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 WP_086510095.1 BZY95_RS11670 carbohydrate ABC transporter permease
Query= TCDB::Q8DT26 (278 letters) >NCBI__GCF_002151265.1:WP_086510095.1 Length = 280 Score = 135 bits (339), Expect = 1e-36 Identities = 86/268 (32%), Positives = 144/268 (53%), Gaps = 6/268 (2%) Query: 13 YALLILLSFIWLFPIIWVILTSFRGEGTAYVPYIIPKTWTLDNYIKLFTNSSFPFGRWFL 72 + L+ L+ + +FP + I TSF G + + P TL NY ++F+ SF + Sbjct: 16 WLLVALIVVVAVFPFYYAIKTSFTPSGDLFRVELWPTRATLANYAQIFSQRSFL--QAIF 73 Query: 73 NTLIVSTATCVLSTSITVAMAYSLSRIKFKHRNGFLKLALVLNMFPGFMSMIAVYYILKA 132 N+++V+T+ ++ + + +Y+L R++F+ R L + L ++MFP + ++ +++A Sbjct: 74 NSILVATSVVFIALLLGITASYALGRVRFRGRTSVLLIILGVSMFPQVAVLSGLFEVIRA 133 Query: 133 LNLTQTLTSLVLVYSSGAA-LTFYIAKGFFDTIPYSLDESAMIDGATRKDIFLKITLPLS 191 LNL L+L Y+ T ++ F +P L+E+A++DGAT K+ LPL Sbjct: 134 LNLYNNPGGLILSYTIFTLPFTVWVLTTFMRQLPLELEEAAIMDGATPWVTITKVFLPLM 193 Query: 192 KPIIVYTALLAFIAPWIDFIFAQVI-LGDATSKYTVAIGLFSMLQADTINNWFMAFAAGS 250 P + T LLAFIA W +F+FA L D+ VAI L S A + W AA S Sbjct: 194 WPAMATTGLLAFIAAWNEFLFALTFTLTDSQRTVPVAIALLSGGSAYEL-PWAPIMAA-S 251 Query: 251 VLIAIPITILFIFMQKYYVEGITGGSVK 278 V++ +P+ +L I Q+ V G+T G+VK Sbjct: 252 VVVTVPLVVLVIIFQRRIVSGLTAGAVK 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: 231 Number of extensions: 14 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 Apr 09 2024. 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