GapMind for catabolism of small carbon sources

 

Protein WP_092349406.1 in Desulfuromusa kysingii DSM 7343

Annotation: NCBI__GCF_900107645.1:WP_092349406.1

Length: 360 amino acids

Source: GCF_900107645.1 in NCBI

Candidate for 55 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
putrescine catabolism potA med PotG aka B0855, component of Putrescine porter (characterized) 44% 76% 258.8 Uncharacterized ABC transporter ATP-binding protein YdcT 53% 254.2
D-maltose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 76% 231.5 PotG aka B0855, component of Putrescine porter 44% 258.8
trehalose catabolism thuK med Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized) 45% 76% 231.5 PotG aka B0855, component of Putrescine porter 44% 258.8
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 41% 79% 221.1 PotG aka B0855, component of Putrescine porter 44% 258.8
D-mannitol catabolism mtlK med SmoK aka POLK, component of Hexitol (glucitol; mannitol) porter (characterized) 42% 86% 218 PotG aka B0855, component of Putrescine porter 44% 258.8
L-arabinose catabolism xacJ med Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 40% 76% 211.1 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 74% 209.5 PotG aka B0855, component of Putrescine porter 44% 258.8
L-fucose catabolism SM_b21106 med ABC transporter for L-Fucose, ATPase component (characterized) 41% 76% 209.1 PotG aka B0855, component of Putrescine porter 44% 258.8
D-sorbitol (glucitol) catabolism mtlK med ABC transporter for D-Sorbitol, ATPase component (characterized) 40% 82% 208 PotG aka B0855, component of Putrescine porter 44% 258.8
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 41% 79% 206.8 PotG aka B0855, component of Putrescine porter 44% 258.8
D-cellobiose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
D-glucose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
lactose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
sucrose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
sucrose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
trehalose catabolism aglK med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
trehalose catabolism aglK' med Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 40% 77% 204.5 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 40% 73% 203 PotG aka B0855, component of Putrescine porter 44% 258.8
N-acetyl-D-glucosamine catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 70% 201.4 PotG aka B0855, component of Putrescine porter 44% 258.8
D-glucosamine (chitosamine) catabolism SMc02869 med N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized) 41% 70% 201.4 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 41% 71% 201.1 PotG aka B0855, component of Putrescine porter 44% 258.8
L-histidine catabolism Ac3H11_2560 med ABC transporter for L-Histidine, ATPase component (characterized) 42% 75% 152.9 PotG aka B0855, component of Putrescine porter 44% 258.8
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 38% 98% 214.2 PotG aka B0855, component of Putrescine porter 44% 258.8
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) 38% 81% 213 PotG aka B0855, component of Putrescine porter 44% 258.8
trehalose catabolism malK 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) 38% 81% 213 PotG aka B0855, component of Putrescine porter 44% 258.8
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) 47% 63% 211.8 PotG aka B0855, component of Putrescine porter 44% 258.8
D-cellobiose catabolism SMc04256 lo ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 35% 98% 211.1 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism malK lo ABC-type maltose transporter (subunit 3/3) (EC 7.5.2.1) (characterized) 37% 94% 209.5 PotG aka B0855, component of Putrescine porter 44% 258.8
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 39% 92% 208 PotG aka B0855, component of Putrescine porter 44% 258.8
L-arabinose catabolism xacK lo Xylose/arabinose import ATP-binding protein XacK; EC 7.5.2.13 (characterized, see rationale) 35% 89% 207.6 PotG aka B0855, component of Putrescine porter 44% 258.8
xylitol catabolism HSERO_RS17020 lo ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 36% 85% 206.1 PotG aka B0855, component of Putrescine porter 44% 258.8
D-cellobiose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 97% 205.3 PotG aka B0855, component of Putrescine porter 44% 258.8
D-glucose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 97% 205.3 PotG aka B0855, component of Putrescine porter 44% 258.8
lactose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 97% 205.3 PotG aka B0855, component of Putrescine porter 44% 258.8
D-maltose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 97% 205.3 PotG aka B0855, component of Putrescine porter 44% 258.8
sucrose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 97% 205.3 PotG aka B0855, component of Putrescine porter 44% 258.8
trehalose catabolism gtsD lo Sugar ABC transporter ATP-binding protein (characterized, see rationale) 36% 97% 205.3 PotG aka B0855, component of Putrescine porter 44% 258.8
D-xylose catabolism gtsD lo ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 43% 61% 204.9 PotG aka B0855, component of Putrescine porter 44% 258.8
lactose catabolism lacK lo ABC transporter for Lactose, ATPase component (characterized) 36% 97% 203 PotG aka B0855, component of Putrescine porter 44% 258.8
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 33% 92% 200.7 PotG aka B0855, component of Putrescine porter 44% 258.8
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) 38% 77% 196.4 PotG aka B0855, component of Putrescine porter 44% 258.8
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 88% 191.8 PotG aka B0855, component of Putrescine porter 44% 258.8
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 88% 191.8 PotG aka B0855, component of Putrescine porter 44% 258.8
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 88% 191.8 PotG aka B0855, component of Putrescine porter 44% 258.8
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 88% 191.8 PotG aka B0855, component of Putrescine porter 44% 258.8
L-proline catabolism opuBA lo 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) 37% 84% 174.5 PotG aka B0855, component of Putrescine porter 44% 258.8
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 34% 83% 174.1 PotG aka B0855, component of Putrescine porter 44% 258.8
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 36% 69% 171.8 PotG aka B0855, component of Putrescine porter 44% 258.8
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 37% 68% 156.4 PotG aka B0855, component of Putrescine porter 44% 258.8
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) 34% 88% 149.1 PotG aka B0855, component of Putrescine porter 44% 258.8
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% 88% 149.1 PotG aka B0855, component of Putrescine porter 44% 258.8
L-histidine catabolism bgtA lo BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized) 37% 95% 145.2 PotG aka B0855, component of Putrescine porter 44% 258.8
myo-inositol catabolism PGA1_c07320 lo Inositol transport system ATP-binding protein (characterized) 32% 86% 113.6 PotG aka B0855, component of Putrescine porter 44% 258.8

Sequence Analysis Tools

View WP_092349406.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

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Sequence

MNNDLSVSNLVKKFGDFTAVDNVTFAVPQGSFFSILGPSGCGKTTLLRMIAGFEEPTSGN
IMIRGKDMAGVGPNLRPVNLVFQHLALFPMMNVEENIAFGLRRRKVDSATIKKKIEAILE
RVGLPDYAKHQIGQLSGGQKQRVAIARSLVLEPSVLLLDEPLGALDLKLREQMKVELKKL
QAKVGTTFVYITHDQSEALVMSDRVVVMNQGRFEQLGTPQELYGQPLTPFVAQFVGDNNL
WSGEITEMSGADAIIRTDEGFIFRSRVQGEVTVGRRADLFLRPETLRIQPEDKEGLNIFN
VTVKTILFDGANSRLLTVTPEDHELLVALPQNRRFDYIQPGQTIEVGWHPEAGVCFAAGD

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