Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate BWI76_RS21205 BWI76_RS21205 MFS transporter
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Koxy:BWI76_RS21205 Length = 478 Score = 296 bits (757), Expect = 1e-84 Identities = 164/465 (35%), Positives = 269/465 (57%), Gaps = 24/465 (5%) Query: 2 GGILFGYDTAVISGAIGSLTSYFHLS-PAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 GG+LFGYD VI GA ++F ++ PA++GWA+S +VGCV G+ +G+ + + GRK Sbjct: 23 GGLLFGYDWVVIGGAKPFYEAWFSITDPAQSGWAMSSALVGCVFGALISGWCADKLGRKL 82 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 L++SA+LF+ SA GT+++ +F FV+YRI+GG+ +GLA+ +SP+Y++EVSP RGR + Sbjct: 83 PLILSAVLFSASAWGTAVASSFDMFVVYRIVGGVGIGLASALSPLYIAEVSPAEKRGRFV 142 Query: 121 SMQQFAIVFGQILIFYVNYKIASIAA---------DTWLIELGWRYMFAAGIIPCILFCI 171 ++ Q IV G + +N IA A +TW ++GWR+MF A ++P + F + Sbjct: 143 AVNQLTIVIGVLAAQLINLMIAEPVATGATQQMIVETWNGQMGWRWMFGAELVPALAFLV 202 Query: 172 LVFLIPESPRWMMMIGREEETLKILTKISNEEHARHLLADIKTSLQNDQLNAHQKLNY-- 229 L+F +PESPRW+M G+ E L +I + ++A +L DI +L+ D + K++Y Sbjct: 203 LMFFVPESPRWLMKAGKPERARAALERIGSADYADRILRDIAHTLEKD----NHKVSYGA 258 Query: 230 -RDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIG 288 V+ I+I+G ++A+ QQ G+NV+ YA + L + GV+ L+ Sbjct: 259 LLAPQVKPIVIIGMVLAVFQQWCGINVIFNYAQEIFASAGFDINSTLKSIVATGVVNLVF 318 Query: 289 SIIGAMIMDKMGRLSLMRKGTIGSIIGLLLTSWALYSQATGYFALFGMLFFMIFYALSWG 348 ++ ++DK+GR LM G G + +L + A G+ L +L + YAL+ Sbjct: 319 TLAALPLVDKIGRRKLMLLGASGLTLIYVLIAGAYAMGIMGWPVLLLVLAAIAIYALTLA 378 Query: 349 VGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPMWIF 408 WVL++EIFPNR+R MS+ +W+A FL++ FP++N + A ++ Sbjct: 379 PVTWVLLAEIFPNRVRGLAMSLGTLALWIACFLLTYTFPLLN------AGLGAAGSFLLY 432 Query: 409 AICCIFSYFFICRYLPETKGISLEKMESVVLAKRRKKLQPIQTER 453 + C Y +I R +PETKG++LE +E LA+R + + E+ Sbjct: 433 GVICAAGYLYILRNVPETKGVTLEALEE-QLAQRHTGVNAAKQEQ 476 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: 650 Number of extensions: 24 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