GapMind for catabolism of small carbon sources

 

Protein WP_013519729.1 in Alicycliphilus denitrificans K601

Annotation: NCBI__GCF_000204645.1:WP_013519729.1

Length: 495 amino acids

Source: GCF_000204645.1 in NCBI

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 95% 383.6 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 95% 383.6 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 95% 383.6 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 95% 383.6 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 43% 92% 382.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 97% 374.8 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 97% 374.8 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 42% 97% 374.8 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 360.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 41% 97% 360.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 98% 355.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 98% 355.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 98% 355.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 98% 355.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 98% 355.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 41% 98% 355.5 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 41% 92% 311.6 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 319.3 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 319.3 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 319.3 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 37% 98% 319.3 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
L-arabinose catabolism xacF lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 39% 98% 311.2 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
D-galacturonate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 39% 98% 311.2 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
D-glucuronate catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 39% 98% 311.2 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8
D-xylose catabolism dopDH lo Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 39% 98% 311.2 4-hydroxymuconic-semialdehyde dehydrogenase (EC 1.2.1.61) 43% 409.8

Sequence Analysis Tools

View WP_013519729.1 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

MPQDSALLPRYEHLYINGEWVTPIDGELVESIDPATGRPWAIAPLGGARDIDRAVEAARR
AFPAWSRKPGHERAALLRRLADLFAAAIPELAVIESHDNGNLVREHRASLTAQVQWYQWF
ASLADKAQGTTIPIDDSVHAFTTRVPVGVVGAIIPWNAPLLATCLKVGAALAAGCTLVVK
PAESTPVSALVLARLVHEAGFPPGVFNVVPGHGRTAGQRLVEHPDVDKVSFTGSTATARR
MVRDGADNLKRFTFELGGKAPHILFADADIDNAINAATASAWRLTGQSCALGSRVLVERS
IYDRVVEAFRERAKAVRVGLPWIDANHMGPQAHQQQLDKTLSYIQYGKEDGAELVTGGRR
IDTPELAAGYFVEPTVFAGVDNGMRIARDEIFGPVASLIPFDGEDEAIAIANDTPYGLTA
GLWTRDVGRAHRVSSRIEAGMVWVNTYSFLRWSTPYGGFKASGWGRENGIDALDPYLETR
TTVISTTGQFPNLYV

This GapMind analysis is from Apr 09 2024. 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