GapMind for catabolism of small carbon sources

 

Protein 199928 in Shewanella oneidensis MR-1

Annotation: SO0742 iron(III) ABC transporter, ATP-binding protein (NCBI ptt file)

Length: 349 amino acids

Source: MR1 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
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 78% 157.1 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 39% 86% 220.3 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 98% 207.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 98% 207.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 98% 207.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 98% 207.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 98% 207.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 35% 98% 207.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 97% 198.7 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 86% 197.6 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 78% 195.7 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 35% 98% 195.3 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 82% 194.9 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 37% 70% 193.7 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 78% 193.4 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 78% 193.4 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 67% 193 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 67% 193 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 32% 96% 185.7 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 36% 89% 183 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 92% 182.6 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
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) 37% 75% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 68% 182.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 42% 56% 177.9 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 77% 176 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 76% 162.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-glucosamine, ATPase component (characterized) 35% 95% 156 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 31% 99% 110.2 Putative iron transport system ATP-binding protein, component of The Fe-hydroxamate-type siderophore uptake porter (transports Fe+3 bound to ferrioxamine, ferrichrome or pyoverdine siderophores) 41% 268.1

Sequence Analysis Tools

View 199928 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

MTSTLNLHQVHSDYQGQQILKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGE
IQINGKTVSGAGQFVPSEQRGIGMIFQDYALFPHLTVAENILFGVAKLTTAQRKARLDDM
LALVKLEGLAKRYPHELSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIR
SILKQRNVSAVFVTHSKDEAFVFADTLAIFSQGVIVQHGRAEDLYAAPNSRYVADFLGSG
NYLPAEVVDGHSVTTPIGQLRSLTPLSQSHAFNGQVFLRPQQLALSADDAGVGTITERRF
LGAFCHYWVKVEAASHAYYLEVRSQIMQFNVGQRVGLSTEPHSLVLFES

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 paper from 2022 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