Align Putative maltose permease, component of MalEFG (K unknown), involved in maltose and maltodextrin uptake (characterized)
to candidate SMc01979 SMc01979 sugar transport system permease ABC transporter protein
Query= TCDB::Q9KZ08 (303 letters) >FitnessBrowser__Smeli:SMc01979 Length = 277 Score = 194 bits (493), Expect = 2e-54 Identities = 109/276 (39%), Positives = 173/276 (62%), Gaps = 3/276 (1%) Query: 31 RSRAASLA-SHGVLTLASLV-ALFPVAWLVYLSLGPDKNDYLHPGRIW-SKMTFDNYAFV 87 R++ A L +H + LA + ALFP+ WL+ +++ P+ Y R+W S+ + +++ FV Sbjct: 2 RAKQAFLTIAHRLAVLAYIAFALFPLFWLLKVAVTPNDLLYSEGIRLWPSRASLEHFDFV 61 Query: 88 LQDTNFFDWLKSSLIVSLGTTVIGVLVAATTGYAVSRMRFPGYRKLMWVLLVTQMFPIAV 147 L+ + F + ++SLIVS T VI ++A+ +GYA+SR RF G L+ ++L+TQMFP+ + Sbjct: 62 LRHSAFPVFFRNSLIVSGSTAVIVTILASLSGYALSRFRFRGKYWLVTLMLLTQMFPLVM 121 Query: 148 LIVPMYQILSKLQLIDNYFGLILVYCSTAVPYCAWLLKGYFDTIPFEIDEAGRVDGLTPF 207 L+ P+++ILS L L ++ GL++VY + VP+ +L++ +FD IP +++EA +DG T F Sbjct: 122 LVAPIFKILSPLGLTNSLTGLVVVYTAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQF 181 Query: 208 GTFFRLILPLARPGLAVAGFYSFITAFGEVAFASTFMLSDTKYTFAVGLQSFVSEHDAQR 267 F ++ILPL PG+A + F A+ E+ F+ + + + TF VGL SFVS+ Sbjct: 182 VAFRQIILPLTLPGIAATLGFVFTAAWSELLFSLMLISGNAQATFPVGLLSFVSKFSVDF 241 Query: 268 NLMAATAVLVAIPVSAFFYLVQKNLVTGLTAGGTKG 303 M A VL IP FF L+Q+ LV GLTAG KG Sbjct: 242 GQMMAAGVLALIPACLFFLLIQRYLVQGLTAGAVKG 277 Lambda K H 0.326 0.139 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: 265 Number of extensions: 14 Number of successful extensions: 2 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: 303 Length of database: 277 Length adjustment: 26 Effective length of query: 277 Effective length of database: 251 Effective search space: 69527 Effective search space used: 69527 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 (21.6 bits) S2: 48 (23.1 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