Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate WP_061945961.1 CPter91_RS07485 ribose ABC transporter permease
Query= TCDB::P23200 (336 letters) >NCBI__GCF_001584185.1:WP_061945961.1 Length = 328 Score = 196 bits (498), Expect = 7e-55 Identities = 124/317 (39%), Positives = 181/317 (57%), Gaps = 20/317 (6%) Query: 13 LKEGGIYVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSA 72 L+ G+ VLL+L+ F ++ NLS I Q+SV I++A G+ +I+T G DLS Sbjct: 22 LRTVGMLPVLLLLVLGFALMSENFFTVQNLSIITQQASVNIVLAAGMTFVILTAGIDLSV 81 Query: 73 GRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNV 132 G + AAVVA +L S+ P+ + IA I G ++GL NG +IA++ + Sbjct: 82 GAILAAAAVVA--MLASLS------PQFGMLGIAAGI----GFGLLLGLANGALIAFMRL 129 Query: 133 TPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALI 192 PFI TLG + + G+ L D + D F+ F LG + ++ AL+ Sbjct: 130 PPFIVTLGALTAMRGLARLLAD---DKTVFNPDLPFA-FIGNDSLLG---VPWLVIIALV 182 Query: 193 AVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGR 252 VA W + +T G I+A+GGN EAA++SG+ V LL +YA+SG+ G ++ A R Sbjct: 183 VVALSWFILRRTVIGVQIYAVGGNHEAARLSGIKVWKVLLFVYAVSGLLAGLGAVMTASR 242 Query: 253 IGSATN-NLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPY 311 + +A LG YELDAIAA ++GG SF+GGVG++ G + G +I V+ GL +GV+ Sbjct: 243 LSAANGLQLGQSYELDAIAAVILGGTSFTGGVGSIGGTLIGALIIAVLTNGLVLLGVSDI 302 Query: 312 WQYIIKGAIIIFAVALD 328 WQYIIKG +II AVALD Sbjct: 303 WQYIIKGIVIIGAVALD 319 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: 14 Number of successful extensions: 4 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: 328 Length adjustment: 28 Effective length of query: 308 Effective length of database: 300 Effective search space: 92400 Effective search space used: 92400 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