GapMind for catabolism of small carbon sources

 

Protein WP_034525974.1 in Lactobacillus oryzae SG293

Annotation: NCBI__GCF_000740055.1:WP_034525974.1

Length: 469 amino acids

Source: GCF_000740055.1 in NCBI

Candidate for 13 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 93% 413.7 Proline-specific permease (ProY) 44% 405.6
L-alanine catabolism cycA med L-alanine and D-alanine permease (characterized) 45% 93% 413.7 Proline-specific permease (ProY) 44% 405.6
L-proline catabolism proY med Proline-specific permease (ProY) (characterized) 44% 99% 405.6 L-alanine and D-alanine permease 45% 413.7
L-threonine catabolism RR42_RS28305 med D-serine/D-alanine/glycine transporter (characterized, see rationale) 42% 96% 385.2 L-alanine and D-alanine permease 45% 413.7
L-histidine catabolism permease med histidine permease (characterized) 41% 97% 382.5 L-alanine and D-alanine permease 45% 413.7
L-tryptophan catabolism aroP med Aromatic amino acid transport protein AroP (characterized, see rationale) 41% 96% 365.5 L-alanine and D-alanine permease 45% 413.7
phenylacetate catabolism H281DRAFT_04042 med Aromatic amino acid transporter AroP (characterized, see rationale) 40% 95% 355.5 L-alanine and D-alanine permease 45% 413.7
L-phenylalanine catabolism aroP lo Aromatic amino acid transport protein AroP (characterized, see rationale) 40% 96% 354.8 L-alanine and D-alanine permease 45% 413.7
L-tyrosine catabolism aroP lo L-tyrosine transporter (characterized) 39% 98% 350.9 L-alanine and D-alanine permease 45% 413.7
D-serine catabolism cycA lo D-serine/D-alanine/glycine transporter (characterized) 39% 93% 339.3 L-alanine and D-alanine permease 45% 413.7
L-serine catabolism serP lo Serine transporter, SerP2 or YdgB, of 459 aas and 12 TMSs (Trip et al. 2013). Transports L-alanine (Km = 20 μM), D-alanine (Km = 38 μM), L-serine, D-serine (Km = 356 μM) and glycine (Noens and Lolkema 2015). The encoding gene is adjacent to the one encoding SerP1 (TC# 2.A.3.1.21) (characterized) 37% 96% 296.2 L-alanine and D-alanine permease 45% 413.7
L-lysine catabolism lysP lo Lysine permease LysP (characterized) 37% 89% 288.1 L-alanine and D-alanine permease 45% 413.7
L-threonine catabolism serP1 lo Serine uptake transporter, SerP1, of 259 aas and 12 TMSs (Trip et al. 2013). L-serine is the highest affinity substrate (Km = 18 μM), but SerP1 also transports L-threonine and L-cysteine (Km values = 20 - 40 μM) (characterized) 36% 97% 273.5 L-alanine and D-alanine permease 45% 413.7

Sequence Analysis Tools

View WP_034525974.1 at NCBI

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

MQRKLSARQMQMIALGGTIGVGLFMGSTSTIKWTGPSVLIAYGIAGIFLYFIMRALGEML
YVDPDTGSFSKFATEYMHPVFGYLTAWSNIFQFIVVGMSEMIAIGGYMEFWWPGLPDWIP
GLIAILFLSLANLISVKMFGELEFWFSLIKVVTIILMIVAGLGLIIFGIGNHMHPIGISN
MWTNGGFFTGGVKGFIFALSIVLASYQGIELIGVTAGEAENPRHTLVKAIQSTVARILIF
YIGAIFVIVSIYPWNKLDALGSPFVETFAKIGITAAASIINFVVVTAALSGSNSGIYSAS
RMAFTLANRGELPKGFLKLNRHGVPYWSVIAISLGIFLGVVLNFLIPIFWPDASNIFVLV
YSSSVLPGMIPWFVILISEIRFRKVHQDKMGDHPFKMPFAPVSNYITIFFLVLTLLFMFV
NPETRVSIIVGVIFLAIMTILYFVKFHGNEEEAIAKSKQGEEAVKNDKF

This GapMind analysis is from Sep 24 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:

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