GapMind for catabolism of small carbon sources

 

Protein WP_034994841.1 in Beijerinckia mobilis UQM 1969

Annotation: NCBI__GCF_000745425.1:WP_034994841.1

Length: 266 amino acids

Source: GCF_000745425.1 in NCBI

Candidate for 56 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-alanine catabolism Pf6N2E2_5405 med ABC transporter for D-Alanine, ATPase component (characterized) 74% 95% 375.6 AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) 71% 374.8
L-asparagine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 71% 99% 374.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-aspartate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 71% 99% 374.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-glutamate catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 71% 99% 374.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-histidine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 71% 99% 374.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-leucine catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 71% 99% 374.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-proline catabolism aapP med AapP, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized) 71% 99% 374.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-asparagine catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 70% 93% 352.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-aspartate catabolism bztD med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 70% 93% 352.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-glutamate catabolism gltL med BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 70% 93% 352.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-lysine catabolism hisP med Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 65% 93% 324.7 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-asparagine catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 63% 99% 303.5 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-aspartate catabolism aatP med ABC transporter for L-Asparagine and possibly other L-amino acids, putative ATPase component (characterized) 63% 99% 303.5 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-asparagine catabolism bgtA med ATPase (characterized, see rationale) 60% 93% 286.6 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-aspartate catabolism bgtA med ATPase (characterized, see rationale) 60% 93% 286.6 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-asparagine catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 256.5 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-aspartate catabolism peb1C med PEB1C, component of Uptake system for glutamate and aspartate (characterized) 53% 99% 256.5 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-asparagine catabolism glnQ med 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) 52% 97% 252.7 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 52% 100% 251.5 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-histidine catabolism bgtA med BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 52% 96% 245.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-glucosamine (chitosamine) catabolism AO353_21725 med ABC transporter for D-Glucosamine, putative ATPase component (characterized) 54% 93% 244.2 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-histidine catabolism hisP med 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) 49% 97% 228.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-citrulline catabolism AO353_03040 med ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 46% 98% 225.7 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-histidine catabolism BPHYT_RS24015 med ABC transporter related (characterized, see rationale) 45% 97% 220.7 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-citrulline catabolism PS417_17605 med 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) 45% 94% 218.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 40% 67% 166 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 38% 56% 156 ABC transporter for D-Alanine, ATPase component 74% 375.6
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 34% 62% 155.2 ABC transporter for D-Alanine, ATPase component 74% 375.6
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 69% 152.9 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 35% 66% 151 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 37% 63% 150.6 ABC transporter for D-Alanine, ATPase component 74% 375.6
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) 38% 57% 150.2 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 67% 149.8 ABC transporter for D-Alanine, ATPase component 74% 375.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 70% 148.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 37% 70% 148.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 64% 148.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 64% 148.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 64% 148.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 35% 64% 148.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 38% 63% 147.1 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 34% 61% 144.4 ABC transporter for D-Alanine, ATPase component 74% 375.6
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% 81% 143.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
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% 81% 143.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
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% 63% 140.2 ABC transporter for D-Alanine, ATPase component 74% 375.6
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% 63% 140.2 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 37% 65% 133.7 ABC transporter for D-Alanine, ATPase component 74% 375.6
D-mannose catabolism TM1749 lo TM1749, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 36% 74% 128.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 34% 77% 115.5 ABC transporter for D-Alanine, ATPase component 74% 375.6
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 33% 63% 111.3 ABC transporter for D-Alanine, ATPase component 74% 375.6
L-proline catabolism HSERO_RS00900 lo ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale) 30% 94% 106.3 ABC transporter for D-Alanine, ATPase component 74% 375.6

Sequence Analysis Tools

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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

MSSTNVHGAKSPNSQMPNSQNWDQELAVSIRGLNKWYGAFQVLRDINLDVGVSEKIILCG
PSGSGKSTLIRCVNRLETFQAGTLTVDGIALTDDLKRIEEVRREVGMVFQHFNLFPHLTI
LENCTLAPIQVRKLSKGRATEIAMHFLERVRIPEQAHKYPGQLSGGQQQRVAIARALCMN
PKIMLFDEPTSALDPEMVQEVLDIMVQLAREGMTMLCVTHEMGFARQIADRIVFMDSGEI
LEIAPPREFFTNPRHPRTKMFLGQIL

This GapMind analysis is from Sep 24 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