Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate BWI76_RS01820 BWI76_RS01820 maltose transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__Koxy:BWI76_RS01820 Length = 296 Score = 119 bits (299), Expect = 6e-32 Identities = 90/284 (31%), Positives = 137/284 (48%), Gaps = 23/284 (8%) Query: 12 YALVAVIILVAVFPFYYAILTSLKSGTAL--------FRIDYWPTDI--SLANYAGIFSH 61 + L+ V I +FP I SL+ G ++W + S+ + G + Sbjct: 17 HLLLLVFIAAIMFPLLMVIAISLREGNFATGSLIPESISWEHWRLALGFSVEHADGRVTP 76 Query: 62 GTF--VRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAV 119 F + L NS+ VA + + L+ T AYA AR+RF G+ LL +L MFP + Sbjct: 77 PPFPVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAVLS 136 Query: 120 LAGLFEL-------IRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIV 172 L L+ L + FVG+ NT +IF+YM + VW + + + +EEAA + Sbjct: 137 LVALYALFDRLGQYVPFVGL-NTHGGVIFAYM-GGIALHVWTIKGYFETIDGSLEEAAAL 194 Query: 173 DGASPWVVITRVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSG 232 DGA+PW V +PL P L +L+FIAA E A T+ V + Sbjct: 195 DGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQYLN 254 Query: 233 GSQFEIPWGNIMAASVIVTVPLVVLVLIFQRRIISGLTAGGVKG 276 + WG+ AA+V+ +P+ V+ L+ QR +++GLTAGGVKG Sbjct: 255 PQNY--LWGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296 Lambda K H 0.332 0.143 0.426 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: 217 Number of extensions: 10 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: 276 Length of database: 296 Length adjustment: 26 Effective length of query: 250 Effective length of database: 270 Effective search space: 67500 Effective search space used: 67500 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 47 (22.7 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