Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate Pf6N2E2_1004 3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Query= curated2:P37079 (267 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1004 Length = 252 Score = 114 bits (286), Expect = 2e-30 Identities = 85/259 (32%), Positives = 132/259 (50%), Gaps = 23/259 (8%) Query: 7 LKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNYHFWSTDISSATEV 66 L + V +VTGG GIG AI + +GA V + D+H + + N D+ D+S + Sbjct: 15 LHNKVALVTGGGMGIGRAIAELFAEEGATVIVGDVHQPEPYKN-DSVVAKHLDVSKLEDW 73 Query: 67 QQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFFM 126 + + +++ ++D LVNNAG LV P L++ + ++++INQ GVF+ Sbjct: 74 ELLVAEVVREHGKVDVLVNNAG------LVGSYLPIDEITLDD--WNRVIDINQNGVFYG 125 Query: 127 SQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIRVV 186 + V M +Q AG IVNVSS G+ G+ G S Y A+KAA+ +++ + GIRV Sbjct: 126 MRTVVPVMKRQHAGSIVNVSSIWGIVGASGVSAYQASKAAVRMMSKNAALSYVANGIRVN 185 Query: 187 GVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEVADFVCYLL 246 + PG++E TP + A +IT + A P+ RA E+A +L Sbjct: 186 SLHPGLVE-----TPMIDRQAA---DITAAVVA------ATPMKRAADPKEIAYAALFLA 231 Query: 247 SARASYITGVTTNIAGGKT 265 S AS+ITG + GG T Sbjct: 232 SDEASFITGAELVVDGGYT 250 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: 177 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: 252 Length adjustment: 24 Effective length of query: 243 Effective length of database: 228 Effective search space: 55404 Effective search space used: 55404 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