GapMind for catabolism of small carbon sources

 

Protein WP_037455545.1 in Skermanella stibiiresistens SB22

Annotation: NCBI__GCF_000576635.1:WP_037455545.1

Length: 376 amino acids

Source: GCF_000576635.1 in NCBI

Candidate for 30 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 58% 98% 416.8 Maltose-transporting ATPase (EC 3.6.3.19) 56% 411.8
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 58% 98% 413.7 Maltose-transporting ATPase (EC 3.6.3.19) 56% 411.8
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 56% 100% 411.8 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
lactose catabolism lacK med LacK, component of Lactose porter (characterized) 56% 100% 395.2 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 57% 99% 377.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-maltose catabolism thuK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 57% 99% 377.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 57% 99% 377.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 57% 99% 377.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
sucrose catabolism thuK med ABC transporter (characterized, see rationale) 52% 99% 368.6 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
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) 54% 98% 358.2 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
trehalose catabolism thuK 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) 54% 98% 358.2 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 53% 99% 355.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 53% 95% 350.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 53% 95% 350.1 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 51% 100% 329.7 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 49% 98% 327.4 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-cellobiose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 309.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-glucose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 309.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
lactose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 309.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-maltose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 309.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
sucrose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 309.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
trehalose catabolism gtsD med Sugar ABC transporter ATP-binding protein (characterized, see rationale) 46% 99% 309.3 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-cellobiose catabolism msiK med MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 47% 98% 307 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 50% 88% 306.2 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 45% 97% 298.9 ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component 58% 416.8

Sequence Analysis Tools

View WP_037455545.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MATVTLRNIRKKYGEVEVIKGVDLDVADREFVVFVGPSGCGKSTLLRMIAGLESITDGDL
MIDGTKANDIGPADRGLAMVFQSYALYPHMTVADNMAFSLRLAGVSKEERMRKVTEAANV
LHLGPLLERRPKELSGGQRQRVAIGRAIVRQPKVFLFDEPLSNLDAALRVQMRIELAKLH
EKLEATMIYVTHDQIEAMTMADKIVVLQGGVVEQVGSPLELYHHPRNLFVAGFIGSPKMN
LMPGRVIGRAEDGITVELANGIPFSVPVRGERVNPGDEVTVGIRPEHLSLSPDGEIAGTV
LVTERLGGLTFLHIQVQGDVVMIVQADGDEAASMHDHVRLSVNPKGCHLFARDGQAVEHV
NRHHLIEPGAAGRRSA

This GapMind analysis is from Sep 24 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:

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