GapMind for catabolism of small carbon sources

 

Protein Synpcc7942_1406 in Synechococcus elongatus PCC 7942

Annotation: Synpcc7942_1406 ATPase

Length: 368 amino acids

Source: SynE in FitnessBrowser

Candidate for 57 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 40% 87% 228.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 74% 209.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 44% 74% 209.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 42% 73% 191.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 74% 189.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
sucrose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 74% 189.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
trehalose catabolism thuK med ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 42% 74% 189.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 98% 211.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 36% 97% 211.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 38% 83% 208.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 44% 64% 206.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 39% 76% 202.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 36% 99% 201.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 42% 61% 200.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 44% 61% 198.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 42% 67% 198 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 77% 197.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 45% 69% 197.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 35% 92% 196.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 36% 95% 195.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 91% 195.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 37% 87% 194.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 40% 79% 194.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized) 43% 63% 190.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 95% 189.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 95% 189.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 95% 189.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 43% 64% 185.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 94% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 36% 89% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 94% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 94% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 94% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 94% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 94% 183.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 33% 94% 174.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 40% 57% 161 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 82% 159.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
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) 39% 84% 155.6 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 40% 92% 153.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 93% 151.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 93% 151.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 37% 75% 149.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 39% 85% 143.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 86% 137.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 86% 137.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-glutamate catabolism gltL lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 37% 86% 137.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-histidine catabolism BPHYT_RS24015 lo ABC transporter related (characterized, see rationale) 36% 87% 135.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-isoleucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 93% 121.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-leucine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 93% 121.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4
L-valine catabolism livG lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 32% 93% 121.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 54% 349.4

Sequence Analysis Tools

View Synpcc7942_1406 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MSQSEVLCLDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESL
QSGSIQLAGETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKGSAAVAR
QALALVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQE
LRDILRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLS
QANFLATEYQGDAWRTVLGDFEAPGGLEGSRTGGEPPVVMVRQEDVLLHPHPEGTGLVRD
RQFLGRDYRYFVQLPAGLEIQVLGPVSEAIAVGTAVQVQLRTGQARLYPYDLPLVLRGTS
TRNAAARA

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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