GapMind for catabolism of small carbon sources

 

Protein 207786 in Desulfovibrio vulgaris Hildenborough

Annotation: DVU2299 glycine/betaine/L-proline ABC transporter, ATP binding protein

Length: 397 amino acids

Source: 882 in MicrobesOnline

Candidate for 46 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) 51% 95% 392.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-proline catabolism proV med Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 49% 99% 367.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-histidine catabolism hutV med HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 58% 96% 293.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
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) 58% 96% 293.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 42% 58% 181 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 39% 64% 176.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 36% 72% 176 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
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) 40% 62% 175.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
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) 40% 62% 175.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 36% 66% 174.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-mannitol catabolism mtlK lo ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized) 34% 83% 172.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 37% 60% 171.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 66% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-cellobiose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 38% 66% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-glucose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
lactose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 44% 60% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
sucrose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
trehalose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 31% 84% 170.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 36% 62% 169.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
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% 85% 169.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 35% 73% 166.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 35% 75% 166.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 61% 166 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 34% 86% 166 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
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) 32% 84% 164.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 34% 78% 164.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism malK lo Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 37% 59% 161.4 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 32% 85% 160.6 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 58% 160.2 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 33% 66% 157.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 34% 75% 157.1 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
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% 72% 152.9 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-histidine catabolism Ac3H11_2560 lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 83% 152.5 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6
L-tryptophan catabolism ecfA1 lo Energy-coupling factor transporter ATP-binding protein EcfA1; Short=ECF transporter A component EcfA; EC 7.-.-.- (characterized, see rationale) 38% 81% 146.7 OtaA, component of The salt-induced glycine betaine OtaABC transporter 57% 430.6

Sequence Analysis Tools

View 207786 at MicrobesOnline

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

MSKLSIRNLTKIFGPHPEKALGLLEQGLGKEEIHRRTSHAVGVDRASFDVEEGEIVVVMG
LSGSGKSTLVRCLNRLIEPTAGTVTVDGRDVTSMPVDELRRLRQRSFGMVFQNFALFPHR
TVLQNAAFGLEAMGVPRAERERQAMVSLERVGLAEWAASRPAQLSGGMQQRVGLARALSL
DPDILLMDEAFSALDPLIRRDMQDELLRLQDDLQKTIVFISHDLDEALKLGDRIVLMRDG
AVVQIGTPEDILTNPADDYVARFVGEADVTKVLTAGSVMKRSEAVAVLGIDGPRTALRKM
RRNAIATLFVLDERHRLVGLITADDAARLAAEGVRELGSIVRRDIATVPPEAPATELISL
MADLPHPLAVVDERGRLAGVIVRGLLLGALAERGGVA

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