Align Major myo-inositol transporter, IolT1, of 456 aas (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)
Query= TCDB::E1WAV3 (456 letters) >FitnessBrowser__Keio:18059 Length = 491 Score = 378 bits (971), Expect = e-109 Identities = 197/473 (41%), Positives = 299/473 (63%), Gaps = 30/473 (6%) Query: 1 MGGILFGYDTAVISGAIGSLTSYF----HLSPAET----GWAVSCVVVGCVIGSFSAGYL 52 +GG+LFGYDTAVISG + SL + F +LS + G+ V+ ++GC+IG GY Sbjct: 19 LGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASALIGCIIGGALGGYC 78 Query: 53 SKRFGRKKSLMVSALLFTISAVGTS---LSYTFTH---------------FVIYRIIGGL 94 S RFGR+ SL ++A+LF IS VG++ L +T + FVIYRIIGG+ Sbjct: 79 SNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGYVPEFVIYRIIGGI 138 Query: 95 AVGLAATVSPMYMSEVSPKNMRGRALSMQQFAIVFGQILIFYVNYKIASIAADTWLIELG 154 VGLA+ +SPMY++E++P ++RG+ +S QFAI+FGQ+L++ VNY IA +WL G Sbjct: 139 GVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFIARSGDASWLNTDG 198 Query: 155 WRYMFAAGIIPCILFCILVFLIPESPRWMMMIGREEETLKILTKISNEEHARHLLADIKT 214 WRYMFA+ IP +LF +L++ +PESPRW+M G++E+ IL KI A + +IK Sbjct: 199 WRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGILRKIMGNTLATQAVQEIKH 258 Query: 215 SLQNDQLNAHQKLNYRDGNVRFILILGCMIAMLQQVTGVNVMMYYAPIVLKDVTGSAQEA 274 SL + + + L + G ++++G M+++ QQ G+NV++YYAP V K + S A Sbjct: 259 SLDHGRKTGGRLLMFGVG----VIVIGVMLSIFQQFVGINVVLYYAPEVFKTLGASTDIA 314 Query: 275 LFQTIWIGVIQLIGSIIGAMIMDKMGRLSLMRKGTIGSIIGLLLTSWALYSQATGYFALF 334 L QTI +GVI L +++ M +DK GR L G +G IG+ A Y+QA G AL Sbjct: 315 LLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGMFSLGTAFYTQAPGIVALL 374 Query: 335 GMLFFMIFYALSWGVGAWVLISEIFPNRMRSQGMSISVGFMWMANFLVSQFFPMINENPY 394 MLF++ +A+SWG WVL+SEIFPN +R + ++I+V W+AN+ VS FPM+++N + Sbjct: 375 SMLFYVAAFAMSWGPVCWVLLSEIFPNAIRGKALAIAVAAQWLANYFVSWTFPMMDKNSW 434 Query: 395 LLSHFHGAFPMWIFAICCIFSYFFICRYLPETKGISLEKMESVVLAKRRKKLQ 447 L++HFH F WI+ + + F+ +++PETKG +LE++E++ + +K Q Sbjct: 435 LVAHFHNGFSYWIYGCMGVLAALFMWKFVPETKGKTLEELEALWEPETKKTQQ 487 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: 703 Number of extensions: 26 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: 491 Length adjustment: 33 Effective length of query: 423 Effective length of database: 458 Effective search space: 193734 Effective search space used: 193734 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