GapMind for catabolism of small carbon sources

 

Protein GFF3990 in Pseudomonas stutzeri RCH2

Annotation: Psest_4063 sulfate ABC transporter, ATP-binding protein

Length: 334 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 27 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 42% 84% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 87% 222.2 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 42% 87% 222.2 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 39% 99% 233 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 40% 84% 229.9 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 47% 67% 222.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 94% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 94% 219.2 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 38% 99% 213 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 42% 68% 211.8 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 44% 64% 209.5 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 67% 183.7 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 67% 183.7 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 67% 183.7 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 41% 67% 183.7 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 36% 63% 172.2 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 37% 89% 170.6 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
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) 36% 87% 157.9 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 39% 77% 136.7 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
L-arabinose catabolism xylGsa lo Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale) 35% 96% 127.9 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 34% 88% 112.8 CysA aka B2422, component of Sulfate/thiosulfate porter 68% 331.3

Sequence Analysis Tools

View GFF3990 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

MSIEISHINKRFGQFQALNTINLHIQSGELVALLGPSGCGKTSLLRIIAGLETPDSGSIV
FHGEDVSSRDVRDRNVGFVFQHYALFRHMTVFENVAFGLRMKPKKQRPSEAVIAEKVHEL
LGLVQLDWLADRYPEQLSGGQRQRIALARALAVEPKVLLLDEPFGALDAKVRKELRRWLA
RLHEDVHLTSVFVTHDQEEAMEVADRIVVMNKGVIEQIGTPAEVYANPASEFVYDFLGDA
NRLQLDDQRSVLFRPHEVALSREAVAEHLAGEVRDIRPLGALTRVTLKVAGQAEPIEAEV
GNDHASLVGVQRGATLYFQPKGQAVRPAAAQQTG

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