Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_090448356.1 BLS63_RS24180 KR domain-containing protein
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_900100495.1:WP_090448356.1 Length = 244 Score = 88.2 bits (217), Expect = 2e-22 Identities = 82/265 (30%), Positives = 116/265 (43%), Gaps = 36/265 (13%) Query: 10 KIITVTGGASGIGLAIVDELLAQGANVQM-IDIHGGDKHQ-------SSGNYNFWPTDIS 61 K+ VTG + GIG AI L A G +V + D Q + G DIS Sbjct: 3 KVAIVTGASRGIGAAIAKRLAADGISVVVNYTSRPADAEQVVRDIVSAGGQAYAVLADIS 62 Query: 62 SASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNINQK 121 + V D +FG ID LVNNAGV P ++ + ++A ++K+ IN K Sbjct: 63 DSVAVEALFDQAELKFGGIDILVNNAGVIQPGMV-------NLADSDDALYQKIFAINTK 115 Query: 122 GVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKELGKH 181 G F + AR + + G IVN S+ G S YAA+KAA+ SFT ++KEL Sbjct: 116 GTFNTLRLAARHL--RDGGRIVNFSTSVVGLALPGYSLYAASKAAVESFTVIFAKELRGR 173 Query: 182 GIRVVGVAPGILEK---TGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSGRLTEV 238 I V +APG G +T E E L PL R G ++ Sbjct: 174 NICVNAIAPGPTATELFLGGKTAEMIERLT----------------KQPPLERLGTPEDI 217 Query: 239 ADFVCYLLSERASYMTGVTTNIAGG 263 A+ V +L+ E+ ++ G + GG Sbjct: 218 ANVVAFLVGEQGGWVNGQVLRVNGG 242 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: 150 Number of extensions: 6 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: 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: 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