Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate BWI76_RS10225 BWI76_RS10225 MFS transporter
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Koxy:BWI76_RS10225 Length = 483 Score = 463 bits (1191), Expect = e-135 Identities = 212/447 (47%), Positives = 327/447 (73%), Gaps = 3/447 (0%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 + GI+ GYD +VISG I LT + L+PA++GWAVS V++GC++G++ G + RFGRK Sbjct: 20 VSGIILGYDASVISGVIDPLTEHLSLTPAQSGWAVSNVILGCIVGAWGVGRFTDRFGRKA 79 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 +L+++A+LF ISA+G++L+ T FV+YR+IGGLAVG+A+ V+P+Y++EVSPK++RGR L Sbjct: 80 TLIITAILFAISAIGSALANDLTWFVVYRMIGGLAVGMASAVTPLYIAEVSPKDLRGRML 139 Query: 121 SMQQFAIVFGQILIFYVNYKIASIAADTWLIELGWRYMFAAGIIPCILFCILVFLIPESP 180 MQQ +V GQ++++ VNY IA A W++ +GWR+M A+ +IPC+LF ++VF +PESP Sbjct: 140 GMQQMLMVGGQLVVYIVNYLIARGMAHEWVVSIGWRWMLASALIPCVLFLVMVFFMPESP 199 Query: 181 RWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQNDQLNAH---QKLNYRDGNVRFI 237 RW M ++E++LK+LT +SN HA L A+I+TS+ D + RD +I Sbjct: 200 RWYAMRNQKEKSLKVLTSLSNPGHAERLYAEIRTSIATDSALLSIPTPRGILRDKKSSYI 259 Query: 238 LILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGSIIGAMIMD 297 L +GC IA+LQQV+G+N++MY+AP +L++VTG+ Q+++FQ+I++G+ L G I + D Sbjct: 260 LWIGCAIAVLQQVSGINILMYFAPSLLQNVTGNTQDSMFQSIFLGLALLAGVSIALVAFD 319 Query: 298 KMGRLSLMRKGTIGSIIGLLLTSWALYSQATGYFALFGMLFFMIFYALSWGVGAWVLISE 357 ++GRL L+R G++G LL TSWA ++ GY + G++ F+ + +SW +GAW+LISE Sbjct: 320 RIGRLPLLRWGSLGCAAFLLFTSWAFMNEVKGYLPIVGLVGFIFVFGMSWSLGAWLLISE 379 Query: 358 IFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPMWIFAICCIFSYF 417 IFPNRMR+ M + MW++NF+V+Q FPM+N NP L+ HFHGAFP+ + + I +++ Sbjct: 380 IFPNRMRAVAMGYAFCSMWVSNFIVTQSFPMMNRNPVLMEHFHGAFPLLLCSGFSIIAFW 439 Query: 418 FICRYLPETKGISLEKMESVVLAKRRK 444 F+ R+LPETKG+SLE +E ++L+K R+ Sbjct: 440 FVGRFLPETKGVSLENIEPLMLSKSRR 466 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: 689 Number of extensions: 37 Number of successful extensions: 2 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: 483 Length adjustment: 33 Effective length of query: 423 Effective length of database: 450 Effective search space: 190350 Effective search space used: 190350 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