GapMind for catabolism of small carbon sources

 

Protein WP_078427781.1 in Alkalihalobacterium alkalinitrilicum DSM 22532

Annotation: NCBI__GCF_002019605.1:WP_078427781.1

Length: 472 amino acids

Source: GCF_002019605.1 in NCBI

Candidate for 28 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 57% 97% 545.8
L-citrulline catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 57% 97% 545.8
putrescine catabolism gabD hi NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 57% 97% 545.8
L-arginine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 56% 97% 545 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 57% 538.1
L-citrulline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 56% 97% 545 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 57% 538.1
L-lysine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 56% 97% 545 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 57% 538.1
L-proline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 56% 97% 545 Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 57% 538.1
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 53% 90% 495 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-arabinose catabolism xacF med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 361.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
D-galacturonate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 361.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
D-glucuronate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 361.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
D-xylose catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 361.3 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 334.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 40% 97% 334.7 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 95% 337.8 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 95% 337.8 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 39% 95% 337.8 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 99% 335.5 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 38% 99% 335.5 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-lysine catabolism amaB lo Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized) 31% 87% 231.9 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 93% 197.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 93% 197.2 NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) 57% 545.8

Sequence Analysis Tools

View WP_078427781.1 at NCBI

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Find functional residues: SitesBLAST

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Sequence

MEHYSIYINGQWLGENFEKIEVSNPATNEIIATVPKGGANEAKQAVDAAYDAFHEWSKYS
AYERAELIRKWYDLINENKEEIAKMMTAEQGKPLKEALGEMTYANGFLSWYAEEAKRIYG
ETIPATQRNKRLFVQKQPVGVVAAITPWNFPAAMITRKVAPALAAGCTVVVKPAEQTPIT
AIKMAELADKAGIPKGVINVVTGDPKAIGKVWLEDDRVRKLTFTGSTEVGKLLMRGAADT
VKKVSLELGGHAPVIVLDDADLDKTVKGVIEAKFRNAGQTCICLNRVYVHESIYETFLEK
LIPKVKELKVGNGFDEGVDIGPLIEQNAVEKVQNHIEDAVKLGAKIEIGGKIKDGLYFEP
TVLSNIDDDMLCMCEETFGPLAPVTSFKSEEEVIKRANNSIFGLAAYVFTENISRGIRIT
EALEYGIIGLNDGLPSTPQAPFGGFKQSGIGREGGHYGLEEYLEVKYISLGL

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