Align ABC transporter for D-Trehalose, permease component 2 (characterized)
to candidate SM_b21150 SM_b21150 sugar uptake ABC transporter permease
Query= reanno::Smeli:SM_b20327 (276 letters) >FitnessBrowser__Smeli:SM_b21150 Length = 285 Score = 177 bits (448), Expect = 3e-49 Identities = 106/282 (37%), Positives = 155/282 (54%), Gaps = 12/282 (4%) Query: 4 AIAKRTAFYALVAVIILVAVF------PFYYAILTSLKSGTALFRIDY--WPTDISLANY 55 A+ R +Y LV + + VF PF L SLK LF Y WP + S Y Sbjct: 5 AMINRYRWYELVGIYGGIFVFLTFILAPFVEGFLVSLKPLGRLFSSPYRFWPENGSFEAY 64 Query: 56 AGIF-SHGTFVRNLGNSLLVATLVVAISLLLAVTAAYALARVRFRGRGLLLLTILSVSMF 114 ++ S F R + NS ++ +V A+ L L V AAYA AR +FRG G LL L+V+MF Sbjct: 65 RTMWVSVPGFARYIFNSFFISIIVTAVVLALVVPAAYAFARFKFRGSGALLAAFLAVNMF 124 Query: 115 PQIAVLAGLFELIRFVGIFNTPLALIFSYMIFTLPFTVWVLTTFMRDLPIEIEEAAIVDG 174 +L LF L+R G+ NT A+I + F +P +W+L T+M +P E++EAA VDG Sbjct: 125 SGAVLLIPLFRLMRSFGVLNTYFAMIVPGVAFLIPSAIWLLRTYMMRIPRELDEAAFVDG 184 Query: 175 ASPWVVITRVFMPLMWPALVTTGLLAFIAAW-NEFLFALTFTSSNTQRTVPVAIALLSGG 233 AS + + RV +P+ P + + FI ++ +F+FALTF S + +PV + G Sbjct: 185 ASHFYTLRRVILPIAMPGITVVAITTFIGSYAQQFIFALTFNSKSEYMPLPVGLFAYFG- 243 Query: 234 SQFEIPWGNIMAASVIVTVPLVVLVLIFQRRIISGLTAGGVK 275 + E+ W +MAAS + P V+++ QR ++SGLTAG VK Sbjct: 244 -RQEVVWNELMAASFVGIAPAVIVIFFLQRYLVSGLTAGAVK 284 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: 206 Number of extensions: 16 Number of successful extensions: 3 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: 285 Length adjustment: 26 Effective length of query: 250 Effective length of database: 259 Effective search space: 64750 Effective search space used: 64750 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