Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate AO353_25690 AO353_25690 3-hydroxy-2-methylbutyryl-CoA dehydrogenase
Query= curated2:P37079 (267 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25690 Length = 253 Score = 105 bits (262), Expect = 9e-28 Identities = 68/214 (31%), Positives = 111/214 (51%), Gaps = 15/214 (7%) Query: 5 LNLKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNY--HFWSTDISS 62 + +++ V +VTGGASG+G A + L+ GA V ++D++ H DIS Sbjct: 1 MQIENKVFLVTGGASGLGAATAEMLVGAGAKVMLVDLNAEAVAAQAKRLGAHCVVADISQ 60 Query: 63 ATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKG 122 + + A + + + GLVN AGV ++ + P A+F +++N+N G Sbjct: 61 EAAAEAAVQAAVAAFGGLHGLVNCAGVVRGEKILGKNGPHAL-----ASFSQVINVNLIG 115 Query: 123 VFFMSQAVARQMVKQRA------GVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSK 176 F M + A + + A GVI+N +S + +G GQ+ YAA+K A+ S T ++ Sbjct: 116 SFNMLRLAAAAIAETEANEDGERGVIINTASVAAFDGQIGQAAYAASKGAIASLTLPAAR 175 Query: 177 ELGKYGIRVVGVAPGILEKTGL--RTPEYEEALA 208 EL +YGIRV+ +APGI E + T E ++LA Sbjct: 176 ELARYGIRVMTIAPGIFETPMMAGMTQEVRDSLA 209 Lambda K H 0.316 0.133 0.386 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: 129 Number of extensions: 7 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: 253 Length adjustment: 24 Effective length of query: 243 Effective length of database: 229 Effective search space: 55647 Effective search space used: 55647 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: 41 (21.6 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