GapMind for catabolism of small carbon sources

 

Protein GFF960 in Marinobacter adhaerens HP15

Annotation: HP15_939 spermidine/putrescine ABC transporter ATPase subunit

Length: 372 amino acids

Source: Marino in FitnessBrowser

Candidate for 36 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) 63% 95% 431.8 Putative ABC transporter component, component of The γ-aminobutyrate (GABA) uptake system, GtsABCD 43% 251.5
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 42% 91% 239.6 PotG aka B0855, component of Putrescine porter 63% 431.8
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 79% 236.5 PotG aka B0855, component of Putrescine porter 63% 431.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 70% 221.9 PotG aka B0855, component of Putrescine porter 63% 431.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 70% 221.9 PotG aka B0855, component of Putrescine porter 63% 431.8
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 41% 78% 220.3 PotG aka B0855, component of Putrescine porter 63% 431.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 77% 219.9 PotG aka B0855, component of Putrescine porter 63% 431.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 75% 216.5 PotG aka B0855, component of Putrescine porter 63% 431.8
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 76% 212.6 PotG aka B0855, component of Putrescine porter 63% 431.8
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 76% 212.6 PotG aka B0855, component of Putrescine porter 63% 431.8
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 43% 76% 212.6 PotG aka B0855, component of Putrescine porter 63% 431.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 76% 197.2 PotG aka B0855, component of Putrescine porter 63% 431.8
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 43% 82% 163.3 PotG aka B0855, component of Putrescine porter 63% 431.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 95% 229.2 PotG aka B0855, component of Putrescine porter 63% 431.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 38% 96% 228.8 PotG aka B0855, component of Putrescine porter 63% 431.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 93% 225.7 PotG aka B0855, component of Putrescine porter 63% 431.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 93% 225.7 PotG aka B0855, component of Putrescine porter 63% 431.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 93% 225.7 PotG aka B0855, component of Putrescine porter 63% 431.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 86% 221.5 PotG aka B0855, component of Putrescine porter 63% 431.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 86% 221.5 PotG aka B0855, component of Putrescine porter 63% 431.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 86% 221.5 PotG aka B0855, component of Putrescine porter 63% 431.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 86% 221.5 PotG aka B0855, component of Putrescine porter 63% 431.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 86% 221.5 PotG aka B0855, component of Putrescine porter 63% 431.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 86% 221.5 PotG aka B0855, component of Putrescine porter 63% 431.8
D-maltose catabolism malK1 lo 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) 39% 93% 221.1 PotG aka B0855, component of Putrescine porter 63% 431.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 35% 97% 215.3 PotG aka B0855, component of Putrescine porter 63% 431.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 37% 86% 211.1 PotG aka B0855, component of Putrescine porter 63% 431.8
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 91% 163.7 PotG aka B0855, component of Putrescine porter 63% 431.8
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) 38% 82% 163.3 PotG aka B0855, component of Putrescine porter 63% 431.8
D-ribose catabolism rbsA lo Ribose import ATP-binding protein RbsA 2, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized) 32% 50% 131.3 PotG aka B0855, component of Putrescine porter 63% 431.8

Sequence Analysis Tools

View GFF960 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

MENGNNTSAQAEVLLSIRGISKSFDGTLAVDNVNLDIHKGEIFALLGGSGSGKSTLLRML
AGFETPNAGSIMLDGQDVTALPPFLRPTNMMFQSYALFPHMTVEQNIAMGLKQDKLPKSE
IRDRVAAMLKLVKMEPYARRKPQQLSGGQQQRVALARSLAKRPKLLLLDEPMGALDKKLR
TEMQLELVEILENVGATCLMVTHDQEEAMTMASRIAIMAQGRIAQIGSPIDIYESPNSRM
TAEFIGSVNIFEAHIREDEADSVTLTSDLLDAPVFIDRGVTTPAESTATLVALRPEKIYL
TPDKPDGENNWSCGTVDNIAYLGDITSYYVKLASGKRVQATMANVERRGERPTWGDRVFV
SWEASSPILLWN

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