GapMind for catabolism of small carbon sources

 

Protein WP_107428579.1 in Streptomyces kebangsaanensis SUK12

Annotation: NCBI__GCF_001906585.1:WP_107428579.1

Length: 479 amino acids

Source: GCF_001906585.1 in NCBI

Candidate for 39 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
4-hydroxybenzoate catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
2'-deoxyinosine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
2-deoxy-D-ribose catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
ethanol catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
L-threonine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
thymidine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
L-tryptophan catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 451.4 NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) 46% 421.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 46% 94% 421.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 46% 94% 421.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 46% 94% 421.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 46% 94% 409.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 96% 387.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 42% 96% 387.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 382.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 382.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 382.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 94% 382.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 95% 360.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 95% 360.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 42% 95% 360.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 37% 96% 319.3 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 312.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 308.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 308.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 308.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 36% 96% 308.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 251.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 251.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 251.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 251.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 35% 92% 251.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 33% 95% 243.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 95% 238.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 95% 238.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 95% 238.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 95% 238.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 95% 238.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 95% 208 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 33% 95% 208 acetaldehyde dehydrogenase (EC 1.2.1.3) 57% 523.1

Sequence Analysis Tools

View WP_107428579.1 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

MTMAFEYAPAPESRAIVDIAPSYGLFIDGEFGEAADGKVFKTVSPSTEEVLSEVAQAGEA
DVDRAVEAARKAFGKWSALPGSERAKYLFRIARIIQERSRELAVLETLDNGKPIKETRDA
DLPLVAAHFFYYAGWADKLDHAGFGPDPKPLGVAGQVIPWNFPLLMLAWKIAPALATGNT
VVLKPAETTPLSALFFADICRQAGLPKGVVNILPGYGDAGAALVAHPDVNKVAFTGSTAV
GKEIARTVAGTRKKLTLELGGKGANIVFDDAPIDQAVEGIVSGIFFNQGQVCCAGSRLLV
QESIHDELLDSLKRRLSTLRLGDPLDKNTDIGAINSAEQLARITALAEQGEAEGAERWSP
ACELPSSGYWFAPTLFTNVTQAHTIARDEIFGPVLSVLTFRTPDEAVAKANNTPYGLSAG
IWTEKGSRILAVANKLRAGVIWSNTFNKFDPTSPFGGYKESGFGREGGRHGLEAYLDVR

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