GapMind for catabolism of small carbon sources

 

Protein YP_004142598.1 in Mesorhizobium ciceri WSM1271

Annotation: NCBI__GCF_000185905.1:YP_004142598.1

Length: 485 amino acids

Source: GCF_000185905.1 in NCBI

Candidate for 21 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 62% 100% 613.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
L-citrulline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 62% 100% 613.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
L-lysine catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 62% 100% 613.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
L-proline catabolism davD hi Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- (characterized) 62% 100% 613.2 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
L-arginine catabolism gabD med NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 60% 100% 595.5 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
L-citrulline catabolism gabD med NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 60% 100% 595.5 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
putrescine catabolism gabD med NAD(P)-dependent succinate-semialdehyde dehydrogenase (EC 1.2.1.16) (characterized) 60% 100% 595.5 3-sulfolactaldehyde dehydrogenase; SLA dehydrogenase; EC 1.2.1.97 59% 595.1
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 55% 92% 534.3 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
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) 44% 97% 386 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
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) 44% 97% 386 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
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) 44% 97% 386 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
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) 44% 97% 386 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 97% 333.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 97% 333.6 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2
L-valine catabolism mmsA lo Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized) 31% 88% 238.4 Glutarate-semialdehyde dehydrogenase; EC 1.2.1.- 62% 613.2

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Predict protein localization: PSORTb

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Sequence

MLQKTSHFMRQANLINGEWVQADSGQTVDVNNPATGLKIGTVPKSGKAETRRAIEAAAEA
FKTWRKTTALERSKLLRKLHDAMMDNQDVLAELLTIEQGKSLFESKGEIGSAASYILWFA
EEGRRTYGDVVPSPWADRRILVTKEPVGVIAAITPWNFPSSMLARKLGPALAAGCTAVVK
PASQTPYSGLAWGALAEEVGFPKGVVNILTGSASEIGDEICANPLVSKITFTGSTEVGKL
LIQKSSVTVKKVSMELGGNAPFIVFDDADLERAVAGAITAKYRNSGQTCVCTNRFLVQAG
VYDKFVEKLAAASNALKVGSGLEDGVQQGPLIDEKAVEKVEELIADATSKGGKIVAGGKR
HALGGSFFQPTVIANATPKMRFMKEEIFGPVAPVFKFETEEEAVALANDTEFGLACYFYT
GDLGRAFRVMEGLKYGMVGVNEGLITTPEAPFGGVKESGLGKEGGHQGIEDYLDTKYVCI
GGLGL

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