GapMind for catabolism of small carbon sources

 

Protein BWI76_RS01825 in Klebsiella michiganensis M5al

Annotation: FitnessBrowser__Koxy:BWI76_RS01825

Length: 514 amino acids

Source: Koxy in FitnessBrowser

Candidate for 7 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-maltose catabolism malF hi Maltose-transporting ATPase (EC 3.6.3.19) (characterized) 100% 100% 1026.5 MalF1; aka Maltose ABC transporter, permease 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 45% 288.9
D-maltose catabolism malF1 lo MalF1; aka Maltose ABC transporter, permease 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) 45% 58% 288.9 Maltose-transporting ATPase (EC 3.6.3.19) 100% 1026.5
trehalose catabolism malF1 lo MalF1; aka Maltose ABC transporter, permease 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) 45% 58% 288.9 Maltose-transporting ATPase (EC 3.6.3.19) 100% 1026.5
D-maltose catabolism malF_Sm lo MalF, 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) 33% 53% 151.4 Maltose-transporting ATPase (EC 3.6.3.19) 100% 1026.5
trehalose catabolism malF lo MalF, 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) 33% 53% 151.4 Maltose-transporting ATPase (EC 3.6.3.19) 100% 1026.5
trehalose catabolism thuF lo ABC-type transporter, integral membrane subunit, component of Trehalose porter. Also binds sucrose (Boucher and Noll, 2011). Induced by glucose and trehalose. Directly regulated by trehalose-responsive regulator TreR (characterized) 30% 89% 125.6 Maltose-transporting ATPase (EC 3.6.3.19) 100% 1026.5
sucrose catabolism thuF lo ABC transporter permease (characterized, see rationale) 31% 68% 118.2 Maltose-transporting ATPase (EC 3.6.3.19) 100% 1026.5

Sequence Analysis Tools

View BWI76_RS01825 at FitnessBrowser

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MDVVKKKHWWQSPQLTWSVIGLLCLLVGYLVVLMYAQGEYLFAIMTLILSSVGLYIFSNR
KAYAWRYVYPGLAGMGLFVLFPLICTIAIAFTNYSSTNQLTFERAQQVLMDRSFQAGKSY
NFALYPAGDEWKLALTDGESGKNYLSDAFKFGGEQKLALKEADALPEGDRATLRVITQNR
TALNQLTAVLPDESKVIMSSLRQFSGTQPLYALANDGTLTNNQSGVKYRPNAEVGFYQAI
NADGSWGSEKLSPGYTVTIGWDNFTRVFQDEGIQKPFFAIFVWTVVFSVLTVILTVAVGM
VLACLVQWEALKGKAIYRVLLILPYAVPSFISILIFKGLFNQSFGEINMMLSALFGIKPA
WFSDPTTARTMIIIVNTWLGYPYMMILCMGLLKAIPDDLYEASAMDGATPFQNFFKITLP
LLIKPLTPLMIASFAFNFNNFVLIQLLTNGGPDRLGTTTPAGYTDLLVSYTYRIAFEGGG
GQDFGLAAAIATLIFLLVGLLAIVNLKATRMKFD

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