Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate GFF2717 PS417_13860 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__WCS417:GFF2717 Length = 255 Score = 110 bits (274), Expect = 4e-29 Identities = 71/216 (32%), Positives = 113/216 (52%), Gaps = 17/216 (7%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHG----GDKHQSSGNYNFWPTDI 60 + ++ KI V+GGASG+G A + L+A GA V ++D++ Q GN DI Sbjct: 1 MQIENKIFLVSGGASGLGAATAEMLVAAGAKVMLVDLNADAVAAKAQQLGGNARSAVADI 60 Query: 61 SSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQ 120 S + V + FG + GLVN AGV ++ + P G A+F +++N+N Sbjct: 61 SQEAAAEAAVQATVAAFGGLHGLVNCAGVVRGEKILGKDGPHGL-----ASFAQVINVNL 115 Query: 121 KGVFLMSQAVARQMVKQRS------GVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSW 174 G F + + A + + + GVI+N +S + +G GQ+ YAA+K A+ S T Sbjct: 116 IGSFNLLRLAAAAIAETEANADGERGVIINTASVAAFDGQIGQAAYAASKGAIASLTLPA 175 Query: 175 SKELGKHGIRVVGVAPGILEKTGL--RTPEYEEALA 208 ++EL + GIRV+ +APGI E + T + E+LA Sbjct: 176 ARELARFGIRVMTIAPGIFETPMMAGMTEQVRESLA 211 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: 145 Number of extensions: 9 Number of successful extensions: 3 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: 255 Length adjustment: 25 Effective length of query: 242 Effective length of database: 230 Effective search space: 55660 Effective search space used: 55660 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