Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate GFF2762 PGA1_c28050 putative sugar transport system, permease protein
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Phaeo:GFF2762 Length = 353 Score = 152 bits (383), Expect = 2e-41 Identities = 98/313 (31%), Positives = 165/313 (52%), Gaps = 17/313 (5%) Query: 21 VLLVLLAIIIFQ---DPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVG 77 +++++L++I+F F S L+ IL Q + I+A + +I+T G DLS G + Sbjct: 45 LIVLVLSVIVFGLLLGSKFFSPFALTLILQQVGIVGIVACAQSLVILTAGIDLSVGAIMV 104 Query: 78 LAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFIT 137 L++VV F +A+ ++C G + G ING ++A + + PFI Sbjct: 105 LSSVVMGQF---------TFRYGLPPEVAVACGLIC--GTICGFINGWLVARMKLPPFIV 153 Query: 138 TLGTMIIVYGINSLYY--DFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVA 195 TLG IV N LY + + + I+ F + + +G +Y + +I V Sbjct: 154 TLGMWQIVLASNFLYSANETIRSQTIAAEAPLLQLFGEK-IKIGGAVFTYGVIFMVILVV 212 Query: 196 FVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGS 255 + + T +G++++A+G +PEAA++SGV V L+ +Y LSG+ AF G GRIGS Sbjct: 213 LLAYVLRHTAWGRHVYAVGDDPEAAELSGVKVTRVLISVYMLSGLICAFAGWAMIGRIGS 272 Query: 256 ATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYI 315 + G + +++I A V+GG+S GG G+++G G +I V GL +G + W Y+ Sbjct: 273 VSPTSGQLANIESITAVVIGGISLFGGRGSILGTFFGALIVGVFTLGLRLLGADAQWTYL 332 Query: 316 IKGAIIIFAVALD 328 + G +II AVA+D Sbjct: 333 LIGLLIIAAVAVD 345 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: 312 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 336 Length of database: 353 Length adjustment: 29 Effective length of query: 307 Effective length of database: 324 Effective search space: 99468 Effective search space used: 99468 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