools

View BWI76_RS17250 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MAVTNVAELNALVERVKKAQREYASFTQEQVDKIFRAAALAAADARIPLAKMAVAESGMG
IVEDKVIKNHFASEYIYNAYKDEKTCGVLSEDDTFGTITIAEPIGIICGIVPTTNPTSTA
IFKSLISLKTRNAIIFSPHPRAKDATNKAADIVLQAAIAAGAPKDLIGWIDQPSVELSNA
LMHHPDINLILATGGPGMVKAAYSSGKPAIGVGAGNTPVVIDETADIKRAVASVLMSKTF
DNGVICASEQSVVVVDSVYDAVRERFSSHGGYLLQGQELKAVQNIILKNGALNAAIVGQP
AYKIAELAGFTVPVSTKILIGEVTDVDESEPFAHEKLSPTLAMYRAKNFEDAVDKAEKLV
AMGGIGHTSCLYTDQDNQPERVAYFGQLMKTARILINTPASQGGIGDLYNFKLAPSLTLG
CGSWGGNSISENVGPKHLINKKTVAKRAENMLWHKLPKSIYFRRGSLPIALDEVITDGHK
RALIVTDRFLFNNGYADQITSVLKAAGVETEVFFEVEADPTLTIVRKGAELANSFKPDVI
IALGGGSPMDAAKIMWVMYEHPETHFEELALRFMDIRKRIYKFPKMGVKAKMVAITTTSG
TGSEVTPFAVVTDDATGQKYPLADYALTPDMAIVDANLVMEMPKSLCAFGGLDAVTHALE
AYVSVLASEFSDGQALQALKLLKENLPASYHEGSKNPVARERVHSAATIAGIAFANAFLG
VCHSMAHKLGSQFHIPHGLANALLISNVIRYNANDNPTKQTAFSQYDRPQARRRYAEIAD
HLGLTAPGDRTAAKIEKLLGWLDEIKAELGIPKSIREAGVQEADFLAHVDKLSEDAFDDQ
CTGANPRYPLIAELKQILLDTFYGRNYVEGGVEEKKEAAPAKAEKKAKKSA

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 (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:

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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