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 AO353_25125 AO353_25125 sugar ABC transporter permease
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25125 Length = 280 Score = 127 bits (318), Expect = 4e-34 Identities = 89/279 (31%), Positives = 147/279 (52%), Gaps = 9/279 (3%) Query: 3 RKKQLQIGSIYALLILLSFIWLFPIIWVILTSFRGEGTAY-VPYIIPKTWTLDNYIKLFT 61 +K L++G + L+ +L +FP + I+TS + + V Y I NY + Sbjct: 7 KKALLRLG-FWCLIGILLLYAVFPFYYAIVTSLKPSSALFEVSYWIDSP-DFSNYAAVLH 64 Query: 62 NSSFPFGRWFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFM 121 SSF R N+L+V+ L+ +++ AY+L R+KF+ R L + L ++MFP Sbjct: 65 QSSFL--RAIGNSLVVALCVVTLALFLSLTAAYALGRVKFRGRGTVLMMVLGVSMFPQVA 122 Query: 122 SMIAVYYILKALNLTQTLTSLVLVYSSGAA-LTFYIAKGFFDTIPYSLDESAMIDGATRK 180 + ++ +++AL L T +L+L Y+ T ++ F +P+ L+E+A++DGA+ Sbjct: 123 VLSGLFEVIRALGLYNTSWALILSYTIFTLPFTVWVLTTFMGQLPHELEEAAIMDGASPW 182 Query: 181 DIFLKITLPLSKPIIVYTALLAFIAPWIDFIFAQVI-LGDATSKYTVAIGLFSMLQADTI 239 ++ LPL P +V T LLAFIA W +F+FA L D VAI L S + Sbjct: 183 VTLTRVLLPLLWPALVTTGLLAFIAAWNEFLFALTFTLTDTQRTVPVAIALISGGSPHEL 242 Query: 240 NNWFMAFAAGSVLIAIPITILFIFMQKYYVEGITGGSVK 278 W + AA SVL+ +P+ IL + Q+ V G+T G++K Sbjct: 243 -PWGLLMAA-SVLVTVPLVILVLIFQRRIVSGLTAGALK 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: 236 Number of extensions: 19 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: 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