Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate Dsui_3259 Dsui_3259 dehydrogenase of unknown specificity, short-chain alcohol dehydrogenase like protein
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__PS:Dsui_3259 Length = 256 Score = 99.8 bits (247), Expect = 5e-26 Identities = 84/275 (30%), Positives = 127/275 (46%), Gaps = 41/275 (14%) Query: 10 KIITVTGGASGIGLAIV----------------DELLAQGANVQMIDIHGGDKHQSSGNY 53 K + +TGG+ GIG A V D AQ ++ D + Sbjct: 3 KTLLITGGSRGIGAATVRLAARAGYAVCFSYRQDAAAAQQLVAEVTRESSRDSGREGAPI 62 Query: 54 NFWPTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFE 113 + DIS E+ QRFG I LVNNAG+ + V++ ++ + Sbjct: 63 LAFQADISREEEIRALFAAAEQRFGPITALVNNAGILELQTRVED--------MDGDRLQ 114 Query: 114 KMVNINQKGVFLMSQAVARQMVKQRSG---VIVNVSSESGLEGSEGQSC-YAATKAALNS 169 ++ N G FL + R++ + G IVN+SS + G+ G+ YAA+KAA+++ Sbjct: 115 RIFATNVIGTFLCCREAVRRLSTRHGGHGGAIVNLSSRAARLGAAGEYVDYAASKAAIDT 174 Query: 170 FTRSWSKELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPL 229 T ++E+ GIRV VAPG+++ T + E VE+LR G IP+ Sbjct: 175 LTLGLAREVAAEGIRVNAVAPGLID-TDIHASGGEPG-------RVERLRTG-----IPM 221 Query: 230 GRSGRLTEVADFVCYLLSERASYMTGVTTNIAGGK 264 R G EVA + +LLSE ASY TG ++AGG+ Sbjct: 222 QRGGTPEEVAKAILWLLSEDASYTTGAILDVAGGR 256 Lambda K H 0.315 0.132 0.378 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: 170 Number of extensions: 9 Number of successful extensions: 4 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: 267 Length of database: 256 Length adjustment: 25 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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: 47 (22.7 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