GapMind for catabolism of small carbon sources

 

Protein WP_110206341.1 in Nocardioides daejeonensis MJ31

Annotation: NCBI__GCF_003194585.1:WP_110206341.1

Length: 498 amino acids

Source: GCF_003194585.1 in NCBI

Candidate for 32 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% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
2'-deoxyinosine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
2-deoxy-D-ribose catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
ethanol catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
L-threonine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
thymidine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
L-tryptophan catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 48% 94% 428.7 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 45% 402.1
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 44% 95% 385.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 94% 384 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 94% 384 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 43% 94% 384 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 43% 98% 377.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 43% 98% 377.9 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 44% 97% 368.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 44% 97% 368.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 44% 97% 368.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 44% 97% 368.2 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 43% 94% 350.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 43% 94% 350.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 43% 94% 350.1 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-lysine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 98% 330.5 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 39% 94% 305.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 291.6 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 98% 291.6 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 89% 253.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 89% 253.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 89% 253.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 89% 253.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 36% 89% 253.8 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 32% 95% 227.3 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 218.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 34% 94% 218.4 acetaldehyde dehydrogenase (EC 1.2.1.3) 54% 501.1

Sequence Analysis Tools

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

MVSTGSTQRVSTGSITGGFDYAPAPESRAIVDIKPSYGLFVNGEFVDGAGASFKTINPAT
EEVLAEIAEANAADVDAAVRAARRAYARVWSKMPGKERAKYLFRIARILQERARELAVLE
SIDNGKPIKEARDVDVPVAAAHFFYYAGWADKLEYALPGNAHSGVRSLGVAAQVIPWNFP
LLMLAWKIAPALAAGNTVVLKPAETTPLTALLFAEICQQADLPAGVVNIVTGAGDTGQAL
VGHADVDKVAFTGSTEVGKAIARTVAGTDKRVTLELGGKAANIVFDDAPLDQAIEGIVSG
IFFNQGHVCCAGSRLLVQESVADEVLERLKSRMGTLRVGDPLDKNTDIGAINSAEQLARI
RELSAIGEQEVAGERWSPPCELPERGFWFPPTIFTGVTQAHRIAREEIFGPVLSVLTFRT
PAEAVEKANNTPYGLSAGVWTEKGSRILWMADQLRAGVVWANTFNKFDPTSPFGGYKESG
YGREGGRHGLEGYLKGTE

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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