GapMind for catabolism of small carbon sources

 

Protein GFF3174 in Phaeobacter inhibens BS107

Annotation: FitnessBrowser__Phaeo:GFF3174

Length: 494 amino acids

Source: Phaeo in FitnessBrowser

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-arginine catabolism kauB med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 50% 96% 471.9 aldehyde dehydrogenase 51% 475.7
L-arginine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 50% 96% 471.9 aldehyde dehydrogenase 51% 475.7
L-citrulline catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 50% 96% 471.9 aldehyde dehydrogenase 51% 475.7
putrescine catabolism puuC med 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 50% 96% 471.9 aldehyde dehydrogenase 51% 475.7
L-arginine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 95% 442.2 aldehyde dehydrogenase 51% 475.7
L-arginine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 95% 442.2 aldehyde dehydrogenase 51% 475.7
L-citrulline catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 95% 442.2 aldehyde dehydrogenase 51% 475.7
L-citrulline catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 95% 442.2 aldehyde dehydrogenase 51% 475.7
putrescine catabolism gabD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 95% 442.2 aldehyde dehydrogenase 51% 475.7
putrescine catabolism patD med 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 49% 95% 442.2 aldehyde dehydrogenase 51% 475.7
L-fucose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 97% 334.3 aldehyde dehydrogenase 51% 475.7
L-rhamnose catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 97% 334.3 aldehyde dehydrogenase 51% 475.7
L-threonine catabolism aldA lo NAD(P)+ L-lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized) 39% 97% 334.3 aldehyde dehydrogenase 51% 475.7
L-phenylalanine catabolism pad-dh lo phenylacetaldehyde dehydrogenase (EC 1.2.1.39) (characterized) 40% 98% 321.2 aldehyde dehydrogenase 51% 475.7
L-arginine catabolism putA lo delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized) 32% 85% 175.6 aldehyde dehydrogenase 51% 475.7
L-citrulline catabolism putA lo delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized) 32% 85% 175.6 aldehyde dehydrogenase 51% 475.7
L-proline catabolism putA lo delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial; EC 1.5.1.12 (characterized) 32% 85% 175.6 aldehyde dehydrogenase 51% 475.7

Sequence Analysis Tools

View GFF3174 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

MDQTKIDTLRAQPVPCFSHLIDGQQVAASDGATMDVLSPIDGRLLTQIARGTVRDMERAI
ASARAAFEDRRWAGQPPAARKKVLMKWAELIEADALNLAVLGVRDNGTEITMALKAEPGS
AAATIRYYAEALDKIYGEIAPTSSDVLGMVHKEPVGVVGAIIPWNFPMMIGAWKLAPALA
MGNSVVLKPSETASLSLMRMVELALEAGLPPGVLNAVTGEGAVVGEALGLSMDVDVLVFT
GSGQTGRRLMEYAARSNLKRVYLELGGKSPNIVFADAPDLADAAKVTAAGIFRNSGQVCV
AGSRLLVEASIHDAFVEEVAKAAQMMRVGDPLRLDTQIGAINSEAQLARNLQFVARAEVE
GGQIITGGQRLLSETGGSYMAPTIVTGVTPDATLAQEEVFGPVLAVTPFETDAEALRIAN
ATVYGLAGAVWTSGLTRAHRMVQGVRTGVMHVNTYGGADGTVPLGGVGQSGNGADKSLHA
IDKYINLKTAWMKL

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