GapMind for catabolism of small carbon sources

 

Protein WP_013707668.1 in Desulfobacca acetoxidans DSM 11109

Annotation: NCBI__GCF_000195295.1:WP_013707668.1

Length: 263 amino acids

Source: GCF_000195295.1 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 hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 36% 81% 138.3 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 31% 60% 138.3 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 88% 136 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 88% 136 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 33% 88% 133.3 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 32% 61% 120.9 Probable ribonucleotide transport ATP-binding protein mkl, component of The Mce/Yrb/Mlk (Mammalian cell entry) ABC-type putative steroid uptake transporter (involved in several aspects of mycobacterial pathogenesis) 42% 184.9

Sequence Analysis Tools

View WP_013707668.1 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

MNGSNGGNHSAAPSEPVIVVEHMASRFGDNLIFQDVSFQVNRGEIFVILGGSGCGKTTLL
KHLIGLYQPAAGRVVVNGIDIATPNLQRLRQVRKNVGMLFQAGALLGSLTLAENVALPLQ
EYTDLSETEIDLIVKMKLALVNLAGYENHLPEEISGGMKKRAGLARAMALDPAILFFDEP
SAGLDPITAVELDLLIKNLNSGLGTTMVIVTHELESIFMIAHRIIMLDKAAKGIIAEGDP
RYLKDHATDPKVVNFFNRKPMTS

This GapMind analysis is from Apr 09 2024. 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