GapMind for catabolism of small carbon sources

 

Protein GFF2209 in Marinobacter adhaerens HP15

Annotation: HP15_2163 sugar ABC transporter, ATP-binding protein

Length: 366 amino acids

Source: Marino in FitnessBrowser

Candidate for 9 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
glycerol catabolism glpT hi GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 52% 100% 369.4 Oligosaccharides import ATP-binding protein MsmX; Maltodextrin import ATP-binding protein MsmX; Melibiose/raffinose/stachyose import ATP-binding protein MsmX; EC 7.5.2.- 36% 233.8
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 95% 230.7 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 37% 94% 220.3 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 37% 90% 218 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 92% 217.6 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 89% 215.3 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 36% 95% 211.8 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
trehalose catabolism malK lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 36% 95% 211.8 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 37% 92% 208.8 GlpT, component of Glycerol uptake porter, GlpSTPQV 52% 369.4

Sequence Analysis Tools

View GFF2209 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

MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ
PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV
HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR
RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF
IGSPGMNLIEVQRCPRGVCFGSTVVSLESWQVDVLQRTRSTNIKIGIRPEFVEVSSVASD
DTFEAEVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHLSFPRQWLKLYVDEF
LVQEQQ

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 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