Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= SwissProt::A0A0H2VG78 (446 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 271 bits (692), Expect = 4e-77 Identities = 158/451 (35%), Positives = 265/451 (58%), Gaps = 13/451 (2%) Query: 1 MKANKYLIF--ILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVG 58 M + KY+IF I+ ALGG L+G+D VISGA FI + L+ T G+ V+ L G ++G Sbjct: 1 MNSKKYVIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQLSDWTHGMAVAIALYGTVIG 60 Query: 59 AGSSGPLADKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPV 118 A G ADK GR+ ++ I +++ I AL A + ++ + R I GL VG S P+ Sbjct: 61 ALFGGIPADKYGRKTSLLWIGVLYFISALGSALAPDVYSFMFFRFIGGLGVGASSVVAPM 120 Query: 119 YLSEMAPTEYRGSLGSLNQLMITIGILAAYLVNY--AFADI-EGWRWMLGLAVVPSVILL 175 Y+SE+AP + RG L +L Q I GIL AY NY AD+ E WRWM+G+ +P++I Sbjct: 121 YISEIAPAKNRGVLVALYQFNIVFGILMAYFSNYLIEMADLNESWRWMMGMEAIPALIYT 180 Query: 176 VGIYFMPESPRWLLENRNE-EAARQVMKITYDDSEIDKELK---EMKEINAISESTWTVI 231 + +P+SPRWL+ + N+ E A Q+++ T D +D+ + E + I + Sbjct: 181 LLSIRVPKSPRWLIAHHNKVEEATQILRKT-DPEGVDEAIHLAIEERNREKIKVGFAVLF 239 Query: 232 KSPWLGRILIVGCIFAIFQQFIGINAVIFYSSSIFAKAGLGEAASILGSVGIGTINVLVT 291 K L + ++ + A+F Q GINA+I+++ +F AG+ + +++L ++GIG +N++ T Sbjct: 240 KHSHL-KTTLLAIMIALFNQLSGINAIIYFAPRVFEMAGIDQKSALLSTIGIGVVNMIAT 298 Query: 292 IVAIFVVDKIDRKKLLVGGNIGMIASLLIMAILIWTIGIASSAWIIIVCLSLFIVFFGIS 351 ++ ++++D+I RKKL+V G+IG I SLL+MA ++ G+ +S ++ + + +FI + Sbjct: 299 MIGLYLIDRIGRKKLMVIGSIGYIISLLLMA-YSFSGGVINSGYLPLF-VFVFIASHAVG 356 Query: 352 WGPVLWVMLPELFPMRARGAATGISALVLNIGTLIVSLFFPILSDALSTEWVFLIFAFIG 411 G V+WV + E+FP R I I +++ FP +++ +F FA + Sbjct: 357 QGSVIWVFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPASIFGFFAVMM 416 Query: 412 VLAMIFVIKFLPETRGRSLEEIEYELRERTG 442 L +++V+ +PET+GRSLEEI+ +L+ + G Sbjct: 417 GLQLLWVLTKMPETKGRSLEEIQQDLKIKQG 447 Lambda K H 0.327 0.144 0.422 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: 560 Number of extensions: 33 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: 446 Length of database: 448 Length adjustment: 33 Effective length of query: 413 Effective length of database: 415 Effective search space: 171395 Effective search space used: 171395 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: 51 (24.3 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