Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 18114 b4086 D-allose transporter subunit (NCBI)
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Keio:18114 Length = 326 Score = 174 bits (441), Expect = 3e-48 Identities = 108/324 (33%), Positives = 172/324 (53%), Gaps = 19/324 (5%) Query: 8 SFLTYLKEGGIYVVLLVLLAIIIFQDPT-FLSLLNLSNILTQSSVRIIIALGVAGLIVTQ 66 +F + + G + +L +++AI P FL+ N++ I QSSV ++I +G I+ Sbjct: 18 NFALFWDKYGTFFILAIIVAIFGSLSPEYFLTTNNITQIFVQSSVTVLIGMGEFFAILVA 77 Query: 67 GTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLI 126 G DLS G + L+ +V A L+ + V P +A M +++ G +G ING + Sbjct: 78 GIDLSVGAILALSGMVTAKLMLA-----GVDPFLAAMIGGVLV------GGALGAINGCL 126 Query: 127 IAYLNVTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYI 186 + + + PFI TLGT I GI + D A+ + GF F F A + Sbjct: 127 VNWTGLHPFIITLGTNAIFRGITLVISD---ANSVYGFSFDFVNF----FAASVIGIPVP 179 Query: 187 TFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGG 246 ++LI +W L + R G+NI+A+GGN +A SG++V ++L+++ +SGV G Sbjct: 180 VIFSLIVALILWFLTTRMRLGRNIYALGGNKNSAFYSGIDVKFHILVVFIISGVCAGLAG 239 Query: 247 MLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYI 306 ++ R+G+A G +E AIA+ ++GG SF GG G + VV G +I IN GL + Sbjct: 240 VVSTARLGAAEPLAGMGFETYAIASAIIGGTSFFGGKGRIFSVVIGGLIIGTINNGLNIL 299 Query: 307 GVNPYWQYIIKGAIIIFAVALDSL 330 V Y+Q ++ G +II AVALD L Sbjct: 300 QVQTYYQLVVMGGLIIAAVALDRL 323 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: 378 Number of extensions: 24 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: 326 Length adjustment: 28 Effective length of query: 308 Effective length of database: 298 Effective search space: 91784 Effective search space used: 91784 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