Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate Ac3H11_2257 Short-chain dehydrogenase/reductase SDR
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2257 Length = 267 Score = 119 bits (298), Expect = 7e-32 Identities = 82/257 (31%), Positives = 125/257 (48%), Gaps = 22/257 (8%) Query: 10 KIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYN--FWPTDISSASEVH 67 ++ VTGGA GIG A V A+GA ++D+ + + D+ ++V Sbjct: 21 RVCIVTGGAQGIGEACVRRFAAEGAKPVIVDVDDARGQALAAELGALYVRCDVGDKAQVD 80 Query: 68 KTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKGVFLMS 127 V ++ GRID LVNNAG+ + E+ EA F+ ++ +N KG FL+ Sbjct: 81 ALVAQVLAAHGRIDVLVNNAGIF---------RAADFLEVTEADFDAVLRVNLKGSFLVG 131 Query: 128 QAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHGIRVVG 187 QAVAR MV G IVN+SS +G+ + Y +K +N TR + L IRV Sbjct: 132 QAVARAMVTSGGGAIVNMSSVNGVLAIPNIASYNVSKGGVNQLTRVMALALADKNIRVNA 191 Query: 188 VAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFVCYLLS 247 VAPG + LA +T ++ + + P+ R G+ +E+AD V +L S Sbjct: 192 VAPGTI----------ATELAAKAVLTSDEAKRKIMSRT-PMKRLGQPSEIADVVAWLAS 240 Query: 248 ERASYMTGVTTNIAGGK 264 + ASY+TG + GG+ Sbjct: 241 DAASYVTGEIVTVDGGR 257 Lambda K H 0.315 0.132 0.378 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: 154 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: 267 Length adjustment: 25 Effective length of query: 242 Effective length of database: 242 Effective search space: 58564 Effective search space used: 58564 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: 42 (22.0 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