Align Sorbitol-6-phosphate 2-dehydrogenase; EC 1.1.1.140; Glucitol-6-phosphate dehydrogenase; Ketosephosphate reductase (uncharacterized)
to candidate HSERO_RS02925 HSERO_RS02925 3-oxoacyl-ACP reductase
Query= curated2:P37079 (267 letters) >FitnessBrowser__HerbieS:HSERO_RS02925 Length = 244 Score = 120 bits (301), Expect = 3e-32 Identities = 87/259 (33%), Positives = 128/259 (49%), Gaps = 32/259 (12%) Query: 9 DNVIIVTGGASGIGLAIVDELLSQGAHVQMIDIHGGDRHHNGDNYHFWSTDISSATEVQQ 68 D V +VTGG GIG AI L + GA V + D H H Y S DI+ A V Q Sbjct: 12 DCVAVVTGGHGGIGAAISARLAAGGAQVVVWDQH----HDAASPYRQQSIDITDAPAVMQ 67 Query: 69 TIDAIIQRWSRIDGLVNNAGVNFPRLLVDEKAPAGRYELNEAAFEKMVNINQKGVFFMSQ 128 ++ RID L+NNAG P + +DE Y++ E + ++V +N GVF + Sbjct: 68 AAQELLADTGRIDFLINNAGYAGPTVPLDE------YDVGE--WHRIVQVNLLGVFHACR 119 Query: 129 AVARQMVKQRAGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKYGIRVVGV 188 +V M R G IVN++S +G EG+ S Y+A KA + + T+S KEL + G+ V + Sbjct: 120 SVTPAMRAARRGRIVNIASLAGKEGTPNASAYSAAKAGVLALTKSLGKELAESGVLVNAI 179 Query: 189 APGILEKTGLRTPEYEEALAWTRNITVEQLREGYTKNAI---PIGRAGKLSEVADFVCYL 245 AP + KT L + Q+ + + I P+ R G + EVAD +L Sbjct: 180 APAAV-KTAL----------------LGQMSPAHVQTMIAKSPMHRLGSVDEVADMCAWL 222 Query: 246 LSARASYITGVTTNIAGGK 264 S S+ TG +++GG+ Sbjct: 223 CSGSCSFNTGAVFDLSGGR 241 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: 147 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: 244 Length adjustment: 24 Effective length of query: 243 Effective length of database: 220 Effective search space: 53460 Effective search space used: 53460 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 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