GapMind for catabolism of small carbon sources

 

Protein GFF501 in Phaeobacter inhibens BS107

Annotation: FitnessBrowser__Phaeo:GFF501

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

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

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 (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