Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate BWI76_RS01820 BWI76_RS01820 maltose transporter permease
Query= TCDB::Q9KZ08 (303 letters) >FitnessBrowser__Koxy:BWI76_RS01820 Length = 296 Score = 144 bits (363), Expect = 2e-39 Identities = 86/215 (40%), Positives = 124/215 (57%), Gaps = 9/215 (4%) Query: 96 WLKSSLIVSLGTTVIGVLVAATT-GYAVSRMRFPGYRKLMWVLLVTQMFPIAVLIVPMYQ 154 WL +S+ V+ G T IG++ +TT YA +RMRFPG L+ +L+ QMFP + +V +Y Sbjct: 84 WLWNSIKVA-GITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLSLVALYA 142 Query: 155 ILSKLQL------IDNYFGLILVYCSTAVPYCAWLLKGYFDTIPFEIDEAGRVDGLTPFG 208 + +L ++ + G+I Y + W +KGYF+TI ++EA +DG TP+ Sbjct: 143 LFDRLGQYVPFVGLNTHGGVIFAYMG-GIALHVWTIKGYFETIDGSLEEAAALDGATPWQ 201 Query: 209 TFFRLILPLARPGLAVAGFYSFITAFGEVAFASTFMLSDTKYTFAVGLQSFVSEHDAQRN 268 F ++LPL+ P LAV SFI A EV AS + YT AVG+Q +++ + Sbjct: 202 AFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLNPQNYLWG 261 Query: 269 LMAATAVLVAIPVSAFFYLVQKNLVTGLTAGGTKG 303 AA AVL AIP++ F L Q+ LV GLTAGG KG Sbjct: 262 DFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296 Lambda K H 0.326 0.139 0.422 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 287 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 303 Length of database: 296 Length adjustment: 27 Effective length of query: 276 Effective length of database: 269 Effective search space: 74244 Effective search space used: 74244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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:
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