GapMind for catabolism of small carbon sources

 

Protein WP_008537404.1 in Megamonas funiformis YIT 11815

Annotation: NCBI__GCF_000245775.1:WP_008537404.1

Length: 379 amino acids

Source: GCF_000245775.1 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
L-proline catabolism opuBA med BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 51% 75% 249.2 Choline transport ATP-binding protein OpuBA 45% 307.0
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 42% 82% 181 Choline transport ATP-binding protein OpuBA 45% 307.0
L-proline catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 41% 82% 176.8 Choline transport ATP-binding protein OpuBA 45% 307.0
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 94% 230.3 Choline transport ATP-binding protein OpuBA 45% 307.0
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 35% 81% 184.9 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism malK1 lo 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) 35% 83% 180.6 Choline transport ATP-binding protein OpuBA 45% 307.0
trehalose catabolism thuK lo 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) 35% 83% 180.6 Choline transport ATP-binding protein OpuBA 45% 307.0
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 38% 79% 174.1 Choline transport ATP-binding protein OpuBA 45% 307.0
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 36% 68% 173.3 Choline transport ATP-binding protein OpuBA 45% 307.0
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 69% 171 Choline transport ATP-binding protein OpuBA 45% 307.0
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 69% 171 Choline transport ATP-binding protein OpuBA 45% 307.0
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 64% 169.9 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 64% 169.1 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 36% 78% 169.1 Choline transport ATP-binding protein OpuBA 45% 307.0
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 64% 169.1 Choline transport ATP-binding protein OpuBA 45% 307.0
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 75% 168.3 Choline transport ATP-binding protein OpuBA 45% 307.0
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 67% 167.9 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 68% 167.5 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 68% 167.5 Choline transport ATP-binding protein OpuBA 45% 307.0
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 68% 167.5 Choline transport ATP-binding protein OpuBA 45% 307.0
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 68% 167.5 Choline transport ATP-binding protein OpuBA 45% 307.0
D-cellobiose catabolism gtsD 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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
D-glucose catabolism gtsD 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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
lactose catabolism gtsD 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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism gtsD 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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
sucrose catabolism gtsD 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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
trehalose catabolism gtsD 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% 64% 166.4 Choline transport ATP-binding protein OpuBA 45% 307.0
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 62% 166 Choline transport ATP-binding protein OpuBA 45% 307.0
L-glutamate catabolism gltL lo GluA aka CGL1950, component of Glutamate porter (characterized) 40% 98% 166 Choline transport ATP-binding protein OpuBA 45% 307.0
D-cellobiose catabolism msiK lo 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) 36% 62% 165.2 Choline transport ATP-binding protein OpuBA 45% 307.0
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 54% 164.1 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 73% 161.4 Choline transport ATP-binding protein OpuBA 45% 307.0
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 37% 62% 158.3 Choline transport ATP-binding protein OpuBA 45% 307.0
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 98% 157.1 Choline transport ATP-binding protein OpuBA 45% 307.0
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 36% 98% 157.1 Choline transport ATP-binding protein OpuBA 45% 307.0
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 61% 156.8 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 36% 61% 156.8 Choline transport ATP-binding protein OpuBA 45% 307.0
trehalose catabolism malK lo 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) 32% 69% 156 Choline transport ATP-binding protein OpuBA 45% 307.0
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 36% 73% 156 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism malK_Sm lo 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) 35% 66% 155.6 Choline transport ATP-binding protein OpuBA 45% 307.0
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 62% 154.1 Choline transport ATP-binding protein OpuBA 45% 307.0
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 62% 154.1 Choline transport ATP-binding protein OpuBA 45% 307.0
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 62% 154.1 Choline transport ATP-binding protein OpuBA 45% 307.0
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 62% 154.1 Choline transport ATP-binding protein OpuBA 45% 307.0
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 62% 154.1 Choline transport ATP-binding protein OpuBA 45% 307.0
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 62% 154.1 Choline transport ATP-binding protein OpuBA 45% 307.0
L-asparagine catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 99% 152.9 Choline transport ATP-binding protein OpuBA 45% 307.0
L-aspartate catabolism aatP lo Glutamate/aspartate transport ATP-binding protein GltL aka B0652, component of Glutamate/aspartate porter (characterized) 37% 99% 152.9 Choline transport ATP-binding protein OpuBA 45% 307.0
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 62% 150.2 Choline transport ATP-binding protein OpuBA 45% 307.0
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 35% 92% 149.1 Choline transport ATP-binding protein OpuBA 45% 307.0
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 92% 146 Choline transport ATP-binding protein OpuBA 45% 307.0
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 35% 68% 139 Choline transport ATP-binding protein OpuBA 45% 307.0

Sequence Analysis Tools

View WP_008537404.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MITFEEVDKAYKEKLVLHKINLTINDGEFVVLIGSSGCGKTTLLKTINKLETVDRGLIKI
DNVSIRQQNTLELRRRIGYVVQDAGLFPHMTIYDNIATVLRINNYDSNNIENRIDELLEM
VDLDPNSYKYLYPCQLSGGQKQRVGVARAFATNPDIILMDEPFSALDPVTRSDLQDAVVK
LQKQFKKTIVFVTHDMDEAIKLADKICIIQKGWIVQYDTPENILKNPANEYVQNFVGKNR
LWSNPEFIKASDIMLKNPCKISVDRTIIQALQVMNHARVDSVLVTEDNKFLGIVWLADLQ
NFDSYSGSLKNFISDDYHAVYENTSLKEITNTVDYNHFGIVPVLDLKNELVGYLTKSRLL
SVLSRQYQDSVRQKDGILA

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