Align Inositol transport system sugar-binding protein (characterized)
to candidate SMa2000 SMa2000 ABC transporter substrate-binding protein
Query= reanno::WCS417:GFF2331 (309 letters) >FitnessBrowser__Smeli:SMa2000 Length = 358 Score = 81.3 bits (199), Expect = 3e-20 Identities = 57/180 (31%), Positives = 86/180 (47%), Gaps = 4/180 (2%) Query: 66 DARADVVKQLSQVENFISQKVDAIIVNPVDTASTANIIKAATAAKIPLVFVNRRPDSQTL 125 DA D KQ++ +E+ I+QKVDAIIV PV + S I+ A AA IP+V R +S+ Sbjct: 94 DAGFDQKKQVADIEDLIAQKVDAIIVQPVTSTSANASIEKAVAAGIPVVLHTGRIESEAY 153 Query: 126 APGVAAVTSDDVEAGKLQMQYIAEKLGGKGNIVILLGDLANNSTTNRTKGVKEVLTKYPG 185 + GK+ ++ ++LGGKGNI +L G + TNR G+K+ L + Sbjct: 154 ---TTEIQGGAEHFGKVMGDFLVKELGGKGNIWVLRGLAGHPEDTNRYNGLKQSL-EGTE 209 Query: 186 IKIEQEQTGIWLRDRGMTLVNDWLTQGRDFQAVLSNNDEMAIGAAMALKSAGKKGVLIAG 245 IKI E+ G W D+ + + + S+ +M K G I+G Sbjct: 210 IKIAAEEHGDWQYDKAKKVCETLYLSDPNVDGIWSSGADMTRACVDVFKQFGSPIPPISG 269 Lambda K H 0.314 0.131 0.357 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: 229 Number of extensions: 10 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: 309 Length of database: 358 Length adjustment: 28 Effective length of query: 281 Effective length of database: 330 Effective search space: 92730 Effective search space used: 92730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 49 (23.5 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