GapMind for catabolism of small carbon sources

 

Protein HSERO_RS17020 in Herbaspirillum seropedicae SmR1

Annotation: FitnessBrowser__HerbieS:HSERO_RS17020

Length: 406 amino acids

Source: HerbieS in FitnessBrowser

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
xylitol catabolism HSERO_RS17020 hi ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 100% 100% 807 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 49% 97% 341.3 AlgS, component of Alginate (MW 27,000 Da) (and Alginate oligosaccharides) uptake porter. Sphingomonas species A1 is a 'pit-forming' bacterium that directly incorporates alginate into its cytoplasm through a pit-dependent transport system, termed a 'superchannel' (Murata et al., 2008). The pit is a novel organ acquired through the fluidity and reconstitution of cell surface molecules, and through cooperation with the transport machinery in the cells. It confers upon bacterial cells a more efficient way to secure and assimilate macromolecules 49% 333.2
D-maltose catabolism malK1 med 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% 98% 333.2 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
trehalose catabolism thuK med 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% 98% 333.2 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-cellobiose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-glucose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
lactose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-maltose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
sucrose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
trehalose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 46% 98% 323.6 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 46% 95% 319.7 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-cellobiose catabolism SMc04256 med ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized) 45% 100% 305.8 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
D-cellobiose catabolism msiK med 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) 47% 100% 305.4 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
putrescine catabolism potA med spermidine/putrescine ABC transporter, ATP-binding protein PotA; EC 3.6.3.31 (characterized) 47% 72% 251.1 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
trehalose catabolism treV med TreV, component of Trehalose porter (characterized) 48% 75% 233 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
glycerol catabolism glpT lo GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized) 36% 92% 218.4 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3
glycerol catabolism glpS lo GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized) 38% 84% 193.4 ABC-type maltose transporter (EC 7.5.2.1) 49% 341.3

Sequence Analysis Tools

View HSERO_RS17020 at FitnessBrowser

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

MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT
LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA
LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL
HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM
NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL
TCPVSVELVEILGADALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFDVESG
ENLSLPDAALTAPGSDDGPHGKETKHESGSGAGPYPPGPIVQGLGA

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:

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