Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Dyella79:N515DRAFT_0382 Length = 472 Score = 268 bits (685), Expect = 3e-76 Identities = 148/453 (32%), Positives = 260/453 (57%), Gaps = 27/453 (5%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 +GG LFG+DTAVI+GA+ ++ F L G+AVSC ++G +G++ AG L+ R+GR + Sbjct: 26 LGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGPLADRWGRVR 85 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 ++ V+A+L ISA+G+ L V++R++GG+ VG+A+ ++P Y++EVSP +RGR Sbjct: 86 TMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVSPARVRGRLG 145 Query: 121 SMQQFAIVFGQILIFYVNYKIASIAADT----WLIELGWRYMFAAGIIPCILFCILVFLI 176 S+QQ AIV G + +A A WL WR+MF ++P +++ LV + Sbjct: 146 SLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPALIYGSLVLGV 205 Query: 177 PESPRWMMMIGREEETLKILTKISN--EEHA-RHLLADIKTSLQNDQLNAHQKLNYRDGN 233 PESPR ++ GR +E ++L ++ + +EHA +H L DI SL+++ + L Sbjct: 206 PESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYRPGLRDLRGSMAG 265 Query: 234 VRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGSIIGA 293 + ++ +G ++++ QQ G+NV+ YY+ + V S +A ++ V+ ++ +++ Sbjct: 266 LLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSVVNVLVTLVAI 325 Query: 294 MIMDKMGRLSLMRKGTIGSIIGLLLTSWALYSQAT------------GYFALFGMLFFMI 341 ++D++GR L+ G+ G + L L +W +SQA G AL +++ Sbjct: 326 ALVDRIGRKPLLAIGSAGMTVTLGLMAWC-FSQAAGSGAALSLPAPWGMVALVAANAYVV 384 Query: 342 FYALSWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHG 401 F+ LSWG WVL+ E+FPNR+R+ ++++ W+ANF+++ FP LS Sbjct: 385 FFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSFP-------ALSELGL 437 Query: 402 AFPMWIFAICCIFSYFFICRYLPETKGISLEKM 434 +F ++A + S F+ + + ETKG+ LE+M Sbjct: 438 SFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470 Lambda K H 0.329 0.141 0.436 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: 592 Number of extensions: 29 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: 456 Length of database: 472 Length adjustment: 33 Effective length of query: 423 Effective length of database: 439 Effective search space: 185697 Effective search space used: 185697 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 (21.8 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