Align MalG, 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)
to candidate 18060 b4032 maltose transporter subunit (NCBI)
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Keio:18060 Length = 296 Score = 134 bits (336), Expect = 3e-36 Identities = 90/284 (31%), Positives = 148/284 (52%), Gaps = 23/284 (8%) Query: 13 YALLILLSFIWLFPIIWVILTSFRGEGTAYVPYIIPKTWTLDNYIKL------------F 60 + LL+L +FP++ V+ S R +G +IP+ + D++ KL Sbjct: 17 HLLLLLFIAAIMFPLLMVVAISLR-QGNFATGSLIPEQISWDHW-KLALGFSVEQADGRI 74 Query: 61 TNSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGF 120 T FP W N++ V+ + + +++ AY+ +R++F + LK L+ MFP Sbjct: 75 TPPPFPVLLWLWNSVKVAGISAIGIVALSTTCAYAFARMRFPGKATLLKGMLIFQMFPAV 134 Query: 121 MSMIAVYYILKALNL------TQTLTSLVLVYSSGAALTFYIAKGFFDTIPYSLDESAMI 174 +S++A+Y + L T ++ Y G AL + KG+F+TI SL+E+A + Sbjct: 135 LSLVALYALFDRLGEYIPFIGLNTHGGVIFAYLGGIALHVWTIKGYFETIDSSLEEAAAL 194 Query: 175 DGATRKDIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSML 234 DGAT F + LPLS PI+ +L+FIA + A ++L D S YT+A+G+ L Sbjct: 195 DGATPWQAFRLVLLPLSVPILAVVFILSFIAAITEVPVASLLLRDVNS-YTLAVGMQQYL 253 Query: 235 QADTINNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 N + FAA +V+ A+PITI+F+ Q++ V G+T G VK Sbjct: 254 NPQ--NYLWGDFAAAAVMSALPITIVFLLAQRWLVNGLTAGGVK 295 Lambda K H 0.330 0.142 0.428 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: 229 Number of extensions: 9 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