GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_2043 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_2043 putative ABC transport system ATP-binding protein

Length: 230 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 25 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 40% 91% 143.7 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-glucosamine, ATPase component (characterized) 40% 86% 140.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 62% 146.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 62% 146.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 62% 146.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 62% 146.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 62% 146.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 62% 146.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 39% 89% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
L-lysine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 39% 89% 136 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
trehalose catabolism thuK lo Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 36% 54% 135.6 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 52% 134.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 36% 56% 133.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 34% 58% 132.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 38% 52% 132.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 58% 129.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 53% 127.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 33% 57% 125.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 35% 60% 125.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 34% 60% 124.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 34% 58% 121.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 53% 121.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
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) 33% 55% 116.3 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 31% 55% 115.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 31% 88% 110.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 44% 200.7

Sequence Analysis Tools

View N515DRAFT_2043 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

MSMGTLIEVRDLSKVYERGKQKVEVLHHINLNIAEGDFLALMGPSGSGKTTLLNLIGGLD
SPTGGSIGVGGQRIDQLGAGALAKWRAANVGFVFQFYNLMPMLTAQRNVELPLLLTKLSA
AQRRKNAAIALQLVGLDERSSHKPSELSGGQQQRVAIARAIVSDPTLLVCDEPTGDLDRQ
SAEDVLGLLRTLNREHGKTIVMVTHDPKAAEYANHTLHLDKGTLVEQALA

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