GapMind for catabolism of small carbon sources

 

Protein GFF501 in Phaeobacter inhibens BS107

Annotation: PGA1_c05130 aldehyde dehydrogenase

Length: 476 amino acids

Source: Phaeo in FitnessBrowser

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-arabinose catabolism xacF hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 65% 99% 621.3
D-galacturonate catabolism dopDH hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 65% 99% 621.3
D-glucuronate catabolism dopDH hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 65% 99% 621.3
D-xylose catabolism dopDH hi Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) (characterized) 65% 99% 621.3
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 95% 332 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 95% 332 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized) 40% 95% 332 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 272.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 272.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 272.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 272.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 272.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 97% 272.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
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) 35% 92% 266.2 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
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) 35% 92% 266.2 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
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) 35% 92% 266.2 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
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) 35% 92% 266.2 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
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) 35% 92% 266.2 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-lysine catabolism amaB lo Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale) 34% 89% 233 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 35% 95% 232.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; EC 1.2.1.71; Succinylglutamic semialdehyde dehydrogenase; SGSD (uncharacterized) 35% 95% 232.3 Ketoglutarate semialdehyde dehydrogenase (EC 1.2.1.26) 65% 621.3

Sequence Analysis Tools

View GFF501 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MEYKNLIAGDWSETVAAAANINPSDTQDVLGYAANSPAEDMERAIAAARDAAPGWASSTP
QQRFDVLDAIGTEILARKAELGKLLSREEGKTLPEGIGEAARAGQIFKFFAGETLRQAGE
ILGSVRPGVGVEVTRSPVGVVGLITPWNFPIAIPAWKIAPALAYGDAVVLKPAELTPGCA
HALAEIINRSGLPEGVFNIVFGTGSTVGQTLVQSRHVDAISFTGSVETGSAIAAACGAQR
KKLQLEMGGKNPMVVLDDADLETAVDASLNGAFFSTGQRCTASSRLIVTEGIHDRFVAAL
GERMTGLRVGNALDDSTQIGPVVDERQLEKDLYYLDVAASEGGQVLGGQTLQRSTKGFYL
APALVTETSNDMRINQEEVFGPLASVIRVADYDEALVVANDTPFGLSAGICTGSLKYATH
FKAHAEAGMAMVNLPTAGVDYHVPFGGTKGSSFGAREQGSHAKEFYTKVKTAYTLA

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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