Align Trehalose/maltose transport system permease protein MalG (characterized)
to candidate BWI76_RS01820 BWI76_RS01820 maltose transporter permease
Query= SwissProt::Q7LYX6 (278 letters) >FitnessBrowser__Koxy:BWI76_RS01820 Length = 296 Score = 127 bits (319), Expect = 3e-34 Identities = 87/285 (30%), Positives = 146/285 (51%), Gaps = 24/285 (8%) Query: 9 ILLIIGAILMAIICLFPFIWMIVVSFAEDPTFLGSPLVEYKS----------TLENYVRV 58 +L+ I AI+ FP + +I +S E GS + E S ++E+ Sbjct: 20 LLVFIAAIM------FPLLMVIAISLREGNFATGSLIPESISWEHWRLALGFSVEHADGR 73 Query: 59 LSDPTLHFPAYLKNSIIIASLVTLTTVSISSLAAYAVSRIEFKGRLLIPIFVLGLSMFPQ 118 ++ P +L NSI +A + + V++S+ AYA +R+ F G+ + +L MFP Sbjct: 74 VTPPPFPVLLWLWNSIKVAGITAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPA 133 Query: 119 ISLVGYLFKFIEKLGW------VNTYQALYFPYVAWTLPLSLWILLSYFSQLPKDLDEAA 172 + + L+ ++LG +NT+ + F Y+ + L +W + YF + L+EAA Sbjct: 134 VLSLVALYALFDRLGQYVPFVGLNTHGGVIFAYMGG-IALHVWTIKGYFETIDGSLEEAA 192 Query: 173 MIDGASRIKTLTTIILPLSAPALFSTALLVFIAAFNEFMFALLFTTDHRARTVPVGIALF 232 +DGA+ + ++LPLS P L +L FIAA E A L D + T+ VG+ + Sbjct: 193 ALDGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNSYTLAVGMQQY 252 Query: 233 QGVHGEIPWGSVMAASVISTIPLVIMALLFQKYIVSGLTAGALKG 277 + WG AA+V+S IP+ ++ LL Q+++V+GLTAG +KG Sbjct: 253 LNPQNYL-WGDFAAAAVLSAIPITVVFLLAQRWLVNGLTAGGVKG 296 Lambda K H 0.329 0.142 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: 249 Number of extensions: 18 Number of successful extensions: 3 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: 278 Length of database: 296 Length adjustment: 26 Effective length of query: 252 Effective length of database: 270 Effective search space: 68040 Effective search space used: 68040 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 (21.8 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