GapMind for catabolism of small carbon sources

 

Protein WP_109968115.1 in Methanospirillum lacunae Ki8-1

Annotation: NCBI__GCF_003173355.1:WP_109968115.1

Length: 329 amino acids

Source: GCF_003173355.1 in NCBI

Candidate for 20 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 94% 135.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 94% 135.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 94% 135.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 34% 94% 128.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-alanine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 123.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-serine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 123.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-threonine catabolism braF lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 95% 123.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-alanine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 92% 121.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-isoleucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 92% 121.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-leucine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 92% 121.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-serine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 92% 121.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-threonine catabolism braG lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 92% 121.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-valine catabolism livF lo High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 35% 92% 121.3 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-phenylalanine catabolism livF lo high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized) 35% 95% 120.6 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 87% 107.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 87% 107.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 31% 87% 107.8 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-arginine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 87% 102.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-glutamate catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 87% 102.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5
L-histidine catabolism braG lo ATP-binding component of a broad range amino acid ABC transporter (characterized, see rationale) 31% 87% 102.1 Linearmycin resistance ATP-binding protein LnrL; EC 7.6.2.- 38% 216.5

Sequence Analysis Tools

View WP_109968115.1 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

MTPIIKTFNLTKIFGSNTAVNSISLEVHKGEVFGLLGPNGAGKTTFLSMLCTILKPTSGT
AVINGYDIVQDSAMVRRSIGIVFQDPSVDTDMTSRENLQMHADLYDVPVSEQASRIQEVL
TLVQLEDRADDFLNTYSGGMRRRLEIARGLLHYPRVLFLDEPTIGLDPQSREHIWSYIRQ
LREREDMTLILTTHYMEEADELCDRIAIIDHGSIVALDTPSALKQTVGCEMILLKTEEPE
KLQSLLAYIPEIDTIRVIDDEVRISIPNADDELPRIMEIAFREGVHMSSVHLSRPDMNDV
FMHYTGREIREEGPESVSRMRMMRRRSRR

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