Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate CCNA_00857 CCNA_00857 glucose/fructose transport protein
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Caulo:CCNA_00857 Length = 478 Score = 269 bits (687), Expect = 2e-76 Identities = 150/451 (33%), Positives = 252/451 (55%), Gaps = 23/451 (5%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 +GG +FGYD+ VI+G L S F+LS TG V +++GC IG+F+AG L+ +GR+ Sbjct: 34 IGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAFAAGRLADVWGRRT 93 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 +++SALLF ISA+GT + + F+I+R+IGGL VG A+ + P+Y+SEV+P N+RGR Sbjct: 94 VMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYISEVTPANIRGRLS 153 Query: 121 SMQQFAIVFGQILIFYVNYKIA----SIAADTWLIELGWRYMFAAGIIPCILFCILVFLI 176 S+QQ I+ G F NY +A S A+ WL WR+MF IIP +F + + I Sbjct: 154 SVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMFWMQIIPAGVFFLCLLGI 213 Query: 177 PESPRWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQNDQLNAHQK-LNYRDGNVR 235 PESPR+++ G++ + IL+++ + +I+ SL D L+ +R Sbjct: 214 PESPRYLVAKGKDAQAEAILSRLFGAGQGAKKVEEIRASLSADHKPTFSDLLDPTTKKLR 273 Query: 236 FILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGSIIGAMI 295 IL G ++A+ QQ+ G+N++ YY ++ + V + ++L I G + ++ ++ + Sbjct: 274 VILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILSGTLSILACLLAIGL 333 Query: 296 MDKMGRLSLMRKGTIGSIIGLLLTSWALYSQAT-----------GYFALFGMLFFMIFYA 344 +DK+GR L+ G+ G + L + +W + T G AL ++IF+ Sbjct: 334 IDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGLTALIAANLYVIFFN 393 Query: 345 LSWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFP 404 LSWG WV++ E+FPN+MR +++ W+ANF +S FP + +++ Sbjct: 394 LSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPALAAASLPMTY------ 447 Query: 405 MWIFAICCIFSYFFICRYLPETKGISLEKME 435 +A+ + S+F + + + ET+G LE M+ Sbjct: 448 -GFYALSAVVSFFLVQKLVHETRGKELEAMQ 477 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: 615 Number of extensions: 27 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: 478 Length adjustment: 33 Effective length of query: 423 Effective length of database: 445 Effective search space: 188235 Effective search space used: 188235 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