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 N515DRAFT_3133 N515DRAFT_3133 carbohydrate ABC transporter membrane protein 2, CUT1 family (TC 3.A.1.1.-)
Query= TCDB::Q8DT26 (278 letters) >FitnessBrowser__Dyella79:N515DRAFT_3133 Length = 273 Score = 142 bits (358), Expect = 8e-39 Identities = 87/269 (32%), Positives = 152/269 (56%), Gaps = 8/269 (2%) Query: 12 IYALLILLSFIWLFPIIWVILTSFR--GEGTAYVPYIIPKTWTLDNYIKLFTNSSFPFGR 69 + LLI + + +FP++W++ SF GE +A P ++P TL NY +LF + GR Sbjct: 10 VNGLLIGSTLVAVFPLLWMLSVSFMRPGEASALPPPLLPTHATLANYHELFERAGM--GR 67 Query: 70 WFLNTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYYI 129 + LN+L VS+A +LS + + Y+ ++++F R ++ L + P ++M+ ++ + Sbjct: 68 YLLNSLGVSSAITLLSLAFNLMAGYAFAKLRFSGRERLFQVLLGGLVIPAQVAMLPLFLL 127 Query: 130 LKALNLTQTLTSLVLVYSSGAALTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKITLP 189 LK L L + ++V V + ++ + + IP L E+A IDGA IF++I LP Sbjct: 128 LKYLGLVNSYAAVV-VPAMATIFGIFLVRQYARGIPDDLMEAARIDGAGELRIFVQIVLP 186 Query: 190 LSKPIIVYTALLAFIAPWIDFIFAQVILGDATSKYTVAIGLFSMLQADTINNWFMAFAAG 249 L KPI+V A+ F+ W DF++ + L YT+ I L S+ + ++ M AG Sbjct: 187 LLKPIMVTLAIFTFLTAWNDFMWPLIAL-TGQEHYTLPIALASLSREHVQDSELM--MAG 243 Query: 250 SVLIAIPITILFIFMQKYYVEGITGGSVK 278 SV+ +P+ +LF+ +Q+YY++G+ GSVK Sbjct: 244 SVVTVLPVLVLFLALQRYYLQGLLLGSVK 272 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: 190 Number of extensions: 13 Number of successful extensions: 5 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: 273 Length adjustment: 25 Effective length of query: 253 Effective length of database: 248 Effective search space: 62744 Effective search space used: 62744 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