Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate N515DRAFT_2414 N515DRAFT_2414 simple sugar transport system permease protein
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Dyella79:N515DRAFT_2414 Length = 358 Score = 122 bits (306), Expect = 1e-32 Identities = 97/317 (30%), Positives = 152/317 (47%), Gaps = 24/317 (7%) Query: 20 VVLLVLLAIIIFQDPTFLSLL--------NLSNILTQSSVRIIIALGVAGLIVTQGTDLS 71 + L++LLA +P FL+L NL +I +++ +++LG+ +I +G D+S Sbjct: 35 LTLILLLAGNGLFNPGFLALQWRDGHLYGNLIDIAHRAAPLALVSLGMTLVIALRGLDIS 94 Query: 72 AGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLN 131 G + +AA VAA + + N +P+ L I A GA+ GL NG ++ Sbjct: 95 VGAVLAIAATVAAWTIGHVSNDG-------LLPLWLAIAAALAAGALCGLWNGWLVVGAG 147 Query: 132 VTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYAL 191 + P + TL M+ GI G ++ + + +S GFV LG L + F Sbjct: 148 MQPIVATLILMVAGRGIAQ---SISGGQILTLYYAPYSFLGNGFV-LG---LPFSLFVVA 200 Query: 192 IAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAG 251 A + + KT G + AIG NP+AA V+GV L Y G+ A G+L + Sbjct: 201 AVFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAITLGAYVFCGIAAALAGLLVSS 260 Query: 252 RIGSA-TNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNP 310 + SA NN G + ELDAI A +GG GG ++ G + G +I + + IGV P Sbjct: 261 NVNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGSLLGALIIQALTTTIYAIGVPP 320 Query: 311 YWQYIIKGAIIIFAVAL 327 +K A+++FAV L Sbjct: 321 QVNLAVK-AVLVFAVML 336 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: 289 Number of extensions: 19 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: 358 Length adjustment: 29 Effective length of query: 307 Effective length of database: 329 Effective search space: 101003 Effective search space used: 101003 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