Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate SM_b20714 SM_b20714 sugar uptake ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Smeli:SM_b20714 Length = 341 Score = 196 bits (497), Expect = 9e-55 Identities = 117/320 (36%), Positives = 184/320 (57%), Gaps = 13/320 (4%) Query: 17 GIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQV 76 GI +V VL + + Q ++ L+ ++ Q SV IIA+GV +I+T G DLS+G V Sbjct: 33 GIALVYEVLGWLFVGQS-FLMNSQRLTIMILQVSVIGIIAVGVTQVIITGGIDLSSGSVV 91 Query: 77 GLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFI 136 G+ A+++A++ Q+ ++P + +P + I + IG + G ING +IA + PFI Sbjct: 92 GMTAMISASVAQASTWPRALYPSLTDLPAIVPIGLGVGIGLLAGFINGQLIARTKIPPFI 151 Query: 137 TTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAF 196 TLG M+ G++ Y P+SG F+ G + F + + F+ IA+ + Sbjct: 152 ATLGMMVSARGVSKWY---TKGQPVSGLTEQFNFIGTGIWPVIVFLVVALIFH--IALRY 206 Query: 197 VWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSA 256 TR+GK +AIG N +AA+VSG+NV +L+ +YA++G+ G++ A R +A Sbjct: 207 -------TRYGKFTYAIGANVQAARVSGINVEAHLVKVYAIAGMLAGLAGVVTAARAQTA 259 Query: 257 TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYII 316 +G MYELDAIAA V+GG S +GGVG V G V G +I V+ G T++ V+ Y+Q I+ Sbjct: 260 QAGMGVMYELDAIAATVIGGTSLTGGVGRVTGTVIGTVILGVMTSGFTFLRVDAYYQEIV 319 Query: 317 KGAIIIFAVALDSLKYARKK 336 KG II+ AV +D + +K Sbjct: 320 KGIIIVAAVVVDVYRQKGRK 339 Lambda K H 0.327 0.143 0.415 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: 328 Number of extensions: 17 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: 336 Length of database: 341 Length adjustment: 28 Effective length of query: 308 Effective length of database: 313 Effective search space: 96404 Effective search space used: 96404 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