Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate SM_b21458 SM_b21458 sugar uptake ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__Smeli:SM_b21458 Length = 291 Score = 288 bits (737), Expect = 9e-83 Identities = 141/270 (52%), Positives = 203/270 (75%), Gaps = 1/270 (0%) Query: 7 KRTAFYALVAVIILVAVFPFYYAILTSLKSGTALFRIDYWPTDISLANYAGIFSHGTFVR 66 K YA VA +++ +FP+Y+AI++S K+G AL++ P + +NY +F + F+ Sbjct: 23 KTAGLYAGVAAVLVYMLFPYYWAIVSSTKTGQALYQFTLLPA-LDFSNYRQLFDNPVFMG 81 Query: 67 NLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMFPQIAVLAGLFEL 126 L NS +VA + A+SL++ + AAYAL R+ F ++L+ +L +S+FPQ+ VL+G+FE+ Sbjct: 82 ALVNSGVVALVSTAVSLVIGILAAYALGRLHFPPGRIVLIAVLMISVFPQVVVLSGMFEV 141 Query: 127 IRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDGASPWVVITRVFM 186 I ++G++N P ALI SY+I TLPFT W+LT+F+RDLP E+EEAA++DG S ++T V + Sbjct: 142 IGWLGLYNRPSALIVSYLILTLPFTTWILTSFIRDLPNELEEAALIDGCSRLRILTHVLL 201 Query: 187 PLMWPALVTTGLLAFIAAWNEFLFALTFTSSNTQRTVPVAIALLSGGSQFEIPWGNIMAA 246 PLM PA+ +TGLL+FI AWNEFLFALTF ++ RTVPVAI LL+G S++E P+G IMAA Sbjct: 202 PLMGPAIASTGLLSFILAWNEFLFALTFILTDENRTVPVAIGLLTGSSRYEYPFGQIMAA 261 Query: 247 SVIVTVPLVVLVLIFQRRIISGLTAGGVKG 276 SV VT+PL+VLVLIFQR+I++GLT+G VKG Sbjct: 262 SVTVTLPLLVLVLIFQRKIVAGLTSGAVKG 291 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: 236 Number of extensions: 11 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: 291 Length adjustment: 26 Effective length of query: 250 Effective length of database: 265 Effective search space: 66250 Effective search space used: 66250 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