Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate BWI76_RS06705 BWI76_RS06705 binding-protein-dependent transport system inner membrane protein
Query= reanno::Smeli:SMc03063 (380 letters) >FitnessBrowser__Koxy:BWI76_RS06705 Length = 283 Score = 115 bits (289), Expect = 1e-30 Identities = 75/246 (30%), Positives = 130/246 (52%), Gaps = 8/246 (3%) Query: 136 GQRIFFTATTPPRFTLDNYAEVLSA-AGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAW 194 G + T+ P + +YA++ + + NS+ ++ + V+ ++ +F AYA + Sbjct: 44 GNSLLSTSIIPENLSFQHYADLFNGNVNYLTWYWNSMKISFMTMVLTLISVSFTAYAFSR 103 Query: 195 MPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPL 254 F GR L + + L ++P +LI + L +G +++ + L + G +P+ Sbjct: 104 FRFKGRQNGLMLFLLLQMIPQFSALIAIFVLSQLLGLI-----NSHLALVLIYVGGMIPM 158 Query: 255 AIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLV 314 +L++ Y+ +P+++ ESAR+DGAS F IF +II+PLS P LA A+F F D ++ Sbjct: 159 NTWLMKGYLDAIPKDLDESARMDGASSFRIFFEIIMPLSKPILAVVALFSFTGPLGDFIL 218 Query: 315 AIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPL-IVFFALQRYLVRGLL 373 + L DK L L NL+ + G A+ + I VP+ I++ ALQ+Y V GL Sbjct: 219 SSTILRT-PDKYTLPIGLYNLVAQKMGASYTTYAAGAVLIAVPVAILYLALQKYFVSGLT 277 Query: 374 AGSVKG 379 +GS KG Sbjct: 278 SGSTKG 283 Score = 29.3 bits (64), Expect = 1e-04 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 4/91 (4%) Query: 130 RMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAG-IGRSFLNSLTVAVPST-VIPILIAAF 187 RM+G+ RIFF P + + S G +G L+S + P +PI + Sbjct: 179 RMDGASSFRIFFEIIMPLSKPILAVVALFSFTGPLGDFILSSTILRTPDKYTLPIGLYNL 238 Query: 188 AAYAL--AWMPFPGRAVLLAVVVGLLVVPLQ 216 A + ++ + AVL+AV V +L + LQ Sbjct: 239 VAQKMGASYTTYAAGAVLIAVPVAILYLALQ 269 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: 253 Number of extensions: 12 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 380 Length of database: 283 Length adjustment: 28 Effective length of query: 352 Effective length of database: 255 Effective search space: 89760 Effective search space used: 89760 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