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 15432 b1312 predicted sugar transporter subunit: membrane component of ABC superfamily (NCBI)
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Keio:15432 Length = 280 Score = 156 bits (394), Expect = 5e-43 Identities = 86/278 (30%), Positives = 156/278 (56%), Gaps = 6/278 (2%) Query: 4 KKQLQIGSIYALLILLSFIWLFPIIWVILTSFRG--EGTAYVPYIIPKTWTLDNYIKLFT 61 K+ L Y L L I LFP +++TSF+G E + P ++P+ WTL++Y+ +F Sbjct: 5 KRTLSRIGFYCGLALFLIITLFPFFVMLMTSFKGAKEAISLHPTLLPQQWTLEHYVDIFN 64 Query: 62 NSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFM 121 FPF +F N+L+VS + V++ + + AY+LSR++FK R + MF G + Sbjct: 65 PMIFPFVDYFRNSLVVSVVSSVVAVFLGILGAYALSRLRFKGRMTINASFYTVYMFSGIL 124 Query: 122 SMIAVYYILKALNLTQTLTSLVLVYSSGAALT-FYIAKGFFDTIPYSLDESAMIDGATRK 180 ++ ++ I+ AL + T +L++ + T ++ K +FDTIP ++E+AM+DG R Sbjct: 125 LVVPLFKIITALGIYDTEMALIITMVTQTLPTAVFMLKSYFDTIPDEIEEAAMMDGLNRL 184 Query: 181 DIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTIN 240 I +IT+PL+ ++ + F+ W D++FA + L A S +T+ +GL ++ T + Sbjct: 185 QIIFRITVPLAMSGLISVFVYCFMVAWNDYLFASIFLSSA-SNFTLPVGLNALF--STPD 241 Query: 241 NWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 + A S++ A+P+ I++ +++ G+T G VK Sbjct: 242 YIWGRMMAASLVTALPVVIMYALSERFIKSGLTAGGVK 279 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: 210 Number of extensions: 12 Number of successful extensions: 4 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: 280 Length adjustment: 26 Effective length of query: 252 Effective length of database: 254 Effective search space: 64008 Effective search space used: 64008 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