Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate HSERO_RS19055 HSERO_RS19055 oxidoreductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__HerbieS:HSERO_RS19055 Length = 256 Score = 128 bits (321), Expect = 1e-34 Identities = 93/265 (35%), Positives = 136/265 (51%), Gaps = 29/265 (10%) Query: 10 KIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSS-----GNYNFWPT--DISS 62 ++ VTGGA GIG +I +L A+G V + DI+ +++ + P D+ S Sbjct: 9 RVALVTGGAMGIGASISQQLAAKGHTVLVADINLDAASKTADALVAAGHRAAPLQMDLGS 68 Query: 63 ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKG 122 + HI + +GR D LVNNAGV +D Y L + + +N+N G Sbjct: 69 PESIAAAFAHIEKDYGRCDVLVNNAGVARTYSFLD-------YPLEN--WLQTMNVNVTG 119 Query: 123 VFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHG 182 V L Q AR MVKQ+ G IVN+SS SG+ G++ Y +KAA+ TR + EL ++G Sbjct: 120 VLLAGQHAARLMVKQQWGRIVNISSISGIRAGAGRTAYGTSKAAVIGLTRQMAIELAQYG 179 Query: 183 IRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFV 242 I V VAPG ++ TP T+ + EQ RE Y + +P+ R G E+A V Sbjct: 180 ITVNSVAPGPVD-----TP-------MTQAMHSEQTRESYYR-LVPMRRYGTTDEIASAV 226 Query: 243 CYLLSERASYMTGVTTNIAGGKTRG 267 CYL +E ++Y+TG + GG G Sbjct: 227 CYLAAEESAYITGHVIPVDGGFVAG 251 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: 149 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: 256 Length adjustment: 25 Effective length of query: 242 Effective length of database: 231 Effective search space: 55902 Effective search space used: 55902 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