Align Glucose transporter GlcP; Glucose/H(+) symporter (characterized)
to candidate 353132 BT3606 sugar-proton symporter (NCBI ptt file)
Query= SwissProt::A0A0H2VG78 (446 letters) >FitnessBrowser__Btheta:353132 Length = 468 Score = 281 bits (719), Expect = 3e-80 Identities = 170/457 (37%), Positives = 264/457 (57%), Gaps = 33/457 (7%) Query: 6 YLIF--ILGALGGLLYGYDNGVISGALLFIHKDIPLNSTTEGIVVSSMLIGAIVGAGSSG 63 Y+IF ++ ALGG L+GYD VISG + + L++ +G V LIG+IVG SG Sbjct: 9 YIIFLSVVAALGGFLFGYDTAVISGTIAQVTHLFQLDTLQQGWYVGCALIGSIVGVLFSG 68 Query: 64 PLADKLGRRRLVMLIAIVFIIGALILAASTNLALLIIGRLIIGLAVGGSMSTVPVYLSEM 123 L+D +GR+R ++L AI+F A+ A + L++ R+I G+ +G P+Y+SE+ Sbjct: 69 ILSDSIGRKRTMILSAILFSTSAIGCAFCIDFNQLVVYRIIGGIGIGVVSIVSPLYISEV 128 Query: 124 APTEYRGSLGSLNQLMITIGILAAYLVNY---AFAD---------------IEGWRWMLG 165 + ++RG + SL QL +T+G L AYLVNY A+++ E WR MLG Sbjct: 129 SVAQFRGRMVSLYQLAVTVGFLGAYLVNYQLLAYSESGNHLPIAWLEKIVVTEVWRGMLG 188 Query: 166 LAVVPSVILLVGIYFMPESPRWLLENRNEEAARQVMKITYDD-SEIDKELKEMKEINAIS 224 + +P++I + I+F+PESPRWL+ E A +++ Y+ E D +L E K + +S Sbjct: 189 METLPAIIFFIIIFFIPESPRWLIVKGQERKATYILEKIYNSFKEADFQLNETKSV-LVS 247 Query: 225 E--STWTVIKSPWLGRILIVGCIFAIFQQFIGINAVIFYSSSIFAKAGLGEAASILGSVG 282 E S W+++ P + + +I+G AI QF+G+NAV++Y SIF AGL S+ V Sbjct: 248 ETRSEWSILLKPGILKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGDSLFYQVL 307 Query: 283 IGTINVLVTIVAIFVVDKIDRKKLLVGGNIGMIASLLIMAILIWTIGIASSAWII--IVC 340 +G +N L TI+A+ ++DK+ RKKL+ G GM+ SL ILI + + +AW I + Sbjct: 308 VGLVNTLTTILALLIIDKVGRKKLIYYGVSGMVVSL----ILIGSYFLFGNAWNISSLFL 363 Query: 341 LSLFIVFF---GISWGPVLWVMLPELFPMRARGAATGISALVLNIGTLIVSLFFPILSDA 397 L+ F+ + IS V++V+L E++P + RG A I+ L IGT ++ P + Sbjct: 364 LAFFLCYVFCCAISICAVIFVLLSEMYPTKIRGLAMSIAGFALWIGTYLIGQLTPWMLQN 423 Query: 398 LSTEWVFLIFAFIGVLAMIFVIKFLPETRGRSLEEIE 434 L+ F +FA + V M+ V K +PET G+SLEEIE Sbjct: 424 LTPAGTFFLFAIMCVPYMLIVWKLVPETTGKSLEEIE 460 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: 626 Number of extensions: 33 Number of successful extensions: 6 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: 468 Length adjustment: 33 Effective length of query: 413 Effective length of database: 435 Effective search space: 179655 Effective search space used: 179655 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