Align The glucose uptake porter, GluP (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= TCDB::Q0SE66 (483 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 524 bits (1350), Expect = e-153 Identities = 271/461 (58%), Positives = 343/461 (74%), Gaps = 7/461 (1%) Query: 20 TSVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAML 79 T+ V IA AALGG LFG+D+AVINGAV A+ G F + + +GFA++ ALLG+A GA Sbjct: 14 TARVVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWY 73 Query: 80 AGRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIA 139 AG +ADR+GR+ TM+ AAV+ +SA+G+G A V LV +R+VGGIGVG+ASVIAP YIA Sbjct: 74 AGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIA 133 Query: 140 EISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCV 199 E+SPARVRGRLGSLQQLAIV GIF +LL D LA AGG+ ++LW GLEAWRWMFL V Sbjct: 134 EVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVV 193 Query: 200 PALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLL---GEKGLDLKIESIRSTLARETQ 256 PAL YG L L +PESPR+L+A+GR+ EA+ +L +L E L K+ I +L E + Sbjct: 194 PALIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYR 253 Query: 257 PSIRDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVIT 316 P +RDL+GS GL+P+VW+GI LSVFQQFVGINVIFYYSS LW +VGF E + I+V+T Sbjct: 254 PGLRDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVT 313 Query: 317 SVVNIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTG 376 SVVN+ TL+AIA +DR+GR+PLL IGSAGM VTL MA+ F A+ L Sbjct: 314 SVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAA----GSGAALSLPA 369 Query: 377 LQGPIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTF 436 G +ALVAAN +VV FG+SWGP+VWVLLGE FPNRIRA AL++AA AQW AN++IT +F Sbjct: 370 PWGMVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSF 429 Query: 437 PSMKDFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAM 477 P++ + L +YG YA A++SLVFV++ V+ETKG+ELE M Sbjct: 430 PALSELGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 Lambda K H 0.324 0.138 0.405 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: 738 Number of extensions: 32 Number of successful extensions: 3 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: 483 Length of database: 472 Length adjustment: 34 Effective length of query: 449 Effective length of database: 438 Effective search space: 196662 Effective search space used: 196662 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 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