GapMind for catabolism of small carbon sources

 

Protein 14980 in Escherichia coli BW25113

Annotation: b0855 ATP-binding component of putrescine transport system (VIMSS)

Length: 377 amino acids

Source: Keio in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 100% 100% 751.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 43% 252.3
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 81% 167.5 PotG aka B0855, component of Putrescine porter 100% 751.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 91% 233 PotG aka B0855, component of Putrescine porter 100% 751.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 40% 83% 233 PotG aka B0855, component of Putrescine porter 100% 751.9
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 87% 232.3 PotG aka B0855, component of Putrescine porter 100% 751.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 38% 91% 217.2 PotG aka B0855, component of Putrescine porter 100% 751.9
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 41% 63% 182.2 PotG aka B0855, component of Putrescine porter 100% 751.9
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 89% 158.3 PotG aka B0855, component of Putrescine porter 100% 751.9
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 40% 80% 146.7 PotG aka B0855, component of Putrescine porter 100% 751.9
L-proline catabolism HSERO_RS00895 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 95% 124.4 PotG aka B0855, component of Putrescine porter 100% 751.9

Sequence Analysis Tools

View 14980 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices: TMHMM

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNDAIPRPQAKTRKALTPLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKST
LLRMLAGFEQPSAGQIMLDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDK
LPKAEIASRVNEMLGLVHMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGAL
DKKLRDRMQLEVVDILERVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEH
PTTRYSAEFIGSVNVFEGVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPE
KIMLCEEPPANGCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWG
DEVRLCWEVDSCVVLTV

This GapMind analysis is from Sep 17 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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