GapMind for catabolism of small carbon sources

 

Protein PfGW456L13_1569 in Pseudomonas fluorescens GW456-L13

Annotation: Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Length: 372 amino acids

Source: pseudo13_GW456_L13 in FitnessBrowser

Candidate for 20 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) 45% 95% 288.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 43% 276.6
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 97% 250 PotG aka B0855, component of Putrescine porter 45% 288.5
D-maltose catabolism malK1 med MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 42% 93% 250 PotG aka B0855, component of Putrescine porter 45% 288.5
trehalose catabolism thuK med MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 42% 93% 250 PotG aka B0855, component of Putrescine porter 45% 288.5
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 86% 249.6 PotG aka B0855, component of Putrescine porter 45% 288.5
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 91% 245.7 PotG aka B0855, component of Putrescine porter 45% 288.5
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 46% 77% 245 PotG aka B0855, component of Putrescine porter 45% 288.5
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 76% 238.8 PotG aka B0855, component of Putrescine porter 45% 288.5
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 41% 92% 238.8 PotG aka B0855, component of Putrescine porter 45% 288.5
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 80% 237.7 PotG aka B0855, component of Putrescine porter 45% 288.5
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 91% 236.5 PotG aka B0855, component of Putrescine porter 45% 288.5
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 97% 238.4 PotG aka B0855, component of Putrescine porter 45% 288.5
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 80% 205.3 PotG aka B0855, component of Putrescine porter 45% 288.5

Sequence Analysis Tools

View PfGW456L13_1569 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 and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNALHSLQTLAVSIRSVRKVYGDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRM
IAGFEFPTEGEILLYGENIADRPPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKV
LHKTQLAERVREMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSAL
DLKLRQAMREELKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYER
PRNRFVADFIGETNFIEGTVTRVEDGLAWFAGPAGHPLPAQPCSDVRVGANVTLSVRPER
LHLVPATTENALPCRIEAQIYLGTDLQYQVSLSDGSRLTVRTPNCVDQSKRFAVGSQAGL
LFDQGSASVLHD

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, the preprint on GapMind for carbon sources, 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