GapMind for catabolism of small carbon sources

 

Protein GFF4209 in Pseudomonas stutzeri RCH2

Annotation: FitnessBrowser__psRCH2:GFF4209

Length: 383 amino acids

Source: psRCH2 in FitnessBrowser

Candidate for 47 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA hi PotG aka B0855, component of Putrescine porter (characterized) 64% 97% 437.6 MalK aka PF1933, component of Maltooligosaccharide porter (Maltose is not a substrate, but maltotriose is.) 42% 264.6
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 92% 250.4 PotG aka B0855, component of Putrescine porter 64% 437.6
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 92% 250.4 PotG aka B0855, component of Putrescine porter 64% 437.6
xylitol catabolism Dshi_0546 med ABC transporter for Xylitol, ATPase component (characterized) 42% 89% 247.7 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 87% 244.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 41% 91% 238.8 PotG aka B0855, component of Putrescine porter 64% 437.6
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 43% 75% 229.9 PotG aka B0855, component of Putrescine porter 64% 437.6
L-arabinose catabolism xacK med Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 40% 86% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
D-maltose catabolism malK med Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 41% 77% 227.3 PotG aka B0855, component of Putrescine porter 64% 437.6
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 71% 224.6 PotG aka B0855, component of Putrescine porter 64% 437.6
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 46% 72% 224.2 PotG aka B0855, component of Putrescine porter 64% 437.6
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 41% 82% 218 PotG aka B0855, component of Putrescine porter 64% 437.6
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 41% 77% 217.6 PotG aka B0855, component of Putrescine porter 64% 437.6
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 42% 76% 217.2 PotG aka B0855, component of Putrescine porter 64% 437.6
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 45% 75% 216.9 PotG aka B0855, component of Putrescine porter 64% 437.6
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 41% 80% 215.7 PotG aka B0855, component of Putrescine porter 64% 437.6
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 89% 177.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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% 175.6 PotG aka B0855, component of Putrescine porter 64% 437.6
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 40% 87% 231.1 PotG aka B0855, component of Putrescine porter 64% 437.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 39% 94% 228.8 PotG aka B0855, component of Putrescine porter 64% 437.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 37% 99% 224.9 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 38% 89% 224.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 38% 89% 224.6 PotG aka B0855, component of Putrescine porter 64% 437.6
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) 38% 89% 222.6 PotG aka B0855, component of Putrescine porter 64% 437.6
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 36% 80% 188.3 PotG aka B0855, component of Putrescine porter 64% 437.6
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 39% 62% 181.4 PotG aka B0855, component of Putrescine porter 64% 437.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 37% 78% 139.8 PotG aka B0855, component of Putrescine porter 64% 437.6
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 38% 82% 139 PotG aka B0855, component of Putrescine porter 64% 437.6
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 113.2 PotG aka B0855, component of Putrescine porter 64% 437.6
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 113.2 PotG aka B0855, component of Putrescine porter 64% 437.6
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 113.2 PotG aka B0855, component of Putrescine porter 64% 437.6
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 32% 90% 113.2 PotG aka B0855, component of Putrescine porter 64% 437.6

Sequence Analysis Tools

View GFF4209 at FitnessBrowser

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

MAVASSAYKKALSGQSKNKQVLLKIDRVTKKFDETVAVDDVSLSIHQGEIFALLGGSGSG
KSTLLRMLAGFERPTEGRIFLDGQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLK
QDGLPKAEIEERVKEMLGLVQMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPM
GALDKKLRSQMQLELVQIIERVGVTCVMVTHDQEEAMTMAERIAIMHLGWIAQVGSPMDI
YETPASRLVCEFIGNVNLFDGELIEDMGDHAVIASPGLENPIYVGHGISTRAEDKQITYA
IRPEKLLIGTELPELERPGYNWAKGVVHDIAYLGGHSVYYIKLPSGGVLQAFMANTERHV
KLPTWEEEVYVYWWDDSGVVLQA

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