GapMind for catabolism of small carbon sources

 

Protein WP_092681530.1 in Rhodopseudomonas pseudopalustris DSM 123

Annotation: NCBI__GCF_900110435.1:WP_092681530.1

Length: 364 amino acids

Source: GCF_900110435.1 in NCBI

Candidate for 53 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 56% 92% 352.4 sn-glycerol-3-phosphate import ATP-binding protein UgpC; EC 7.6.2.10 51% 351.7
D-mannitol catabolism mtlK med ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 50% 97% 349.7 ABC transporter for Lactose, ATPase component 56% 352.4
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) 50% 99% 342 ABC transporter for Lactose, ATPase component 56% 352.4
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) 50% 99% 342 ABC transporter for Lactose, ATPase component 56% 352.4
D-sorbitol (glucitol) catabolism mtlK med MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized) 49% 97% 341.3 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 96% 337 ABC transporter for Lactose, ATPase component 56% 352.4
D-cellobiose catabolism gtsD med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-glucose catabolism gtsD med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
lactose catabolism gtsD med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism gtsD med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism thuK med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-mannose catabolism TT_C0211 med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
sucrose catabolism gtsD med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
sucrose catabolism thuK med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
trehalose catabolism gtsD med 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) 51% 97% 330.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 49% 99% 328.6 ABC transporter for Lactose, ATPase component 56% 352.4
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 49% 99% 328.6 ABC transporter for Lactose, ATPase component 56% 352.4
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 49% 99% 328.6 ABC transporter for Lactose, ATPase component 56% 352.4
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) 46% 100% 325.1 ABC transporter for Lactose, ATPase component 56% 352.4
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 49% 99% 325.1 ABC transporter for Lactose, ATPase component 56% 352.4
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 51% 94% 316.6 ABC transporter for Lactose, ATPase component 56% 352.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 94% 316.2 ABC transporter for Lactose, ATPase component 56% 352.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 48% 94% 316.2 ABC transporter for Lactose, ATPase component 56% 352.4
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 45% 95% 314.3 ABC transporter for Lactose, ATPase component 56% 352.4
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 44% 95% 314.3 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 47% 100% 313.5 ABC transporter for Lactose, ATPase component 56% 352.4
trehalose catabolism malK med MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 47% 100% 309.3 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 50% 85% 304.7 ABC transporter for Lactose, ATPase component 56% 352.4
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 43% 90% 303.9 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism malK_Sm med MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 46% 100% 302 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 49% 87% 299.3 ABC transporter for Lactose, ATPase component 56% 352.4
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 46% 94% 298.5 ABC transporter for Lactose, ATPase component 56% 352.4
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 45% 100% 296.2 ABC transporter for Lactose, ATPase component 56% 352.4
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 89% 293.5 ABC transporter for Lactose, ATPase component 56% 352.4
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 89% 293.5 ABC transporter for Lactose, ATPase component 56% 352.4
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 89% 293.5 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 89% 293.5 ABC transporter for Lactose, ATPase component 56% 352.4
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 89% 293.5 ABC transporter for Lactose, ATPase component 56% 352.4
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 49% 89% 293.5 ABC transporter for Lactose, ATPase component 56% 352.4
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 95% 278.9 ABC transporter for Lactose, ATPase component 56% 352.4
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 43% 94% 250.8 ABC transporter for Lactose, ATPase component 56% 352.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 44% 87% 240.7 ABC transporter for Lactose, ATPase component 56% 352.4
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 43% 83% 233 ABC transporter for Lactose, ATPase component 56% 352.4
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 33% 94% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 39% 81% 209.1 ABC transporter for Lactose, ATPase component 56% 352.4
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 36% 89% 184.9 ABC transporter for Lactose, ATPase component 56% 352.4

Sequence Analysis Tools

View WP_092681530.1 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

MANVVLRNVRKTYPGGFEAIKGVDFEVGDGQFCVLVGPSGCGKSTLLRMVAGLETITSGE
IDIGGRVVNDVEPADRDIAMVFQNYALYPHMSVYNNMAYGLRNRGMAKPEIEARVQEAAR
ILEIGAMLDRKPRQLSGGQRQRVAMGRAIVRQPKVFLFDEPLSNLDAKLRVAMRVEIRKL
QRRLSTTAIYVTHDQLEAMTLADILVVMNAGQVEQIGSPLDVYAKPATTFVASFIGAPPM
NLIPLDAEGVRARFGGAVTEAGVLGVRPEDLAISSEPPAPGGLTLDLAVEAIERVGPETF
VYGTRSPGGDLAAISSKPGELPPDEIIIRIPGQEAPAIGERISVVALRHNLHLFSADGRR
RIAV

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