Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_037452166.1 N825_RS13095 ribose ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_000576635.1:WP_037452166.1 Length = 338 Score = 193 bits (490), Expect = 6e-54 Identities = 116/331 (35%), Positives = 188/331 (56%), Gaps = 27/331 (8%) Query: 2 SALNKKSFLTYLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAG 61 +A K++ T ++ G+ VL+++ F FL+ N+S ++ Q+S+ I++A G+ Sbjct: 21 AATRKQNLHTIIQVVGMLPVLILICIGFEFATGKFLTARNISIVMQQASINIVLATGLTF 80 Query: 62 LIVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGL 121 +I+T G DL+ G + ++AV A ++ + P++A +P+AL++ G +G Sbjct: 81 VILTGGIDLAVGAVLAVSAVTAVSMTLTG------MPDLA-IPLALLV------GLALGA 127 Query: 122 INGLIIAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGS- 180 +NG +IA+ + PFI TLG M V G++ L S D+ A F +G+ Sbjct: 128 VNGSLIAFFRLPPFIVTLGAMTAVRGLSRL----------SANDTTVFNAALPFAWIGNS 177 Query: 181 --FRLSYITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALS 238 F + ++ AL VA W + +T G I+ +GGNP+AA++SG+ V LL +YA+S Sbjct: 178 QLFGIPWMVIIALAVVAISWFVLRRTVLGVWIYGVGGNPDAARLSGIKVWAVLLFVYAIS 237 Query: 239 GVFYAFGGMLEAGRIGSATN-NLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFT 297 G+ G++ A R SA LG YELDAIAA ++GG SF GG+G++ G + G +I Sbjct: 238 GMLAGLAGVMSAARTLSANGAQLGMGYELDAIAAVILGGTSFVGGIGSIFGTLIGALIIA 297 Query: 298 VINYGLTYIGVNPYWQYIIKGAIIIFAVALD 328 V++ GL + V+ WQ IIKG +I+ AVALD Sbjct: 298 VLSNGLILMNVSEVWQLIIKGLVIVGAVALD 328 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: 287 Number of extensions: 18 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: 338 Length adjustment: 28 Effective length of query: 308 Effective length of database: 310 Effective search space: 95480 Effective search space used: 95480 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