GapMind for catabolism of small carbon sources

 

Protein 8500851 in Desulfovibrio vulgaris Miyazaki F

Annotation: FitnessBrowser__Miya:8500851

Length: 354 amino acids

Source: Miya in FitnessBrowser

Candidate for 52 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 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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
trehalose 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) 44% 95% 258.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
lactose catabolism lacK med ABC transporter for Lactose, ATPase component (characterized) 40% 94% 236.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 43% 79% 229.2 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 43% 71% 225.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
trehalose catabolism malK 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) 43% 71% 225.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism malK med Maltose/maltodextrin import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 42% 83% 221.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 86% 219.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
sucrose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 86% 219.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
trehalose catabolism aglK med ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 42% 86% 219.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 42% 75% 216.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 40% 72% 211.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-cellobiose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-galactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-glucose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
lactose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-mannose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
sucrose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
trehalose catabolism glcV med monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 41% 81% 210.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 48% 66% 236.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 47% 69% 233.8 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 39% 96% 231.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 98% 230.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 89% 226.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 96% 225.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 40% 96% 225.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 39% 96% 224.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 93% 223.4 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
putrescine catabolism potA lo Spermidine/putrescine import ATP-binding protein PotA, component of The spermidine/putrescine uptake porter, PotABCD (characterized) 39% 86% 221.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 86% 217.6 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 46% 62% 215.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 91% 211.5 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 39% 80% 209.9 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 88% 205.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 88% 205.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 88% 205.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 88% 205.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 88% 205.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 37% 88% 205.3 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
L-proline catabolism opuBA lo 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) 37% 80% 179.1 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 65% 173.7 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
L-histidine catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 37% 85% 155.6 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7
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) 37% 85% 155.6 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 44% 282.7

Sequence Analysis Tools

View 8500851 at FitnessBrowser

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Find functional residues: SitesBLAST

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSYVRLVNVTKRFGGVTAVDSLNLEIGRGECFSMLGPSGCGKTTTLRMVAGFEDLDDGEI
HVGDRLLSARRNNYYLPPEKRDFGMVFQAFAVWPHLSVYENVAFPLRIRRLSAAEIDRRT
REALHHTSLADVAQKSPDDLSGGGKQRVALARALAINPDVMLLDEPLSSLDPHLREEMRF
EIKDLQRTFGFSILYVTHDQSEAMALSDRIMVMRNGVVQQVGTPLDVYTNPANSFVFGFI
GLSNFLDVNLTPEGLVRVNGGDARVTPATPPSARLVSAGRAALASRPSEIDFTAEGGLRG
VVRRRAYLGEIVDYRIDVSGQEVRVQKGRRAPGPAEGDACGLVFLRPHWYDPAA

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:

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