GapMind for catabolism of small carbon sources

 

Protein WP_004117779.1 in Rhizobium freirei PRF 81

Annotation: NCBI__GCF_000359745.1:WP_004117779.1

Length: 365 amino acids

Source: GCF_000359745.1 in NCBI

Candidate for 12 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-fucose catabolism SM_b21106 hi ABC transporter for L-Fucose, ATPase component (characterized) 77% 100% 567.8 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 53% 379.0
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) 53% 99% 379 ABC transporter for L-Fucose, ATPase component 77% 567.8
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) 53% 99% 379 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-glucosamine (chitosamine) catabolism SM_b21216 med ABC transporter for D-Glucosamine, ATPase component (characterized) 51% 100% 353.6 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-maltose catabolism malK_Aa med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 51% 97% 352.1 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-maltose catabolism malK_Sm med 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) 50% 100% 351.3 ABC transporter for L-Fucose, ATPase component 77% 567.8
trehalose catabolism malK med 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) 50% 100% 351.3 ABC transporter for L-Fucose, ATPase component 77% 567.8
xylitol catabolism HSERO_RS17020 med ABC-type sugar transport system, ATPase component protein (characterized, see rationale) 47% 90% 340.1 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-xylose catabolism gtsD med ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized) 49% 95% 338.2 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-galactose catabolism PfGW456L13_1897 med ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 48% 95% 332.8 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-maltose catabolism malK_Bb med ABC-type maltose transport, ATP binding protein (characterized, see rationale) 50% 99% 329.7 ABC transporter for L-Fucose, ATPase component 77% 567.8
D-maltose catabolism musK med ABC-type maltose transporter (EC 7.5.2.1) (characterized) 53% 86% 321.2 ABC transporter for L-Fucose, ATPase component 77% 567.8

Sequence Analysis Tools

View WP_004117779.1 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

Fitness BLAST: loading...

Sequence

MAQVSLKKLVKRYGALEIVHGIDLDIADKEFIALVGPSGCGKSTTLRMIAGLEEVSGGTI
EIGDTVVNDLPPRDRNISMVFQSYALYPHMTVRENMGFSLKIAKQPQAEIDKRVNEAAAI
LSLEALMDRRPAQLSGGQRQRVAMGRAIVRQPEVFLFDEPLSNLDAKLRTQMRTEIKKLH
AKVQSTVVYVTHDQVEAMTLADRIVIMRDGYIEQVGTPDEVFKRPATRFVAGFIGSPPMN
IEEATLKGGELTFKNGERLPLPSQFAGKVKEGEKVAFGLRPDDIFPTGHGLHSGAETAVY
ELTLPVAITEPLGNETLVFVEFAGREWVSRMLNPRSLKSGEQLKMSFDLSQAHLFSTETG
KSLAI

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