GapMind for catabolism of small carbon sources

 

Protein CA265_RS07485 in Pedobacter sp. GW460-11-11-14-LB5

Annotation: CA265_RS07485 macrolide ABC transporter ATP-binding protein

Length: 252 amino acids

Source: Pedo557 in FitnessBrowser

Candidate for 63 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 40% 96% 155.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 42% 78% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 42% 78% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 40% 84% 141.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 74% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 39% 65% 153.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 39% 89% 151 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 40% 83% 149.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 57% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 38% 95% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 36% 97% 143.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 92% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 37% 92% 143.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 37% 58% 141.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-asparagine catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 36% 98% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-aspartate catabolism aatP lo ABC transporter for L-aspartate, L-asparagine, L-glutamate, and L-glutamine, ATPase component (characterized) 36% 98% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 61% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 61% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 61% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 61% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 61% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 34% 61% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 39% 62% 139.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 56% 138.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 81% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 37% 81% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 35% 58% 137.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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% 62% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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% 62% 137.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 35% 55% 135.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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% 55% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 34% 58% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 58% 134.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 36% 55% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 52% 133.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 57% 132.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 58% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 37% 58% 132.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-citrulline catabolism PS417_17605 lo ATP-binding cassette domain-containing protein; SubName: Full=Amino acid transporter; SubName: Full=Histidine ABC transporter ATP-binding protein; SubName: Full=Histidine transport system ATP-binding protein (characterized, see rationale) 35% 89% 131.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 60% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 36% 60% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 37% 54% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 38% 59% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 35% 65% 129.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 39% 55% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 51% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 35% 90% 124.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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) 33% 56% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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) 34% 53% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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) 35% 55% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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% 74% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 31% 57% 121.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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) 36% 51% 118.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
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) 34% 81% 113.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 61% 105.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 52% 101.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
citrate catabolism fecE lo iron(III) dicitrate transport ATP-binding protein FecE (characterized) 31% 78% 97.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-fructose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 92% 94.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-mannose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 92% 94.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
D-ribose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 92% 94.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3
sucrose catabolism frcA lo Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized) 30% 92% 94.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 257.3

Sequence Analysis Tools

View CA265_RS07485 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

MEKPLITIKEIGRKYVIGSEVIHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDT
PSSGTYVLNGTNVSHMSDDALAEVRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKK
DRDARAARALENVGLGNRMDHKPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKT
SIEIMGLLEEIHSKGNTIILVTHEEDIAQHAHRIVRMRDGLIENDYLNTDIKNVSPRLQA
LKDNGSDWEKIN

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, the preprint 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