GapMind for catabolism of small carbon sources

 

Protein WP_087505828.1 in Neiella marina J221

Annotation: NCBI__GCF_002165625.1:WP_087505828.1

Length: 493 amino acids

Source: GCF_002165625.1 in NCBI

Candidate for 49 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 44% 99% 416.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-fucose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 44% 99% 416.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-rhamnose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 44% 99% 416.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-threonine catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 44% 99% 416.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
D-xylose catabolism aldA med lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 44% 99% 416.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 40% 98% 362.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 40% 98% 362.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
putrescine catabolism gabD lo succinate-semialdehyde dehydrogenase (NAD+) (EC 1.2.1.24) (characterized) 40% 98% 362.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 99% 357.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 99% 357.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-lysine catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 99% 357.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-proline catabolism davD lo glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 39% 99% 357.1 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
4-hydroxybenzoate catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
2'-deoxyinosine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
2-deoxy-D-ribose catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
ethanol catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-threonine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
thymidine catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-tryptophan catabolism adh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 39% 90% 349.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-phenylalanine catabolism pad-dh lo aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 37% 92% 320.9 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arabinose catabolism xacF lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 37% 99% 317.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
D-galacturonate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 37% 99% 317.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
D-glucuronate catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 37% 99% 317.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
D-xylose catabolism dopDH lo Alpha-ketoglutarate semialdehyde dehydrogenase; KGSADH; EC 1.2.1.26 (characterized) 37% 99% 317.8 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 37% 97% 309.3 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 37% 97% 309.3 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
putrescine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19); betaine-aldehyde dehydrogenase (EC 1.2.1.8) (characterized) 37% 97% 309.3 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 96% 296.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 34% 96% 296.2 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 98% 288.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 98% 288.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 98% 288.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
putrescine catabolism puuC lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 36% 98% 288.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-lysine catabolism patD lo aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 36% 98% 277.3 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-tryptophan catabolism nbaE lo 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized) 32% 100% 268.5 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 253.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 253.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 253.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 253.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 32% 91% 253.4 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 240.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 240.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 240.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 240.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 240.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 31% 98% 240.7 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
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% 89% 240 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 94% 183 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 30% 94% 183 3,6-anhydro-alpha-L-galactose dehydrogenase; AHG dehydrogenase; EC 1.2.1.92 74% 726.9

Sequence Analysis Tools

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Predict transmenbrane helices: Phobius

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Sequence

MLRPAQSQHGAQAVKDYQLFINGQWQDSVTGATVEVLSPSTGEVVATIQDGNEVDAEAAL
KAAEQAQQQWKKLPARQRADLLRDFCTEIKNNREKLATLLTSEQGKLLKVARFEVDVCCS
FIEYACDWARQMDGDIVQSDNANEHIWIHKIPRGVVVGITAWNFPLALAGRKIGPALVAG
NTIVLKPTSETPLATLELADIANKVGIPPGVLNIVTGPGRTMGDALCRHPITKMVSMTGS
TPAGQAIIKATADNMAHCQLELGGKAPFIVLEDADLEQAANAALHSRFDNCGQVCTCNER
MYVQESVYDEFMNIFMPKVKALKVGDPMDESVDMGPKVNKKELDHMKELVAVSVKEGATV
AYGGKEAAVEGFEGGNWFEPTILTDVTQDMTIVHEESFGPILPVVKFTTLEQAIEYANDA
DYGLAAMVCTKDMKNIMRLTDELECGEIYINRGHGEQHQGFHNGYKLSGTGGEDGKYGFE
QYLEKKTFYVNYD

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