Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_004124021.1 RHSP_RS23175 ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_000359745.1:WP_004124021.1 Length = 350 Score = 199 bits (507), Expect = 7e-56 Identities = 115/326 (35%), Positives = 188/326 (57%), Gaps = 12/326 (3%) Query: 15 EGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGR 74 EG + L+V++A+ F P + +L N + + ++ I+A+G+ +I+ G DLS G Sbjct: 28 EGRAFFALIVIIAVFSFLSPNYFTLGNFLTMSSHVAIFGILAIGMLLVILNGGIDLSVGS 87 Query: 75 QVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTP 134 +GLA VA L+Q + ++ F + P+ V+++ CA GA+IG +NG+++AYL V Sbjct: 88 TLGLAGCVAGFLMQGVTLSS--FGVILYPPVWAVVVLTCAFGAIIGAVNGVLVAYLRVPA 145 Query: 135 FITTLGTMIIVYGI-----NSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFY 189 F+ +LG + + GI N L Y+ +G P G ++GF GF L +S I Sbjct: 146 FVASLGVLYVARGIALLMTNGLTYNNLGGRPELG-NTGFGWL--GFNRLAGIPISVIVLA 202 Query: 190 ALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLE 249 AL + ++ ++T FG+ ++A GGN AA +SGV V +++Y LSGV A G++ Sbjct: 203 ALAIIC--GLVLSRTAFGRWLYASGGNERAADLSGVPVKRVKIIVYVLSGVCAAIAGLVL 260 Query: 250 AGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVN 309 + ++ SA G YEL AIAA V+GG + +GG GT G + G + ++ GL IGV+ Sbjct: 261 SSQLTSAGPTAGTTYELTAIAAVVIGGAALTGGRGTTRGTMLGAFVIGFLSDGLVIIGVS 320 Query: 310 PYWQYIIKGAIIIFAVALDSLKYARK 335 YWQ + GA+I+ AV ++S++Y R+ Sbjct: 321 AYWQTVFTGAVIVLAVLMNSIQYGRR 346 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: 337 Number of extensions: 16 Number of successful extensions: 4 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: 350 Length adjustment: 29 Effective length of query: 307 Effective length of database: 321 Effective search space: 98547 Effective search space used: 98547 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