Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate 349964 BT0436 arabinose-proton symporter (NCBI ptt file)
Query= TCDB::P15729 (468 letters) >FitnessBrowser__Btheta:349964 Length = 468 Score = 293 bits (749), Expect = 1e-83 Identities = 166/469 (35%), Positives = 269/469 (57%), Gaps = 20/469 (4%) Query: 9 QSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSA 68 +ST N +++ +S VAALGGFLFG+DTAVI+G +A + + FQ D+L G V AL+GS Sbjct: 2 KSTINFGYLIFLSVVAALGGFLFGYDTAVISGTIAQVTQLFQLDTLQQGWYVGCALIGSI 61 Query: 69 LGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIA 128 +G AG ++D+ GR TMI++A LF+ S++G + + +R++GG+G+G S+++ Sbjct: 62 VGVLFAGILSDKLGRKMTMIISATLFSTSALGCAISADFTQLVVYRIIGGVGIGVVSIVS 121 Query: 129 PAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMA--GGSAQNPWL---FGAA 183 P YI+EV+ A RGRL SL QLA+ G A L N+ + A G WL F Sbjct: 122 PLYISEVAVAQYRGRLVSLYQLAVTVGFLGAYLINYQLLAYAESGNQLSMDWLNKIFVTE 181 Query: 184 AWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEG--GDVPSRIEEI 241 WR M E +PA+L+ + F IPESPR+L+ +G+ EKA IL ++ + S+++E Sbjct: 182 VWRGMLGMETLPAVLFFIIIFFIPESPRWLIVRGKEEKAVNILERIYNSVSEAASQLKET 241 Query: 242 QATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEE 301 ++ ++ + K ++ L+ + G+ V IG+ ++ L QF+G+N + YY ++ + G + Sbjct: 242 KSVLTSETKSEWAMLM--KPGIFKAVIIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGG 299 Query: 302 KSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSV--VFGGATVVN 359 SL V+ G +N LTT++A+ +D+ GRK L+ G GM ++L ++ V +FG + Sbjct: 300 DSLFYQVLVGLVNTLTTVLALVIIDRVGRKQLVYYGVSGMVVSLLLIGVYFLFGDS---- 355 Query: 360 GQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIAN 419 G + + LV YVF S +V+VLL EM+ K+R A+S+A WI Sbjct: 356 -----WGVSSLFLLVFFLFYVFCCAVSICAVVFVLLSEMYPTKVRGLAMSIAGFALWIGT 410 Query: 420 FIISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468 ++I P +L + + L+A + +W V ET GK+LE++ Sbjct: 411 YLIGQLTPWMLQNLTPAGTFFLFAVMCVPYMLIVWKLVPETTGKSLEEI 459 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: 513 Number of extensions: 21 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: 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 Apr 09 2024. 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