Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate BWI76_RS17835 BWI76_RS17835 sugar ABC transporter permease
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Koxy:BWI76_RS17835 Length = 279 Score = 120 bits (302), Expect = 3e-32 Identities = 71/235 (30%), Positives = 129/235 (54%), Gaps = 4/235 (1%) Query: 146 PPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVLLA 205 P +F+ +N+ G+ + LNS+ V TV+ + ++A AAYALA F G A++ Sbjct: 48 PNQFSFENFIFAWMDIGVWQYLLNSILVVFFGTVLQVSVSALAAYALARKKFRGVALVSL 107 Query: 206 VVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSA-KTYMGIWLAHTGFGLPLAIYLLRNYMA 264 V++ +++P ++ IPL + N F S +Y+G+ L G+ +I++L +M+ Sbjct: 108 VILSTMMLPEEVIAIPLYMIINWRLPFIDASLYNSYLGMILPVVGWAF--SIFVLTEFMS 165 Query: 265 GLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDD 324 +P+E+ E+AR+DGA+++ IF +ILPL PAL + F F+ W+ L+ ++ + D Sbjct: 166 AIPKELEEAARIDGANEWQIFFHVILPLVKPALGTVVTFGFIMIWDQYLLPLIVVNQ-DS 224 Query: 325 KLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIVFFALQRYLVRGLLAGSVKG 379 + L L I A + ++ +IV+ LQ++ RG+++G+VKG Sbjct: 225 LNTIPVILGTLRTDESITPNIFIAITLLAMLPSIIVYLGLQKHFNRGIMSGAVKG 279 Lambda K H 0.324 0.139 0.418 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: 255 Number of extensions: 13 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: 380 Length of database: 279 Length adjustment: 28 Effective length of query: 352 Effective length of database: 251 Effective search space: 88352 Effective search space used: 88352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 48 (23.1 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