GapMind for catabolism of small carbon sources

 

Protein Pf1N1B4_691 in Pseudomonas fluorescens FW300-N1B4

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

Length: 351 amino acids

Source: pseudo1_N1B4 in FitnessBrowser

Candidate for 38 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 44% 96% 271.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 267.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 267.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 267.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 47% 89% 267.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
trehalose catabolism thuK med Trehalose import ATP-binding protein SugC; EC 7.5.2.- (characterized) 44% 91% 260.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 42% 96% 257.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-sorbitol, ATPase component (characterized) 44% 90% 253.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 43% 92% 253.1 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 46% 83% 251.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 46% 83% 251.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 46% 83% 251.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 46% 83% 251.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 46% 83% 251.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 46% 83% 251.9 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 95% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 43% 95% 248.4 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
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) 46% 86% 246.5 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 42% 81% 240 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-cellobiose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 45% 78% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-glucose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 45% 78% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
lactose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 45% 78% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-maltose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 45% 78% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
sucrose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 45% 78% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
trehalose catabolism gtsD med GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 45% 78% 239.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 81% 238.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-maltose catabolism malK_Sm med MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 45% 81% 235.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
trehalose catabolism malK med MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 45% 81% 235.3 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 40% 92% 238.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 39% 92% 229.2 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
L-proline catabolism opuBA lo BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 37% 93% 183.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
L-isoleucine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 33% 98% 131.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
L-phenylalanine catabolism livG lo High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale) 33% 98% 131.7 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
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% 100% 130.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
L-leucine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 130.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
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% 100% 130.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
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% 100% 130.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9
L-valine catabolism livG lo High-affinity branched-chain amino acid transport ATP-binding protein BraF, component of Branched chain amino acid uptake transporter. Transports alanine (characterized) 32% 100% 130.6 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 42% 271.9

Sequence Analysis Tools

View Pf1N1B4_691 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

MTGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLTGGEI
RLDGEDIGHTPAHQRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL
IQLQEMIDRPVAKLSGGQRQRVAIARAIASRPKILLLDEPLSALDAKLRESMQVEIRQLQ
QRLNITTIMVTHDQREAMTMADIVVVLGEHRVQQVGSPIEIYRHPANEFVADFIGSGNIF
PATALGNGKVSLPGGDALQVPICSSIVVGEKVKMLIRPEDLQLSQPQATAGNRLLGKVTF
VRDIGATIETTVECSGVSFTALSTPCQGVGLSIGNPVSVTLPAEACRVLSA

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