Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 17810 b3750 ribose ABC transporter permease protein (NCBI)
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Keio:17810 Length = 321 Score = 193 bits (491), Expect = 4e-54 Identities = 116/323 (35%), Positives = 183/323 (56%), Gaps = 21/323 (6%) Query: 12 YLKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLS 71 +L E + LLVL+AI+ P F ++ NL NIL Q+SV I+A+G+ +I+T G DLS Sbjct: 16 WLMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLS 75 Query: 72 AGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLN 131 G + L VAA+++ NA + + A+GA IG + G+I+A Sbjct: 76 VGSLLALTGAVAASIVGIEVNA------------LVAVAAALALGAAIGAVTGVIVAKGR 123 Query: 132 VTPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFR-LSYITFYA 190 V FI TL M+++ G+ +Y SP++ +GF+ A F G R L T Sbjct: 124 VQAFIATLVMMLLLRGVTMVY---TNGSPVN---TGFTENADLFGWFGIGRPLGVPTPVW 177 Query: 191 LIAVAFV--WVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGML 248 ++ + F+ W + + TR G+ I+A+GGN A ++SG+NV +++Y+L G+ + G++ Sbjct: 178 IMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGII 237 Query: 249 EAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGV 308 E R+ SA G YELDAIAA V+GG S +GG G ++G + G +I +N GL +GV Sbjct: 238 EVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGV 297 Query: 309 NPYWQYIIKGAIIIFAVALDSLK 331 + Y+Q I+K +I+ AV +D+ K Sbjct: 298 SSYYQMIVKAVVILLAVLVDNKK 320 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: 296 Number of extensions: 22 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: 321 Length adjustment: 28 Effective length of query: 308 Effective length of database: 293 Effective search space: 90244 Effective search space used: 90244 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