Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate AO356_19860 AO356_19860 short-chain dehydrogenase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_19860 Length = 253 Score = 112 bits (280), Expect = 8e-30 Identities = 79/263 (30%), Positives = 131/263 (49%), Gaps = 26/263 (9%) Query: 10 KIITVTGGASGIGLAIVDELLAQGANVQM--IDIHGGDKHQSS-----GNYNFWPTDISS 62 ++ VTGGA+GIG A A+G V + +D+ GG++ S G F +++ Sbjct: 8 QVAVVTGGAAGIGCATAQAFAAEGLKVVVADLDVAGGERTVQSIRDGGGEALFVRCNVTL 67 Query: 63 ASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQKG 122 S+V +D +I+ +GR+D NNAG+ EK L+E F+ ++ +N KG Sbjct: 68 ESDVQHLMDEVIKAYGRLDYAFNNAGIEI------EKGKLADGTLDE--FDAIMGVNVKG 119 Query: 123 VFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKHG 182 V+L + ++ Q G IVN +S +GL + S YAA+K A+ T+S + E + Sbjct: 120 VWLCMKYQLPLLLAQGGGAIVNTASVAGLGAAPKMSIYAASKHAVIGLTKSAAIEYARKK 179 Query: 183 IRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEVADFV 242 IRV V P +++ R R + + ++ P+GR G++ E+A V Sbjct: 180 IRVNAVCPAVIDTDMFR-----------RAYEADPKKGEFANAMHPVGRIGKVEEIASAV 228 Query: 243 CYLLSERASYMTGVTTNIAGGKT 265 YL S+ A++ TG + + GG T Sbjct: 229 LYLCSDGAAFTTGHSLAVDGGVT 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: 164 Number of extensions: 9 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: 253 Length adjustment: 24 Effective length of query: 243 Effective length of database: 229 Effective search space: 55647 Effective search space used: 55647 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