GapMind for catabolism of small carbon sources

 

Protein WP_024981057.1 in Flavobacterium sp. LM5

Annotation: NCBI__GCF_002017945.1:WP_024981057.1

Length: 220 amino acids

Source: GCF_002017945.1 in NCBI

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 artP lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 85% 141.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 37% 85% 141.4 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 35% 84% 137.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 33% 57% 130.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 32% 56% 124.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 58% 122.9 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-isoleucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-leucine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-valine catabolism livF lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 86% 112.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 90% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 32% 90% 108.2 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 32% 86% 102.8 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 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) 32% 86% 100.5 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 85% 92 lipoprotein releasing system, ATP-binding protein; EC 3.6.3.- 46% 200.7

Sequence Analysis Tools

View WP_024981057.1 at NCBI

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

MILAKNIHKFYDQLEVLKGVDLHITKGEIVSIVGASGAGKTTLLQILGTLDRPTSNENSS
LLINGEDVLKMNDKALSRFRNLNLGFIFQFHQLLPEFTALENVCIPAFIAGKNKLETEIE
AKKLLDYLGLSHRHHHKPNELSGGEQQRVAVARALINKPDILFADEPSGNLDTTSAENLH
QLFFKLRDELGQTFVIVTHNEELANMADRKLVMVDGQISA

This GapMind analysis is from Sep 24 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