Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_011384506.1 AMB_RS10625 3-oxoacyl-[acyl-carrier-protein] reductase
Query= curated2:P37079 (267 letters) >NCBI__GCF_000009985.1:WP_011384506.1 Length = 245 Score = 105 bits (263), Expect = 7e-28 Identities = 79/265 (29%), Positives = 128/265 (48%), Gaps = 33/265 (12%) Query: 6 NLKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRH-------HNGDNYHFWST 58 +L +VTG + GIG AI L ++GA V +HG R G+ H Sbjct: 3 DLTGKTALVTGASGGIGGAIAKALHARGATV---GLHGTRREALDALAAELGERVHVLPA 59 Query: 59 DISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNI 118 ++S A V+Q +D LVNNAG+ L++ + + ++ ++++ Sbjct: 60 NLSDAAAVEQLAKDAEAAMGSVDILVNNAGLTKDGLVL---------RMKDEDWQTVLDV 110 Query: 119 NQKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178 N F +S+A + +K+R G I+N++S G+ G+ GQ YAA+KA + +++ ++E+ Sbjct: 111 NLTAAFRLSRAAVKGQMKRRWGRIINITSIVGVTGNPGQVNYAASKAGMIGMSKALAQEV 170 Query: 179 GKYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEV 238 I V VAPG + A T ++ EQ + IP GR G E+ Sbjct: 171 ASRNITVNCVAPGFVSS------------AMTDVLSDEQKTK--LNAGIPAGRMGTADEI 216 Query: 239 ADFVCYLLSARASYITGVTTNIAGG 263 A V YL SA A+Y+TG T ++ GG Sbjct: 217 AAAVVYLASAEAAYVTGQTLHVNGG 241 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: 160 Number of extensions: 8 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: 245 Length adjustment: 24 Effective length of query: 243 Effective length of database: 221 Effective search space: 53703 Effective search space used: 53703 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