Align MglC aka B2148, component of Galactose/glucose (methyl galactoside) porter (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= TCDB::P23200 (336 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 204 bits (519), Expect = 2e-57 Identities = 118/309 (38%), Positives = 177/309 (57%), Gaps = 8/309 (2%) Query: 20 VVLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGLA 79 + L++L ++ FL+L N N++ Q SV I I++G+ +I+T G DLS G + L Sbjct: 11 IALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSVGSILALC 70 Query: 80 AVVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITTL 139 V A+L+++ + + P+ VIL V +G +G NG I V PF+ TL Sbjct: 71 GAVTASLIKNGIAVEGLNLHIGFAPLGAVILGV-GLGFGLGWFNGWTITRFKVPPFVATL 129 Query: 140 GTMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAFVWV 199 + I G+ L+ G PI+G F+ G+ LG +IT + VA + Sbjct: 130 AMLTIARGLTMLW---TGGFPINGLGEDFAFLGTGWF-LGIPMPVWIT---AVIVALAVL 182 Query: 200 LWNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSATNN 259 L KT+FG+ ++AIGGN AA++SG+N+ + +YA++G A GGM+ R+ SA N Sbjct: 183 LTKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPN 242 Query: 260 LGFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYIIKGA 319 G YELDAIAA V+GG S SGG GT++G V G II V+N GL + V+P+WQ ++KGA Sbjct: 243 AGISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGA 302 Query: 320 IIIFAVALD 328 +I+ AV +D Sbjct: 303 VILLAVVID 311 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: 308 Number of extensions: 16 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: 318 Length adjustment: 28 Effective length of query: 308 Effective length of database: 290 Effective search space: 89320 Effective search space used: 89320 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: 48 (23.1 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