Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_004127101.1 RHSP_RS28500 ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_000359745.1:WP_004127101.1 Length = 341 Score = 211 bits (537), Expect = 2e-59 Identities = 135/328 (41%), Positives = 189/328 (57%), Gaps = 20/328 (6%) Query: 15 EGGIYVVLLVLLAII-----IFQDPTFL-SLLNLSNILTQSSVRIIIALGVAGLIVTQGT 68 E GI++VL+ + + IF +FL +L L ++ Q SV II++GV +I+T G Sbjct: 24 ELGIFLVLIGIALLCEILGWIFVGQSFLMNLQRLKIMILQVSVIGIISVGVTQVIITGGI 83 Query: 69 DLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIA 128 DLS+G VGL A+VAA+ QS A V+P + MP + I I IG V G ING +I Sbjct: 84 DLSSGSVVGLTAMVAASFAQSSTWARAVYPALTDMPFFVPIGIGLLIGLVAGYINGQLIT 143 Query: 129 YLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITF 188 + PFI TLG M+ G++ LY PISG F+ G + Sbjct: 144 RTKIPPFIATLGMMVSARGLSKLY---TKGQPISGLTDQFNFIGSGIWP--------VVV 192 Query: 189 YALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGML 248 + +IAV F VL TR+GK +AIG N +AA+VSG+NV +L+ +YA++G+ G++ Sbjct: 193 FLIIAVVFHIVL-RYTRYGKFTYAIGANVQAARVSGINVEGHLVKVYAIAGLLAGLAGII 251 Query: 249 EAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGV 308 A R+ +A +G YELDAIAA V+GG S +GGVG + G V G II V+ G T++ V Sbjct: 252 TAARVQTAQAGMGVTYELDAIAAAVIGGTSLTGGVGRIAGTVIGTIILGVMISGFTFLNV 311 Query: 309 NPYWQYIIKGAIIIFAVALDSLKYARKK 336 + Y+Q I KG III AVA+D Y +KK Sbjct: 312 DAYYQEIAKGVIIIAAVAID--VYRQKK 337 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: 334 Number of extensions: 22 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: 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 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