GapMind for catabolism of small carbon sources

 

Protein WP_012591146.1 in Methylocella silvestris BL2

Annotation: NCBI__GCF_000021745.1:WP_012591146.1

Length: 312 amino acids

Source: GCF_000021745.1 in NCBI

Candidate for 70 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 BilEA aka OpuBA protein, component of A proline/glycine betaine uptake system. Also reported to be a bile exclusion system that exports oxgall and other bile compounds, BilEA/EB or OpuBA/BB (required for normal virulence) (characterized) 42% 94% 224.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-histidine catabolism hutV med ABC transporter for L-Histidine, ATPase component (characterized) 41% 86% 177.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 40% 89% 171.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
sucrose catabolism thuK lo ABC transporter (characterized, see rationale) 44% 62% 196.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 35% 82% 182.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-proline catabolism proV lo Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized) 35% 74% 180.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 68% 179.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
trehalose catabolism thuK lo Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 40% 68% 179.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
putrescine catabolism potA lo spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 41% 67% 179.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism malK_Bb lo ABC-type maltose transport, ATP binding protein (characterized, see rationale) 37% 81% 178.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 38% 75% 177.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 69% 177.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
N-acetyl-D-glucosamine catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 70% 176 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-fucose catabolism SM_b21106 lo ABC transporter for L-Fucose, ATPase component (characterized) 39% 66% 176 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-glucosamine (chitosamine) catabolism SMc02869 lo N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 39% 70% 176 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
sucrose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
trehalose catabolism aglK lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 36% 75% 172.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 42% 57% 171.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 37% 65% 169.9 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 68% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 68% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 68% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 68% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-mannitol catabolism mtlK lo SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 37% 72% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 68% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 39% 68% 167.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 38% 64% 164.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 38% 67% 163.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 38% 69% 161.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 39% 63% 160.6 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 35% 76% 160.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 38% 63% 159.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-glucosamine (chitosamine) catabolism SM_b21216 lo ABC transporter for D-Glucosamine, ATPase component (characterized) 31% 84% 158.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
trehalose catabolism treV lo TreV, component of Trehalose porter (characterized) 33% 82% 156.8 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-alanine catabolism Pf6N2E2_5405 lo ABC transporter for D-Alanine, ATPase component (characterized) 38% 94% 156.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 38% 63% 155.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 34% 74% 153.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 37% 60% 152.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 38% 92% 149.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 38% 92% 149.4 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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% 65% 149.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-arginine catabolism artP lo Arginine transport ATP-binding protein ArtP; EC 7.4.2.- (characterized) 37% 99% 147.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 38% 57% 147.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-histidine catabolism aapP lo ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, ATPase component (characterized) 35% 92% 146.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 31% 77% 146 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 35% 92% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-asparagine catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 90% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 35% 92% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-aspartate catabolism bztD lo BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized) 35% 90% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 35% 92% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 35% 92% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 35% 92% 144.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-lysine catabolism hisP lo Amino-acid ABC transporter, ATP-binding protein (characterized, see rationale) 35% 92% 143.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 35% 96% 142.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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) 36% 89% 140.2 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-asparagine catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 98% 138.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-aspartate catabolism peb1C lo PEB1C, component of Uptake system for glutamate and aspartate (characterized) 35% 98% 138.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-asparagine catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 94% 137.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-aspartate catabolism aatP lo PP1068, component of Acidic amino acid uptake porter, AatJMQP (characterized) 35% 94% 137.5 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 32% 76% 136.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
L-histidine catabolism hisP lo histidine transport ATP-binding protein hisP (characterized) 34% 95% 136.3 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 31% 80% 132.1 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9
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% 121.7 Glycine betaine uptake system ATP-binding protein YehX; EC 7.4.2.- 48% 283.9

Sequence Analysis Tools

View WP_012591146.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MIELDGVAKFFGPMAAVETVSLEVAAGDFCVLLGPSGCGKSTVLRMINAMIAPDRGRIAI
RGVDIATLDPIALRRGVGYCIQSVGLFPHWTVEHNIAAVPRLLGWGSAKIAARMAEVVAA
MQIDEALLPRYPRELSGGQQQRIGVARALAADPDIILMDEPFAALDPISRAALQDEMRRL
HEASGKTFLFVTHDINEALRLATRIVVMNKGRVAQAGTPADILMRPVDEFVRGFLGRDEL
PLRLLDLVEIRDRIRPLSHRPSTTAIGGNATLRAALNMMLDHHVSRLAVADETGEIIGEI
SLADIVAGGAPQ

This GapMind analysis is from Apr 09 2024. 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