GapMind for catabolism of small carbon sources

 

Protein WP_148648326.1 in Sphingobium czechense LL01

Annotation: NCBI__GCF_001046645.1:WP_148648326.1

Length: 495 amino acids

Source: GCF_001046645.1 in NCBI

Candidate for 42 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) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
2'-deoxyinosine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
2-deoxy-D-ribose catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
ethanol catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
L-threonine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
thymidine catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
L-tryptophan catabolism adh hi Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized) 52% 96% 495 aldehyde dehydrogenase [NAD(P)+] (EC 1.2.1.5) 52% 468.0
L-phenylalanine catabolism pad-dh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 50% 94% 446.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 96% 410.2 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 96% 410.2 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 96% 410.2 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 45% 96% 410.2 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
4-hydroxybenzoate catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 43% 97% 409.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-tryptophan catabolism praB med 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 43% 97% 409.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 45% 96% 401 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 45% 96% 401 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 45% 96% 401 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-fucose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 95% 394.4 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-rhamnose catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 95% 394.4 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-threonine catabolism aldA med NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 44% 95% 394.4 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arginine catabolism davD med Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 98% 355.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-citrulline catabolism davD med Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 98% 355.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-lysine catabolism davD med Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 98% 355.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-proline catabolism davD med Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 41% 98% 355.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-tryptophan catabolism nbaE med aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 40% 96% 344.4 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 38% 99% 325.5 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arabinose catabolism xacF lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 319.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
D-galacturonate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 319.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
D-glucuronate catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 319.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
D-xylose catabolism dopDH lo Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized) 38% 97% 319.3 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 92% 263.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 92% 263.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 92% 263.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 92% 263.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 33% 92% 263.8 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 93% 258.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 93% 258.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 93% 258.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 93% 258.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 35% 93% 258.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 35% 94% 258.1 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0
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) 30% 86% 202.6 Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 52% 495.0

Sequence Analysis Tools

View WP_148648326.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MNMMTIPPRPALLDTPDQDMLIDGQRVPALSGKRFETRNPATGELLATIAQGGPEDVDRA
VKAARAAFEGPWRRMKPVERQRIMLRLADLVEAHFEELAMLDTLDLGAPYSRTIMGKARA
GALLRYYAGQAMLITGDTIDNNAPGDVLSHTLKEPIGVVAAINPWNGPIGMSVWKAGPVL
ATGCTLVMKPAEQTPLSALRFGELCLEAGVPEGVINIVTGLGDAGAALSSHPDVDKIAFT
GSTGVGEKILHAAAASMKRVTVELGGKSPNIVFADADLDKAVPAAAMAVFANAGQICSAG
TRLFVQNAIHDEFMERLAAFTKTIKVGDPLDPTTQMGPVVSAPQMDKILAFIAGANTEGA
RPLTGGGRMSGAGYDAGYFIEPTIFTHVADDMTIAREEIFGPVLSAFTFDTVDEVLARAN
ATEFGLGSGVWTRDLGTAHRMARGIRAGSVWVNCYQMLDPAVPFGGYKMSGFGRESGPHH
IEDYLETKAVWINLD

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