Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate 349964 BT0436 arabinose-proton symporter (NCBI ptt file)
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Btheta:349964 Length = 468 Score = 285 bits (729), Expect = 2e-81 Identities = 155/450 (34%), Positives = 265/450 (58%), Gaps = 23/450 (5%) Query: 1 MGGILFGYDTAVISGAIGSLTSYFHLSPAETGWAVSCVVVGCVIGSFSAGYLSKRFGRKK 60 +GG LFGYDTAVISG I +T F L + GW V C ++G ++G AG LS + GRK Sbjct: 19 LGGFLFGYDTAVISGTIAQVTQLFQLDTLQQGWYVGCALIGSIVGVLFAGILSDKLGRKM 78 Query: 61 SLMVSALLFTISAVGTSLSYTFTHFVIYRIIGGLAVGLAATVSPMYMSEVSPKNMRGRAL 120 ++++SA LF+ SA+G ++S FT V+YRIIGG+ +G+ + VSP+Y+SEV+ RGR + Sbjct: 79 TMIISATLFSTSALGCAISADFTQLVVYRIIGGVGIGVVSIVSPLYISEVAVAQYRGRLV 138 Query: 121 SMQQFAIVFGQILIFYVNYKIASIAAD------TWLIEL----GWRYMFAAGIIPCILFC 170 S+ Q A+ G + + +NY++ + A WL ++ WR M +P +LF Sbjct: 139 SLYQLAVTVGFLGAYLINYQLLAYAESGNQLSMDWLNKIFVTEVWRGMLGMETLPAVLFF 198 Query: 171 ILVFLIPESPRWMMMIGREEETLKILTKISNE-EHARHLLADIKTSLQNDQLNAHQKLNY 229 I++F IPESPRW+++ G+EE+ + IL +I N A L + K+ L ++ + L Sbjct: 199 IIIFFIPESPRWLIVRGKEEKAVNILERIYNSVSEAASQLKETKSVLTSETKSEWAML-M 257 Query: 230 RDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEALFQTIWIGVIQLIGS 289 + G + + I+G IA+L Q GVN ++YY P + ++ S ++LF + +G++ + + Sbjct: 258 KPGIFKAV-IIGVCIAILGQFMGVNAVLYYGPSIFENAGLSGGDSLFYQVLVGLVNTLTT 316 Query: 290 IIGAMIMDKMGRLSLMRKGTIGSIIGLLLTS-WALYSQATGYFALFGMLFFMIFY---AL 345 ++ +I+D++GR L+ G G ++ LLL + L+ + G +LF ++FF+ + A+ Sbjct: 317 VLALVIIDRVGRKQLVYYGVSGMVVSLLLIGVYFLFGDSWGVSSLFLLVFFLFYVFCCAV 376 Query: 346 SWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPYLLSHFHGAFPM 405 S +VL+SE++P ++R MSI+ +W+ +L+ Q P++L + A Sbjct: 377 SICAVVFVLLSEMYPTKVRGLAMSIAGFALWIGTYLIGQL------TPWMLQNLTPAGTF 430 Query: 406 WIFAICCIFSYFFICRYLPETKGISLEKME 435 ++FA+ C+ + + +PET G SLE++E Sbjct: 431 FLFAVMCVPYMLIVWKLVPETTGKSLEEIE 460 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: 641 Number of extensions: 38 Number of successful extensions: 7 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 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