GapMind for catabolism of small carbon sources

 

Protein WP_018372458.1 in Streptococcus massiliensis 4401825

Annotation: NCBI__GCF_000341525.1:WP_018372458.1

Length: 209 amino acids

Source: GCF_000341525.1 in NCBI

Candidate for 22 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-asparagine catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 43% 86% 185.3 glutamine ABC transporter, ATP-binding protein GlnQ 43% 184.1
L-aspartate catabolism aatP med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 43% 86% 185.3 glutamine ABC transporter, ATP-binding protein GlnQ 43% 184.1
L-glutamate catabolism gltL med Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 43% 86% 185.3 glutamine ABC transporter, ATP-binding protein GlnQ 43% 184.1
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 44% 87% 176.8 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 44% 87% 176.8 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 43% 78% 175.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 43% 78% 175.3 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 42% 80% 172.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 42% 80% 172.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 42% 80% 172.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-histidine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 42% 80% 172.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 42% 80% 172.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 42% 80% 172.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 40% 81% 164.5 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 41% 83% 158.7 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-arginine catabolism artP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 39% 84% 167.5 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 39% 84% 167.5 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 40% 81% 164.1 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 39% 82% 162.2 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 38% 61% 144.8 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 40% 54% 140.6 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 62% 136 Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter 43% 185.3

Sequence Analysis Tools

View WP_018372458.1 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

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Sequence

MLELRNISKKFGNKQILTNFNLVVPENKILAIVGPSGGGKTTLLRMLAGLEKIDSGQVFF
NGEELPLDELENRSPLGFVFQDFQLFPHLSVMENLTLSPIQTMKLSQSDAETRALKLLKR
LNLAEHVNAYPFSLSGGQKQRVALARAMMIEPQIIGYDEPTSALDPALRQEVEKLIVQNR
EMGITQIVVTHDMQFAQDIADEILEVQPK

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