GapMind for catabolism of small carbon sources

 

Protein GFF4127 in Marinobacter adhaerens HP15

Annotation: HP15_4067 spermidine/putrescine ABC transporter ATPase subunit

Length: 362 amino acids

Source: Marino in FitnessBrowser

Candidate for 31 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 40% 93% 238.4 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 81% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 81% 236.9 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 43% 85% 231.1 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism malK med ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 42% 80% 219.9 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 42% 81% 219.5 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 75% 214.2 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-mannitol catabolism mtlK med ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 42% 80% 210.3 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 45% 71% 207.2 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 74% 203 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 51% 60% 231.5 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 78% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 98% 228 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 91% 226.5 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-mannose catabolism TT_C0211 lo Sugar-binding transport ATP-binding protein aka MalK1 aka TT_C0211, component of The trehalose/maltose/sucrose/palatinose porter (TTC1627-9) plus MalK1 (ABC protein, shared with 3.A.1.1.24) (Silva et al. 2005; Chevance et al., 2006). The receptor (TTC1627) binds disaccharide alpha-glycosides, namely trehalose (alpha-1,1), sucrose (alpha-1,2), maltose (alpha-1,4), palatinose (alpha-1,6) and glucose (characterized) 40% 88% 224.6 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 38% 86% 223.4 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 97% 221.1 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 100% 220.7 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 40% 80% 217.2 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 91% 208 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 91% 208 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 91% 208 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 64% 204.1 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 45% 64% 204.1 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 37% 79% 137.1 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 31% 90% 107.8 Uncharacterized ABC transporter ATP-binding protein YdcT 49% 249.2

Sequence Analysis Tools

View GFF4127 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

MDSDLFCEGLVRRFGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGD
IHIRGERMNDVPPNRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLE
QVGLPDLEHRNPQELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHL
QKQFGTTFVYITHDQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVGDNNR
LSGELVSVRDSLAELRLDDGVLVQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFSS
MQAKVRTTLFDGANSRVEAETCGQPVYARLPQDGSAPRLSVDSSIRLAWNPSLARVFGAE
SL

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 (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 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