Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate 5208820 Shew_1322 short-chain dehydrogenase/reductase SDR (RefSeq)
Query= curated2:P37079 (267 letters) >FitnessBrowser__PV4:5208820 Length = 242 Score = 102 bits (254), Expect = 8e-27 Identities = 76/261 (29%), Positives = 123/261 (47%), Gaps = 30/261 (11%) Query: 12 IIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDR----HHNGDNYHFWSTDISSATEVQ 67 IIVTGG+ G+GLAIV LL+QG V + N+ ++ +I +A + Sbjct: 4 IIVTGGSRGLGLAIVTHLLAQGYKVSTCSRATTSTIEALEQSNPNFKWFPCEIGNAEQTS 63 Query: 68 QTID--AIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFF 125 Q + I S + GL+NNAG+ +L + ++ +N G + Sbjct: 64 QFVKEACIWANESPLWGLINNAGIAKEGVLAT---------FPNIESDALIQVNLNGALY 114 Query: 126 MSQAVARQMVKQR-AGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIR 184 ++ V R ++Q AG I+N+SS G G G + Y+A+KA L+ TR+ ++E G+ I Sbjct: 115 TAREVLRVFLRQNSAGRIINISSIIGSRGYTGLAAYSASKAGLDGLTRALARENGRRNIT 174 Query: 185 VVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEVADFVCY 244 V +APG L+ + T+ + P+ R GK+ ++ + + Sbjct: 175 VNSIAPGYLDT--------------EMSSTLSDKKRDQIIRRTPMHRLGKVDDITPAISF 220 Query: 245 LLSARASYITGVTTNIAGGKT 265 LLS A++ITG T I GG T Sbjct: 221 LLSDGAAFITGQTLTIDGGIT 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: 161 Number of extensions: 10 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: 242 Length adjustment: 24 Effective length of query: 243 Effective length of database: 218 Effective search space: 52974 Effective search space used: 52974 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