Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate RR42_RS32890 RR42_RS32890 ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Cup4G11:RR42_RS32890 Length = 322 Score = 179 bits (453), Expect = 1e-49 Identities = 107/317 (33%), Positives = 173/317 (54%), Gaps = 20/317 (6%) Query: 18 IYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVG 77 ++ + L+ L + + D FL+L N+ N+L Q+S+ ++A GV +I+T G DLS G V Sbjct: 21 LFALGLLCLLLAVASD-AFLTLGNILNVLRQASLLFLLASGVTLVILTGGLDLSVGANVA 79 Query: 78 LAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFIT 137 ++A VAAT+++ AT L + GA+IGL NGL++A L + PFI Sbjct: 80 MSACVAATVMK------------ATGSTMLGVGAGLGTGALIGLANGLLVAMLRIPPFIA 127 Query: 138 TLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAFV 197 T G + +++G+ Y F+ I GF F G++ + + + L+ + Sbjct: 128 TYGMLWVLHGVT---YWFMAGETIHGFPPAFRAIGSGYL----WGVPIPVYLMLVFLVAG 180 Query: 198 WVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSAT 257 + KT +G+ I+AIG NP AA++SGV V L+++Y +SG ++ R+ SA Sbjct: 181 TAMSQKTTYGQEIYAIGANPVAARLSGVPVRRRLVLVYLVSGAMAGIASLVFLARLNSAE 240 Query: 258 NNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYIIK 317 ++G L AIAA ++GG S GGVG V G + G II T++ G+ + V+ WQ ++ Sbjct: 241 GDIGEALTLPAIAAVLIGGTSLFGGVGRVSGTLVGAIILTLVLNGMNLLTVSANWQPLVT 300 Query: 318 GAIIIFAVALDSLKYAR 334 G I++ AV LD+L R Sbjct: 301 GVIVVLAVFLDTLSRKR 317 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: 19 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: 322 Length adjustment: 28 Effective length of query: 308 Effective length of database: 294 Effective search space: 90552 Effective search space used: 90552 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