GapMind for catabolism of small carbon sources

 

Protein 200919 in Shewanella oneidensis MR-1

Annotation: SO1755 phosphoglucomutase/phosphomannomutase family protein (NCBI ptt file)

Length: 573 amino acids

Source: MR1 in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism pgmA med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 38% 338.6
2'-deoxyinosine catabolism deoB med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) 39% 334.7
D-galactose catabolism pgmA med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 38% 338.6
lactose catabolism pgmA med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 38% 338.6
sucrose catabolism pgmA med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 38% 338.6
thymidine catabolism deoB med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) (EC 5.4.2.2) 39% 334.7
trehalose catabolism pgmA med Phosphoglucomutase-2; PGM 2; Glucose phosphomutase 2; Phosphodeoxyribomutase; Phosphoglucomutase-1; Phosphopentomutase; EC 5.4.2.2; EC 5.4.2.7 (characterized) 37% 92% 342.4 Probable phosphoribomutase; PRM; Phosphoglucomutase 3 homolog; PGM 3 homolog; EC 5.4.2.7 38% 338.6

Sequence Analysis Tools

View 200919 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNTHLQLQIQHWLKNDPDPSTQAQLQALIDSGNEAELAARFAGRLEFGTAGLRGVVGAGP
MGMNRLVIRQTSAGLGAYLLEQIHDVAERGVVIGYDGRHDSYTFAHDTASVLTAMGIKVR
LTAKVAPTPLVAFGVKHFNAAAGIVVTASHNPPQYNGYKVYWENGAQIIPPHDSGIAAKI
EQAATQAIPFMELDDAIKQGKLIWLNDDYYETYRRGVMHAKVLQNHTAPEKVSLAYTAMH
GVGADMAETVLKDAGFTQVYSVAAQREPDGDFPTVNFPNPEEKGAMDLVIAEAKKHSAML
ACANDPDADRFAVAVRKDDGEYQMLTGDQVGVLFGHYLLSHASADQRLVGTTIVSSSLLS
KIANGFGVESYTTLTGFKWLMNVGIAQSQPDNQFLFAYEEALGYTVGNMVWDKDGLSALV
AFAQLTAELAAKGQTIWDRLEQIYREQGFHLNAQASIALKPETPNIGAYLREHPPLTIGE
HAVVSTDDLKALSRRFADGKVENINLPASDVLTYRLSNGARVIVRPSGTEPKIKCYYEVV
EPMTAQDTLATAQARATQAMEAFISAHQASLPK

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, the preprint on GapMind for carbon sources, 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