Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate HSERO_RS05255 HSERO_RS05255 ribose ABC transporter permease
Query= TCDB::P23200 (336 letters) >FitnessBrowser__HerbieS:HSERO_RS05255 Length = 347 Score = 184 bits (468), Expect = 2e-51 Identities = 114/321 (35%), Positives = 170/321 (52%), Gaps = 18/321 (5%) Query: 19 YVVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGL 78 + LL+++ F P F+ + NL +IL ++V ++A+ +I+T G DLS G + Sbjct: 40 FASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTF 99 Query: 79 AAVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITT 138 AV+A +L + MP+ L I GA+ G I+G++IA L V PFI T Sbjct: 100 CAVMAGVVLTNWG-----------MPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIAT 148 Query: 139 LGTMIIVYGINSLYYDFVGASPISGFDS-GFSTFAQGFVA---LGSFRLSYITFYALIAV 194 LG M+++ G++ + G PI D+ GFS AQ + + S + + Sbjct: 149 LGMMMLLKGLSLV---ISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVA 205 Query: 195 AFVWVLWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIG 254 ++ NKT FG+ FA+G N EA ++SGV V + +Y SG G++ A R+ Sbjct: 206 IGASIILNKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLN 265 Query: 255 SATNNLGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQY 314 SA LG YELDAIAA V+GG S SGG GT++G + G I +V+ GL + V WQ Sbjct: 266 SAQPALGQGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQT 325 Query: 315 IIKGAIIIFAVALDSLKYARK 335 ++ G III AV LD L+ R+ Sbjct: 326 VVTGVIIILAVYLDILRRRRR 346 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: 285 Number of extensions: 18 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: 347 Length adjustment: 29 Effective length of query: 307 Effective length of database: 318 Effective search space: 97626 Effective search space used: 97626 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