Align Trehalose/maltose transport system permease protein MalG (characterized)
to candidate WP_086511010.1 BZY95_RS16615 carbohydrate ABC transporter permease
Query= SwissProt::Q7LYX6 (278 letters) >NCBI__GCF_002151265.1:WP_086511010.1 Length = 275 Score = 148 bits (373), Expect = 1e-40 Identities = 92/278 (33%), Positives = 148/278 (53%), Gaps = 4/278 (1%) Query: 1 MREEVLKRILLIIGAILMAIICLFPFIWMIVVSFAEDPTFLGSPL-VEYKSTLENYVRVL 59 M + L +I IL+A + + P + F + +PL + +NYV + Sbjct: 1 MSSATFRNTLRVIVLILVASLVIGPLLASFFGGFKTNAELRTNPLWLPDAWNPQNYVAIF 60 Query: 60 SDPTLHFPAYLKNSIIIASLVTLTTVSISSLAAYAVSRIEFKGRLLIPIFVLGLSMFPQI 119 D +F Y+ NS I+S+ L T+ + + AAY S+I F G +I ++L MFP Sbjct: 61 LDG--NFWRYMGNSFFISSMTVLLTLVVGAAAAYVFSQIRFFGSRMIHSYLLLGLMFPFA 118 Query: 120 SLVGYLFKFIEKLGWVNTYQALYFPYVAWTLPLSLWILLSYFSQLPKDLDEAAMIDGASR 179 + + LF + LG ++TY A+ P A+ L L++ + ++F QLPK+L EAA +DG S Sbjct: 119 AAILPLFIKVRDLGLLDTYWAVILPQTAFGLSLAILLFKAFFDQLPKELFEAAYVDGCSY 178 Query: 180 IKTLTTIILPLSAPALFSTALLVFIAAFNEFMFALLFTTDHRARTVPVGIALFQGVHGEI 239 ++ + LPLS P L + + VF+ ++N F+ L+ D T P+G+ FQG + Sbjct: 179 LRFFWSFTLPLSTPILATVGVFVFVQSWNNFLLPLVVLNDRSIYTWPLGMMQFQGEY-LT 237 Query: 240 PWGSVMAASVISTIPLVIMALLFQKYIVSGLTAGALKG 277 W ++A ++ P VI L QKYIV+GLT G++KG Sbjct: 238 QWNMILAFVTLTITPAVIFFLAAQKYIVAGLTGGSVKG 275 Lambda K H 0.329 0.142 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: 189 Number of extensions: 13 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: 278 Length of database: 275 Length adjustment: 25 Effective length of query: 253 Effective length of database: 250 Effective search space: 63250 Effective search space used: 63250 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 24 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