Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate WP_086511015.1 BZY95_RS16640 MFS transporter
Query= TCDB::E1WAV3 (456 letters) >NCBI__GCF_002151265.1:WP_086511015.1 Length = 468 Score = 279 bits (713), Expect = 2e-79 Identities = 152/451 (33%), Positives = 260/451 (57%), Gaps = 24/451 (5%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 +GG LFG+D+ VI+G + L + F TG+ V+ +++GC +G+F AG L+ RFGR+ Sbjct: 22 IGGFLFGFDSGVINGTVDGLQAAFGSDSVGTGFNVASMLLGCAVGAFFAGRLADRFGRRT 81 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 L+V+A+LF +SA G+ ++ + FV YR++GG+AVG A+ ++P Y+SEV+P RGR Sbjct: 82 LLIVAAILFLVSAWGSGVAGSSLEFVFYRVLGGMAVGAASVMTPAYISEVAPAAYRGRLA 141 Query: 121 SMQQFAIVFGQILIFYVNYKIASIA----ADTWLIELGWRYMFAAGIIPCILFCILVFLI 176 ++QQ AI+ G + F NY +A ++ A+ WL WR+MF ++P +F + + I Sbjct: 142 TIQQVAIISGLFVAFLSNYVLAHVSGSAMAELWLGFATWRWMFWIELLPATVFLLALLFI 201 Query: 177 PESPRWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQND-QLNAHQKLNYRDGNVR 235 PESPR+++ G++ E ++L + E +A+I +L D + L+ G V Sbjct: 202 PESPRYLISSGKQGEARRVLGLVMPEGEVSAKMAEIDATLARDHKPRLRDVLDRTTGKVH 261 Query: 236 FILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGSIIGAMI 295 I+ +G +A+ QQ+ G+NV+ YY ++ + V S +AL + G + + ++ + Sbjct: 262 GIVWVGIGLAVFQQLVGINVVFYYGAVLWQSVGFSEGDALLINVISGAVSIGACLLAIAL 321 Query: 296 MDKMGRLSLMRKGTIGSIIGLLLTSWALYSQAT------------GYFALFGMLFFMIFY 343 +DK+GR L+ G++G + L ++A +S AT G AL ++ F+ Sbjct: 322 IDKIGRKPLLWAGSVGMALTLACMAFA-FSTATLIDGRLRLGDDMGVLALLAANAYVFFF 380 Query: 344 ALSWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAF 403 +SWG WV++ E+FPN+MR G++I+ F W+ANF ++ FP+ +L+ A Sbjct: 381 NVSWGPVMWVMLGEMFPNQMRGSGLAIAGLFQWLANFGITMTFPI------MLATIGLAG 434 Query: 404 PMWIFAICCIFSYFFICRYLPETKGISLEKM 434 +A+C + S FF+ R + ET+G LE+M Sbjct: 435 AYGFYALCAVVSVFFVLRLVKETRGKELEEM 465 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: 602 Number of extensions: 30 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: 468 Length adjustment: 33 Effective length of query: 423 Effective length of database: 435 Effective search space: 184005 Effective search space used: 184005 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 24 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