Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate HSERO_RS03645 HSERO_RS03645 ribose ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__HerbieS:HSERO_RS03645 Length = 339 Score = 192 bits (488), Expect = 1e-53 Identities = 114/316 (36%), Positives = 177/316 (56%), Gaps = 24/316 (7%) Query: 18 IYVVLLVL---LAIIIFQDPT--FLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSA 72 + VVL +L L + + D T F S N NIL Q ++ +++A G+ +I+T G DLS Sbjct: 32 VLVVLYLLFYGLTLYLSGDGTSNFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSV 91 Query: 73 GRQVGLAAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNV 132 G + ++AV+ + + P + + + + G V+G++NG ++A LN+ Sbjct: 92 GSVLAVSAVLGMQV------------SLGAAPGWAIPMFIFS-GLVMGMVNGAMVALLNI 138 Query: 133 TPFITTLGTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALI 192 F+ TLGTM G L D G + ++ F G + ++ + A+ Sbjct: 139 NAFVVTLGTMTAFRGAAYLLAD--GTTVLNNDIPSFEWIGNG----DFLHVPWLIWVAVA 192 Query: 193 AVAFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGR 252 V WV+ KT G +I+AIGGN +AA+++G+ VGL LL +Y++SG+F G + A R Sbjct: 193 VVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLLFVYSISGLFSGLAGAMSASR 252 Query: 253 IGSATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYW 312 + A N G YELDAIAA V+GG S GGVG++ G V G +I V+N GLT +G++ +W Sbjct: 253 LYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVGALIIGVMNNGLTILGLSSFW 312 Query: 313 QYIIKGAIIIFAVALD 328 QY+ KGA+I+ AV LD Sbjct: 313 QYVAKGAVIVLAVILD 328 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: 306 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: 339 Length adjustment: 28 Effective length of query: 308 Effective length of database: 311 Effective search space: 95788 Effective search space used: 95788 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