Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate BPHYT_RS27190 BPHYT_RS27190 sugar ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__BFirm:BPHYT_RS27190 Length = 343 Score = 169 bits (428), Expect = 9e-47 Identities = 115/328 (35%), Positives = 165/328 (50%), Gaps = 39/328 (11%) Query: 22 LLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAG--LIVTQGTDLSAGRQVGLA 79 L+VL+ F S+ NL + Q V I LGVA +I+T G DLS G + LA Sbjct: 33 LVVLIVAFSLTSAAFFSVGNLMTVALQ--VTSIAYLGVAATCVIITGGIDLSVGSVLALA 90 Query: 80 AVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITTL 139 V AA L++ A +PI + +L +GA G +NG+ + + + PFI TL Sbjct: 91 GVAAALLVK------------AGVPIPVAMLGGMLVGAACGWVNGICVTRMGLPPFIATL 138 Query: 140 GTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYI------------- 186 G M++ G L GA P+SG F G + FR+S+I Sbjct: 139 GMMLVARG---LALQITGARPVSGLGDAFGELGNGAL----FRISHIGADGFPDTVFPGI 191 Query: 187 ---TFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYA 243 ++ A V +L ++T G++I+A+G N EAA++SGVNV L Y LSG+ Sbjct: 192 PYPVVIMVVLFAAVSILLSRTSLGRHIYAVGSNAEAARLSGVNVQGVKLFTYVLSGLLAG 251 Query: 244 FGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGL 303 G + R+ +A N G MYELDAIA+ V+GG S GGVGT+ G G + V+ GL Sbjct: 252 ATGCVLMSRLVTAQPNEGVMYELDAIASAVIGGTSLMGGVGTISGTAIGAFVIGVLRNGL 311 Query: 304 TYIGVNPYWQYIIKGAIIIFAVALDSLK 331 GV+ + Q II G +I+ V +D L+ Sbjct: 312 NMNGVSSFIQQIIIGVVILGTVWIDQLR 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: 294 Number of extensions: 18 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: 343 Length adjustment: 28 Effective length of query: 308 Effective length of database: 315 Effective search space: 97020 Effective search space used: 97020 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