GapMind for catabolism of small carbon sources

 

Protein YP_004139497.1 in Mesorhizobium ciceri WSM1271

Annotation: NCBI__GCF_000185905.1:YP_004139497.1

Length: 479 amino acids

Source: GCF_000185905.1 in NCBI

Candidate for 17 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arabinose catabolism xacF hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 80% 100% 763.5
D-galacturonate catabolism dopDH hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 80% 100% 763.5
D-glucuronate catabolism dopDH hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 80% 100% 763.5
D-xylose catabolism dopDH hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 80% 100% 763.5
L-isoleucine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 273.5 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
myo-inositol catabolism mmsA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 273.5 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
propionate catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 273.5 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-threonine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 273.5 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-valine catabolism iolA lo malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized) 36% 96% 273.5 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-arginine catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 37% 91% 272.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-arginine catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 37% 91% 272.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-citrulline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 37% 91% 272.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-citrulline catabolism rocA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 37% 91% 272.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-proline catabolism putA lo 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized) 37% 91% 272.7 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 37% 94% 245.4 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 37% 94% 245.4 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5
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) 32% 89% 233.8 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 80% 763.5

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MTLFRKNLIDGEWVGDAGSRNINPSDTGDVVGDYASAGVEQAQQAIAAAKAAFPAWSRSG
PLARHAVLKKASDEILARKDEIGRNLAREEGKTLAEGIGETIRAAQIFDFFAGETLRLTG
EVVPSVRPGVGVEMTREAVGVVGIITPWNFPIAIPAWKIAPALTHGNTVVFKPAELVPES
AWTIVDILHRAGLPKGVLNLVMGKGSVVGQAMLDSPDVNAISFTGSVGTGKRVAAASIEH
MRKFQLEMGGKNPLVVLDDADLAIAVDCALNGAFFSTGQRCTASSRLIVADGIHDRFVDA
LKDRMSKLVIGDALDAQTQIGPVVDATQLKQDEDYIAIGVREGATLAFGGERLDRKTPGF
YLQPALLTEATNAMRSSREEIFGPVASVIRVKDYDEALSVANDTPFGLTSGICTSSLKHA
THFKRNSEAGMVMVNLPTAGVDFHVPFGGRKGSSYGPREQGHYAAEFYTTVKTAYTFAG

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