Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate H281DRAFT_02703 H281DRAFT_02703 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Burk376:H281DRAFT_02703 Length = 333 Score = 188 bits (478), Expect = 1e-52 Identities = 118/324 (36%), Positives = 172/324 (53%), Gaps = 20/324 (6%) Query: 16 GGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQ 75 G ++ L+++ + P FL+ L+NI+ Q SV I A+G +I+T G DLS G Sbjct: 27 GPLFAALVIICIALSIASPEFLTTSTLTNIMVQVSVVGIAAVGGTFVIITSGIDLSVGSL 86 Query: 76 VGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCA---IGAVIGLINGLIIAYLNV 132 V L +VAAT++ I L I +CA +GA G +NGL +A+L + Sbjct: 87 VALTGMVAATVMAGSSPG----------AIGLGIAGLCAALAVGAAAGALNGLAVAWLRL 136 Query: 133 TPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALI 192 PFI TL M + G+ D G + F + F+ F VA L L+ Sbjct: 137 VPFIVTLAMMAMARGLTLAISD--GRTKFD-FPNAFTAFGAKTVA----GLPMPMIVMLV 189 Query: 193 AVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGR 252 VL KT FG +FA+GGN EAA+++G+ V + + Y L+GV A G++ AGR Sbjct: 190 IFVIGHVLLRKTTFGHQVFAVGGNQEAARLAGIPVHRVVFLTYMLAGVTAAIAGIVLAGR 249 Query: 253 IGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYW 312 + SA + EL IAA V+GG S +GG G+++G GV++ VIN GL+ +GVNP+W Sbjct: 250 LNSALPSAANGLELQVIAAVVIGGTSLAGGRGSIVGTFIGVVLIGVINVGLSLLGVNPFW 309 Query: 313 QYIIKGAIIIFAVALDSLKYARKK 336 I+G +I AV LD+L RK+ Sbjct: 310 TQFIQGGVIFAAVLLDALSQRRKQ 333 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: 293 Number of extensions: 17 Number of successful extensions: 5 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: 333 Length adjustment: 28 Effective length of query: 308 Effective length of database: 305 Effective search space: 93940 Effective search space used: 93940 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