Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate WP_010632451.1 RH97_RS11210 SDR family oxidoreductase
Query= curated2:P37079 (267 letters) >NCBI__GCF_000246965.1:WP_010632451.1 Length = 246 Score = 129 bits (323), Expect = 8e-35 Identities = 92/267 (34%), Positives = 146/267 (54%), Gaps = 25/267 (9%) Query: 1 MNTWLNLKDNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGD--RHHNGDNYHFWST 58 MN ++N +++TGG SGIGLA +S+GA V ++D + RH + D Y Sbjct: 1 MNRFVNKS---VLITGGGSGIGLATAKLFISEGAAVSVLDYKVSEALRHLDCDTYQ---A 54 Query: 59 DISSATEVQQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNI 118 DI A +V++ + +I++ +ID LVN AG+ A + E A++++++ Sbjct: 55 DIRKADQVEEAVTKVIKKKKQIDILVNTAGIELV---------ASLEQTTEDAWDRVLDT 105 Query: 119 NQKGVFFMSQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178 N KGVF +++AV +K+ GVIVN +S+ GS + Y A+KAA+ +FTRS + E+ Sbjct: 106 NLKGVFLVTRAVL-PFLKETHGVIVNTASQLAYVGSALFTAYTASKAAILNFTRSLAIEM 164 Query: 179 GKYGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEV 238 K GIRV V PG ++ T L ++E + T++ L + PIGR GK E+ Sbjct: 165 AKDGIRVNSVCPGAVD-TPLLNRQFENGKTGPQG-TIDDLIRMH-----PIGRLGKPEEI 217 Query: 239 ADFVCYLLSARASYITGVTTNIAGGKT 265 A + +L S AS++TG + GG T Sbjct: 218 ARPILFLCSDDASFMTGSALVVDGGYT 244 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: 136 Number of extensions: 6 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: 246 Length adjustment: 24 Effective length of query: 243 Effective length of database: 222 Effective search space: 53946 Effective search space used: 53946 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 24 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