GapMind for catabolism of small carbon sources

 

Protein Echvi_1022 in Echinicola vietnamensis KMM 6221, DSM 17526

Annotation: Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Length: 345 amino acids

Source: Cola in FitnessBrowser

Candidate for 67 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 34% 89% 196.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 32% 88% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 35% 84% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 32% 88% 185.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 33% 88% 176.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 31% 95% 173.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 71% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 71% 171.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 30% 95% 166 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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) 33% 89% 164.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 30% 92% 160.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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) 35% 63% 159.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
sucrose catabolism thuK 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) 35% 63% 159.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 35% 62% 158.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 97% 157.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 97% 157.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 31% 97% 157.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 36% 60% 157.1 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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) 34% 66% 156 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 38% 72% 154.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 34% 70% 154.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 33% 69% 154.8 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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) 32% 72% 153.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 62% 153.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 32% 74% 151.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 30% 97% 149.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 35% 64% 149.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 67% 149.4 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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% 83% 148.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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% 83% 148.7 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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) 37% 57% 148.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
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) 32% 66% 147.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-arginine catabolism artP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 33% 97% 146 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-histidine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 33% 97% 146 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-lysine catabolism hisP lo Probable ATP-binding component of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized) 33% 97% 146 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 65% 145.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 35% 79% 130.2 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-isoleucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 117.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-leucine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 117.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-valine catabolism livF lo ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized) 34% 94% 117.9 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-alanine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 110.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-histidine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 110.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-leucine catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 110.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-proline catabolism natA lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 110.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-serine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 110.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-threonine catabolism braF lo NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized) 32% 94% 110.5 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 32% 88% 101.3 FutC aka SLL1878, component of Ferric iron (Fe3+) porter 33% 201.8

Sequence Analysis Tools

View Echvi_1022 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

MSLLQLHGISKKFPQTKQFAVKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDKG
EIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQESRNARQIAMDS
LALAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEISEDIR
DIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANFFGKR
NELLATPTEDGFYAGFGFIPHPDSASYTDKVKILFRSEDAKIKKSTEQPLSGIVTRVLFY
GDHQIVKLEDDEGKQISIKAAPGRNFEMGARMFFTIDKFEIETAF

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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, 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