Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate 3608790 Dshi_2182 3-oxoacyl-(acyl-carrier-protein) reductase (RefSeq)
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Dino:3608790 Length = 245 Score = 105 bits (262), Expect = 9e-28 Identities = 80/262 (30%), Positives = 121/262 (46%), Gaps = 27/262 (10%) Query: 6 NLKEKIITVTGGASGIGLAIVDELLAQGANVQM----IDIHGGDKHQSSGNYNFWPTDIS 61 +L K VTG + GIG AI L AQGA V + +D + + P ++S Sbjct: 3 DLTGKTALVTGASGGIGGAIATALHAQGATVGLSGTRVDPLEALAAELGERAHVLPCNLS 62 Query: 62 SASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQK 121 A V + G +D LVNNAG+ L + +++ + ++++N Sbjct: 63 DADAVEALPKQAVAAMGSVDILVNNAGITRDNLFM---------RMSDEEWASVLDVNLT 113 Query: 122 GVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKH 181 + + V R M+K R G IVN+SS G G+ GQ YAA+KA + ++S + E+ Sbjct: 114 STMRLCRGVLRGMMKARWGRIVNISSVVGATGNPGQGNYAASKAGMVGMSKSLAYEVASR 173 Query: 182 GIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADF 241 GI V VAPG + + A T +T +Q + +P GR G E+A Sbjct: 174 GITVNAVAPGFI------------STAMTDKLTDDQ--KDKLLVQVPSGRMGEPGEIAAA 219 Query: 242 VCYLLSERASYMTGVTTNIAGG 263 V YL S A Y+TG ++ GG Sbjct: 220 VVYLASPEAGYVTGSVLHVNGG 241 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: 156 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: 245 Length adjustment: 24 Effective length of query: 243 Effective length of database: 221 Effective search space: 53703 Effective search space used: 53703 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