Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate CA265_RS08605 CA265_RS08605 short-chain dehydrogenase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Pedo557:CA265_RS08605 Length = 262 Score = 113 bits (282), Expect = 5e-30 Identities = 88/267 (32%), Positives = 133/267 (49%), Gaps = 26/267 (9%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKH-------QSSGNYNFWP 57 L LKEK+I +TG A GIG +I + + A ++ D + G + Sbjct: 3 LQLKEKVIVITGAAKGIGRSIAEVFAKENAIAVIVGRKAEDNQIVVDAIATNGGKAAQFV 62 Query: 58 TDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVN 117 ++S+ + V +I+ +FGRIDGLVNNAGVN L SG Y+ A+ K Sbjct: 63 AELSNPEDCETVVKNIVAQFGRIDGLVNNAGVNDGVGL-----ESGNYKDFMASLHK--- 114 Query: 118 INQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKE 177 N +LM+ V +++K + G IVN++S++ G S YAA N+ TR W+ E Sbjct: 115 -NVVHYYLMAHHVLPELIKSK-GAIVNITSKTAETGQGNTSAYAAANGGRNALTREWAVE 172 Query: 178 LGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPL-GRSGRLT 236 L K+GIRV V TP YE + T + E+L+E +K IPL R Sbjct: 173 LLKYGIRVNAVV-----VAECWTPAYETWIE-TLDNAEEKLKEITAK--IPLENRMTTAE 224 Query: 237 EVADFVCYLLSERASYMTGVTTNIAGG 263 E+A+ +L+S ++S+ TG ++ GG Sbjct: 225 EIANMTAFLMSSKSSHTTGQIIHVDGG 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: 168 Number of extensions: 11 Number of successful extensions: 3 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: 262 Length adjustment: 25 Effective length of query: 242 Effective length of database: 237 Effective search space: 57354 Effective search space used: 57354 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