Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 187 bits (476), Expect = 2e-52 Identities = 101/313 (32%), Positives = 176/313 (56%), Gaps = 11/313 (3%) Query: 33 ITEYSLIVIFVVMFATMSLTVDHFFSIENMLGLALSISQIGMVSCTMMFCLASRDFDLSV 92 I ++ ++ +++ +SL D F ++ N + +S +S M + + DLSV Sbjct: 4 IAKFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSV 63 Query: 93 GSTVAFAGVLCA-MVLNATG----NTFI------AIVAAVAAGGVIGFVNGAVIAYLRIN 141 GS +A G + A ++ N N I A++ V G +G+ NG I ++ Sbjct: 64 GSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVP 123 Query: 142 ALITTLATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLSFFGVSLPIWVTLLCFIVFGVM 201 + TLA + I RGL + + G + + F LG F G+ +P+W+T + + ++ Sbjct: 124 PFVATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLL 183 Query: 202 LNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNA 261 +T +GR AIGGN A+RL+GIN+ R ++ ++ I G + A+ G+I+ SR+ S QPNA Sbjct: 184 TKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNA 243 Query: 262 AQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLMNIDAFYQYLVRGAI 321 +EL+ I+A V+GG SL GG+ TI G V+G +I+G + N + L+N+ F+Q +V+GA+ Sbjct: 244 GISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAV 303 Query: 322 LLAAVLLDQLKNR 334 +L AV++D+ ++ Sbjct: 304 ILLAVVIDKANSK 316 Lambda K H 0.326 0.139 0.396 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: 310 Number of extensions: 20 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: 338 Length of database: 318 Length adjustment: 28 Effective length of query: 310 Effective length of database: 290 Effective search space: 89900 Effective search space used: 89900 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: 49 (23.5 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