Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 155 bits (391), Expect = 2e-42 Identities = 106/335 (31%), Positives = 170/335 (50%), Gaps = 32/335 (9%) Query: 7 KSFLTYLKEGGIYVVLLVLLAII----IFQDPTFLSLLNLSNILTQSSVRIIIALGVAGL 62 + F L + V L+VL+A I + F S L+ IL Q + I+A + + Sbjct: 34 RKFQHALHQTPALVPLIVLVAAIAVFGLLLGSKFFSPFALTLILQQVQIVGIVAAAQSLV 93 Query: 63 IVTQGTDLSAGRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLI 122 I+T G DLS G + +++VV F +P+ + + G ++G I Sbjct: 94 ILTAGIDLSVGAIMVMSSVVMGQ-----------FTFRYGLPVEVAVACGLLCGTLLGFI 142 Query: 123 NGLIIAYLNVTPFITTLGTMIIVYGINSLY--------YDFVGASPISGFDSGFSTFAQG 174 NG ++A + + PFI TLG IV N LY D +P+ F F T + Sbjct: 143 NGWLVAKVKLPPFIVTLGMWQIVLAANFLYSRNETIRSQDIRDQAPLLQF---FGTTLE- 198 Query: 175 FVALGSFRLSY-ITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLM 233 +G RL+Y + F L+ + + L T +G++++A+G +PEAA++SGV V L+ Sbjct: 199 ---IGGARLTYGVIFMVLLVIVLAYAL-RHTAWGRHVYAVGDDPEAAELSGVQVSRTLIS 254 Query: 234 IYALSGVFYAFGGMLEAGRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGV 293 +Y LSG+ AF G GRIGS + G + +++I A V+GG+S GG G+++G G Sbjct: 255 VYMLSGLICAFAGWALIGRIGSVSPTSGQLANIESITAVVIGGISLFGGRGSILGAFFGA 314 Query: 294 IIFTVINYGLTYIGVNPYWQYIIKGAIIIFAVALD 328 +I V GL +G + W +++ G +II AVA+D Sbjct: 315 LIVGVFTLGLRLLGADAQWTFLLIGLLIIAAVAVD 349 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: 289 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: 357 Length adjustment: 29 Effective length of query: 307 Effective length of database: 328 Effective search space: 100696 Effective search space used: 100696 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