Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_108223269.1 C8J29_RS11820 ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_003046325.1:WP_108223269.1 Length = 363 Score = 152 bits (383), Expect = 2e-41 Identities = 97/318 (30%), Positives = 160/318 (50%), Gaps = 20/318 (6%) Query: 20 VVLLVLLAII-IFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGL 78 +VL+V ++I F S L+ IL Q ++ I+ +++T G DLS G + L Sbjct: 49 IVLVVSVSIFGALLGQKFFSAFTLTLILQQVAIVGIVGAAQTLVVLTAGIDLSVGAIMVL 108 Query: 79 AAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITT 138 ++V+ F +P L +L A GA IG +NG ++A + + PFI T Sbjct: 109 SSVIMGQ-----------FTFRYGIPAPLSVLCGLAAGAGIGFVNGTLVARMKLPPFIVT 157 Query: 139 LGTMIIVYGINSLY--------YDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYA 190 LG IV N LY D +PI F G +Y Sbjct: 158 LGMWQIVLAANFLYSANETIRSQDISAQAPILQFFGNTFRLGADEAGRGGAVFTYGAVLL 217 Query: 191 LIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEA 250 ++ V + + +T +G++++A+G +P+AA+++GV L+ +Y LSG+ A G + Sbjct: 218 ILLVLVIAYVLRQTAWGRHVYAVGDDPDAAELAGVQTRNVLVTVYTLSGLICALAGWVMI 277 Query: 251 GRIGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNP 310 GR+GS + G +++I A V+GG+S GG G+V+G++ G +I V + GL +G +P Sbjct: 278 GRLGSVSPTAGQFANIESITAVVIGGISLFGGRGSVLGMLFGALIVGVFSLGLKLMGTDP 337 Query: 311 YWQYIIKGAIIIFAVALD 328 W Y++ G +II AVA+D Sbjct: 338 QWTYLLIGMLIIAAVAVD 355 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: 283 Number of extensions: 10 Number of successful extensions: 2 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: 363 Length adjustment: 29 Effective length of query: 307 Effective length of database: 334 Effective search space: 102538 Effective search space used: 102538 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 24 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