Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_085635685.1 MGEO_RS05330 ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_002115805.1:WP_085635685.1 Length = 358 Score = 142 bits (357), Expect = 2e-38 Identities = 100/326 (30%), Positives = 166/326 (50%), Gaps = 41/326 (12%) Query: 21 VLLVLLAIIIFQ---DPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVG 77 +++++ AIIIF F S L+ IL Q + ++A + +I+T G DLS VG Sbjct: 48 LIVLVAAIIIFGIALGSKFFSPFALTLILQQVQIVGVLAAAQSLIILTAGIDLS----VG 103 Query: 78 LAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFIT 137 AV+++ ++ F +P + + AIG IG +NG +++ + + PFI Sbjct: 104 AMAVISSVIMGQ-------FTFRYGLPAPMAVAAGLAIGTAIGALNGWLVSRVKLPPFIV 156 Query: 138 TLGTMIIVYGINSLYY--DFVGASPISG-----------FDSGFSTFAQGFVALGSFRLS 184 TLG IV N L+ + + A I F G +TF G + + Sbjct: 157 TLGMWQIVLAANYLFSRNETIRAQDIEANAPFLHFMGYKFQIGGATFTLGVLVM------ 210 Query: 185 YITFYALIAVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAF 244 L+ + +VL N T +G++++A+G +PEAA+++GV+V L+ +Y L G A Sbjct: 211 -----ILLVLLLAYVLRN-TAWGRHVYAVGDDPEAAQLAGVDVHKTLMSVYMLVGFICAL 264 Query: 245 GGMLEAGRIGSATNNL--GFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYG 302 G + GR GS + + G M + +I A V+GG+S GG G+++G G +I V G Sbjct: 265 AGWVMIGRFGSVSPSASTGMMGNIQSITAVVIGGISLFGGRGSILGAFFGALIVGVFELG 324 Query: 303 LTYIGVNPYWQYIIKGAIIIFAVALD 328 L G +P W +++ GA+II AV++D Sbjct: 325 LRMAGADPQWTFLLIGALIIAAVSVD 350 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: 303 Number of extensions: 15 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: 358 Length adjustment: 29 Effective length of query: 307 Effective length of database: 329 Effective search space: 101003 Effective search space used: 101003 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