Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate Echvi_1862 Echvi_1862 Dehydrogenases with different specificities (related to short-chain alcohol dehydrogenases)
Query= curated2:P37079 (267 letters) >FitnessBrowser__Cola:Echvi_1862 Length = 246 Score = 115 bits (289), Expect = 7e-31 Identities = 79/261 (30%), Positives = 126/261 (48%), Gaps = 24/261 (9%) Query: 11 VIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGD----RHHNGDNYHFWSTDISSATEV 66 + +VTGGASG+GLA + +I + + G N H+++ D++ + Sbjct: 5 IALVTGGASGLGLATAKKFCDHDITTIIIGRNESKLAKAQEELGPNCHYYAFDLNDLPNI 64 Query: 67 QQTIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFFM 126 I+ I +ID LVNNAG+N + + E+ + F++++ N VF + Sbjct: 65 PDLINTITTEHGKIDILVNNAGINMKKPFI---------EVTDEEFQQIITTNVFAVFSL 115 Query: 127 SQAVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIRVV 186 S+ +A+ M Q+ G IVN+SS + G Y A+K+A+ T++ + EL GIRV Sbjct: 116 SREIAKTMASQKHGAIVNISSMASQYGIPKVIAYTASKSAIEGMTKAMAVELSPLGIRVN 175 Query: 187 GVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAIPIGRAGKLSEVADFVCYLL 246 VAPG + E A N E+ ++ ++ P+G G + +AD V YL Sbjct: 176 CVAPGFIA---------TEMSAKALNGDPERKQKVLSRT--PMGALGTPANIADAVYYLA 224 Query: 247 SARASYITGVTTNIAGGKTRG 267 S ASYITG + GG G Sbjct: 225 SESASYITGTILPVDGGNAIG 245 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: 133 Number of extensions: 5 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 Apr 09 2024. 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