Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate SMc01979 SMc01979 sugar transport system permease ABC transporter protein
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__Smeli:SMc01979 Length = 277 Score = 174 bits (440), Expect = 2e-48 Identities = 96/276 (34%), Positives = 156/276 (56%), Gaps = 8/276 (2%) Query: 3 VAIAKRTAFYALVAVIILVAVFPFYYAILTSLKSGTALFR--IDYWPTDISLANYAGIFS 60 + IA R A A +A A+FP ++ + ++ L+ I WP+ SL ++ + Sbjct: 8 LTIAHRLAVLAYIAF----ALFPLFWLLKVAVTPNDLLYSEGIRLWPSRASLEHFDFVLR 63 Query: 61 HGTFVRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVL 120 H F NSL+V+ I +LA + YAL+R RFRG+ L+ +L MFP + ++ Sbjct: 64 HSAFPVFFRNSLIVSGSTAVIVTILASLSGYALSRFRFRGKYWLVTLMLLTQMFPLVMLV 123 Query: 121 AGLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVV 180 A +F+++ +G+ N+ L+ Y F +PF +++ +F +P ++EEAA++DGA+ +V Sbjct: 124 APIFKILSPLGLTNSLTGLVVVYTAFNVPFATFLMQSFFDGIPKDLEEAAMIDGATQFVA 183 Query: 181 ITRVFMPLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPW 240 ++ +PL P + T F AAW+E LF+L S N Q T PV LLS S+F + + Sbjct: 184 FRQIILPLTLPGIAATLGFVFTAAWSELLFSLMLISGNAQATFPV--GLLSFVSKFSVDF 241 Query: 241 GNIMAASVIVTVPLVVLVLIFQRRIISGLTAGGVKG 276 G +MAA V+ +P + L+ QR ++ GLTAG VKG Sbjct: 242 GQMMAAGVLALIPACLFFLLIQRYLVQGLTAGAVKG 277 Lambda K H 0.332 0.143 0.426 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: 185 Number of extensions: 8 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: 276 Length of database: 277 Length adjustment: 25 Effective length of query: 251 Effective length of database: 252 Effective search space: 63252 Effective search space used: 63252 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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