Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate WP_086511015.1 BZY95_RS16640 MFS transporter
Query= TCDB::P15729 (468 letters) >NCBI__GCF_002151265.1:WP_086511015.1 Length = 468 Score = 471 bits (1213), Expect = e-137 Identities = 235/455 (51%), Positives = 329/455 (72%), Gaps = 3/455 (0%) Query: 16 FVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAFGAG 75 ++ +I +AA+GGFLFGFD+ VING V LQ F +DS+ TG +V+ LLG A+GAF AG Sbjct: 12 YIFMICCIAAIGGFLFGFDSGVINGTVDGLQAAFGSDSVGTGFNVASMLLGCAVGAFFAG 71 Query: 76 PIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEV 135 +ADR GR +I+AA+LF +S+ GSG+ + +F+F+RVLGG+ VGAASV+ PAYI+EV Sbjct: 72 RLADRFGRRTLLIVAAILFLVSAWGSGVAGSSLEFVFYRVLGGMAVGAASVMTPAYISEV 131 Query: 136 SPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIP 195 +PA RGRL ++QQ+AI+SG+F+A LSN+ +A ++G + WL G A WRWMFW EL+P Sbjct: 132 APAAYRGRLATIQQVAIISGLFVAFLSNYVLAHVSGSAMAELWL-GFATWRWMFWIELLP 190 Query: 196 ALLYGVCAFLIPESPRYLVAQG-QGEKAAAILWKVEGGDVPSRIEEIQATVSLDHKPRFS 254 A ++ + IPESPRYL++ G QGE + + G+V +++ EI AT++ DHKPR Sbjct: 191 ATVFLLALLFIPESPRYLISSGKQGEARRVLGLVMPEGEVSAKMAEIDATLARDHKPRLR 250 Query: 255 DLLSRRGGLLP-IVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGFI 313 D+L R G + IVW+G+GL+ QQ VGINV+FYY +VLW+SVGF+E +LLI VI+G + Sbjct: 251 DVLDRTTGKVHGIVWVGIGLAVFQQLVGINVVFYYGAVLWQSVGFSEGDALLINVISGAV 310 Query: 314 NILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIAL 373 +I L+AIA +DK GRKPLL GS+GM +TL ++ F AT+++G+ L G++AL Sbjct: 311 SIGACLLAIALIDKIGRKPLLWAGSVGMALTLACMAFAFSTATLIDGRLRLGDDMGVLAL 370 Query: 374 VTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDTV 433 + AN YVF F SWGP++WV+LGEMF N++R + L++A QW+ANF I+ TFP +L T+ Sbjct: 371 LAANAYVFFFNVSWGPVMWVMLGEMFPNQMRGSGLAIAGLFQWLANFGITMTFPIMLATI 430 Query: 434 GLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 GL AYG YA A +S+FF+ VKET+GK LE+M Sbjct: 431 GLAGAYGFYALCAVVSVFFVLRLVKETRGKELEEM 465 Lambda K H 0.325 0.140 0.430 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: 645 Number of extensions: 26 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: 468 Length of database: 468 Length adjustment: 33 Effective length of query: 435 Effective length of database: 435 Effective search space: 189225 Effective search space used: 189225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 51 (24.3 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