Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_068003992.1 PsAD2_RS06355 SDR family oxidoreductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_001623255.1:WP_068003992.1 Length = 263 Score = 128 bits (322), Expect = 1e-34 Identities = 91/271 (33%), Positives = 135/271 (49%), Gaps = 32/271 (11%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDI--HGGDKHQSS----GNYNFWPT 58 + L K+ VTGGA GIG AI L GA V + D G+ Q + G+ F Sbjct: 1 MKLDRKVAIVTGGAQGIGYAIAQRFLEDGAKVMISDADERAGEAAQEALSEFGHVAFCHC 60 Query: 59 DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118 D+ +V V + + FG ID LVNNAGV A L+E F++++ + Sbjct: 61 DVGVRLDVRNMVANTLDEFGDIDVLVNNAGVT---------AAGDFLTLSEDDFDRVLQV 111 Query: 119 NQKGVFLMSQAVARQMVKQ-----RSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRS 173 N KG FL SQAVAR MV++ +G+I+N+SS + + Q Y +K LN T Sbjct: 112 NLKGAFLCSQAVARHMVEKIEEGGSAGIIINISSVNSVLAIPEQVPYTVSKGGLNQLTNV 171 Query: 174 WSKELGKHGIRVVGVAPGILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSG 233 + L K+GIRV G+ PG +E L+ +E+ ++ + S+ PLGR G Sbjct: 172 SAVALAKYGIRVNGIGPGSIETDMLKAVVQDES----------KMNKVLSRT--PLGRLG 219 Query: 234 RLTEVADFVCYLLSERASYMTGVTTNIAGGK 264 + +E+A +L S+ ASY++G T G + Sbjct: 220 QPSEIAGVASFLASDDASYVSGQTIFADGAR 250 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: 173 Number of extensions: 10 Number of successful extensions: 5 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: 263 Length adjustment: 25 Effective length of query: 242 Effective length of database: 238 Effective search space: 57596 Effective search space used: 57596 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 24 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