Align ABC transporter for D-Trehalose, permease component 1 (characterized)
to candidate WP_011648808.1 RL_RS32980 sugar ABC transporter permease
Query= reanno::Smeli:SM_b20326 (328 letters) >NCBI__GCF_000009265.1:WP_011648808.1 Length = 312 Score = 171 bits (434), Expect = 2e-47 Identities = 96/299 (32%), Positives = 167/299 (55%), Gaps = 20/299 (6%) Query: 32 WLFLAPTFLVLALVAGWPLIRTIYFSFTNASLTNLSGAEFVGFANYLSWITLKSGRTIYR 91 W F+ P +V+A V +P + T++ S + +L F G NY Sbjct: 29 WPFVIPALIVIAAVIVFPWVFTLWMSVNSWTLGQ--SQVFAGLDNYAR------------ 74 Query: 92 GLLADPAWWNAVWNTLKFTVLSVSIETALGLIVALVLNAQFPGRGLVRAAILIPWAIPTI 151 L+ D +W+++W+T+ +T LSV + LG + AL+ +AQFP RGL+R ++P + Sbjct: 75 -LVVDMRFWDSLWHTVLYTTLSVVVPLFLGTLAALIFDAQFPLRGLIRGIFVMPMMATPV 133 Query: 152 VSAKMWAWMLNDQFGILNDMLIGLGLIGEKIAWTASPDTAMIAELIVDVWKTTPFMALLI 211 A +W M + Q G+LN +L +G+ ++ W + + + + ++V+ W+ TP + L++ Sbjct: 134 AIALVWTMMYHPQLGVLNYLLSFIGIGPQE--WIYNQSSVIPSLVLVETWQWTPLIMLIV 191 Query: 212 LAGLQMVPGDIYEAAKIDGVHPVRVFWRVTLPLIRPALMVAVIFRMLDALRIFDLIYVLT 271 L GL VP + YE+A+IDG + + F +TLP+I P LM+AVI R +DA++ FD+IY +T Sbjct: 192 LGGLAAVPREPYESAEIDGANVWQKFRYLTLPMIAPFLMIAVIIRSIDAVKSFDIIYAMT 251 Query: 272 PNNAQT--KTMSVMARENLFDFDKFAYGAAASTMLFLIIATITILYMWL-GRLNLSGGE 327 T +T+++ F + YG+A + + F++I ++ + M L R+N S GE Sbjct: 252 QGGPGTASETINIYLYNTAFAYYDIGYGSAMAVVFFILIVLLSFVLMMLRQRVNWSDGE 310 Lambda K H 0.328 0.140 0.438 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: 349 Number of extensions: 20 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: 328 Length of database: 312 Length adjustment: 28 Effective length of query: 300 Effective length of database: 284 Effective search space: 85200 Effective search space used: 85200 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 (21.7 bits) S2: 48 (23.1 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