GapMind for catabolism of small carbon sources

 

Protein WP_048081777.1 in Methanobacterium arcticum M2

Annotation: NCBI__GCF_000746075.1:WP_048081777.1

Length: 226 amino acids

Source: GCF_000746075.1 in NCBI

Candidate for 14 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 35% 66% 152.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 84% 151.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 36% 84% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 89% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 89% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-alanine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-isoleucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-leucine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-proline catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-serine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-threonine catabolism braG lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-valine catabolism natE lo NatE, component of The neutral amino acid permease, N-1 (transports pro, phe, leu, gly, ala, ser, gln and his, but gln and his are not transported via NatB) (characterized) 32% 73% 100.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
D-alanine catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 77% 92.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4
L-proline catabolism AZOBR_RS08250 lo Leucine//isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale) 31% 77% 92.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 47% 201.4

Sequence Analysis Tools

View WP_048081777.1 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

MNGLINGNELWKTYKLDSTEVHALRGLNITVGEGEFVSIMGPSGSGKSTLLNMIGGLDNP
TKGDLFIDGKDISRMSEGELTRMRAEKIGFIFQTFNLLPALTVRDNVEFPMRNLNGSKKM
NKSSRIKKAEECIEIVGLGDRMDYLPAKLSGGERQRVAVARALVNNPKFILADEPTGNLD
SESTENIINLLHEVNQNETTVIMVTHDAETTKNTRIMKIRDGKIAE

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