GapMind for catabolism of small carbon sources

 

Protein WP_109939172.1 in Methanospirillum stamsii Pt1

Annotation: NCBI__GCF_003173335.1:WP_109939172.1

Length: 376 amino acids

Source: GCF_003173335.1 in NCBI

Candidate for 57 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-proline catabolism opuBA med 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) 50% 91% 372.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-proline catabolism proV med glycine betaine/l-proline transport atp-binding protein prov (characterized) 45% 94% 344 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 55% 89% 281.2 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
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) 51% 89% 271.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 41% 71% 186 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-histidine catabolism PA5503 med Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 41% 72% 175.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 41% 60% 173.7 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 91% 171.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-maltose catabolism thuK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 91% 171.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 91% 171.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 34% 91% 171.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 38% 62% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 38% 71% 169.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-cellobiose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 57% 167.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-glucose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 57% 167.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
lactose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 57% 167.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-maltose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 57% 167.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
sucrose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 57% 167.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
trehalose catabolism gtsD lo GtsD (GLcK), component of Glucose porter, GtsABCD (characterized) 41% 57% 167.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 37% 63% 167.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
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) 42% 59% 166.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
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) 42% 59% 166.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 41% 56% 165.2 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtM (characterized) 37% 98% 162.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 68% 162.2 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 34% 88% 161 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 88% 159.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 32% 93% 159.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 38% 98% 156.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 38% 98% 156.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-glutamate catabolism gltL lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 38% 98% 156.8 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 61% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 61% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 61% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 37% 90% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 61% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 61% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 61% 155.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
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) 36% 96% 154.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-glucosamine (chitosamine) catabolism AO353_21725 lo ABC transporter for D-Glucosamine, putative ATPase component (characterized) 35% 93% 152.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 95% 145.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 37% 90% 144.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 34% 95% 144.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 87% 139.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 87% 139.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
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% 88% 138.7 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 36% 88% 138.7 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-asparagine catabolism aapP lo 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) 34% 89% 137.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-aspartate catabolism aapP lo 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) 34% 89% 137.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-glutamate catabolism aapP lo 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) 34% 89% 137.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-leucine catabolism aapP lo 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) 34% 89% 137.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
L-proline catabolism aapP lo 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) 34% 89% 137.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-mannose catabolism TM1750 lo TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized) 33% 70% 132.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 75% 121.3 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 33% 88% 120.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
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) 30% 84% 116.7 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4
D-cellobiose catabolism cbtF lo CbtF, component of Cellobiose and cellooligosaccharide porter (characterized) 32% 72% 114 OtaA, component of The salt-induced glycine betaine OtaABC transporter 60% 441.4

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Sequence

MLTHLQKGCTTKEIRERTGHVVALKNISFSVKKGEIFVLMGLSGCGKSTLLRCLNRLISP
TAGSILLDGEDIASVSTERMRTIRRSRMGMVFQSFALLPHKNIQDNVAFGLEIQGISAEE
RAGIAKETLDLVGLSGYENSYPDQLSGGMKQRVGLARAIASSPDILLMDEAFSALDPMIR
RDMQNELLDIQDRLEKTIIFVSHDLDEALKLGTRIGLMKAGEIVQIGTPEEILTQPKNEF
VERFVEDVDLSRVLTAKDVMKVPDPMIHASSGPHVALRMMKEAGISTIFVVAKNRELKGI
ITADDALRAGKEGLTLQDIIIPDVVTLSLDTPVADIIPVIADSKFPIAVINEEKRLKGVI
VRGSVLAALGRTGASL

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