GapMind for catabolism of small carbon sources

 

Protein WP_109968015.1 in Methanospirillum lacunae Ki8-1

Annotation: NCBI__GCF_003173355.1:WP_109968015.1

Length: 473 amino acids

Source: GCF_003173355.1 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
L-fucose catabolism aldA lo Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 35% 97% 292.7 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-rhamnose catabolism aldA lo Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 35% 97% 292.7 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-threonine catabolism aldA lo Lactaldehyde dehydrogenase; EC 1.2.1.22 (uncharacterized) 35% 97% 292.7 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arginine catabolism gabD lo 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 (characterized) 35% 89% 270.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-citrulline catabolism gabD lo 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 (characterized) 35% 89% 270.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
putrescine catabolism gabD lo 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 (characterized) 35% 89% 270.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arginine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 250.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-citrulline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 250.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-lysine catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 250.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-proline catabolism davD lo Glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 35% 94% 250.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 34% 96% 248.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
4-hydroxybenzoate catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
2'-deoxyinosine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
2-deoxy-D-ribose catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
ethanol catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-threonine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
thymidine catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-tryptophan catabolism adh lo Phosphonoacetaldehyde dehydrogenase; EC 1.2.1.- (characterized) 32% 95% 246.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 31% 98% 238.4 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 31% 98% 238.4 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arginine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 93% 233.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 93% 233.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-citrulline catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 93% 233.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 93% 233.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
putrescine catabolism patD lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 93% 233.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 34% 93% 233.8 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 31% 93% 231.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 32% 95% 231.1 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 220.7 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 31% 96% 220.7 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 31% 95% 220.7 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arabinose catabolism xacF lo 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) 32% 98% 219.9 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
D-galacturonate catabolism dopDH lo 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) 32% 98% 219.9 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
D-glucuronate catabolism dopDH lo 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) 32% 98% 219.9 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
D-xylose catabolism dopDH lo 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) 32% 98% 219.9 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized) 30% 92% 194.9 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
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% 81% 192.2 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 89% 182.6 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 31% 89% 182.6 Sulfoacetaldehyde dehydrogenase; EC 1.2.1.73 38% 309.7

Sequence Analysis Tools

View WP_109968015.1 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

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Sequence

MDDWACIVGGVERRSEDRYLVVNPFSGEVVGQVSRCSAEDIEEALQAATAGSTVTAELAA
HQRATVLRRLVDLMTAHREEFITLLIAEGGKPRRNAEGETARAIETILISAEEAVRIGGE
VIPLDRTVPGEGCIGIVQRFPVGVVLGITPFNFPLNLACHKLGPAVASGNAIILKPASAT
PLSSLLLGRLLLEAGYPPAAVSVLICSPDDAERLAADQRIGCFSFTGSPEVGWHLRSRAT
YAKVTLELGGNGAVIVHEDCDLSHAASRIIEGGFSQAGQVCISVQRVFVHRPVFEPLLTR
LGELADGLVVGDPSDPKTDVGSMISKEAAEHALKRIQDACSAGATLIKGGSLSGSLLQPT
ILTGTKAGMEVNCREVFAPIITVTPYDTFEQAVADVNDSVYGLQAGVFTRDLLRVRYAFS
HLKVGTVVIGDIPTFRVDMMPYGGVKRSGSGREGPRYAIEEMTDTRMMIIRDP

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