Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_013430493.1 CALKRO_RS07790 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_000166775.1:WP_013430493.1 Length = 248 Score = 140 bits (353), Expect = 3e-38 Identities = 93/270 (34%), Positives = 139/270 (51%), Gaps = 41/270 (15%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYN-----------F 55 LK+K+ +TG + GIG AI + GANV I+ + N Sbjct: 4 LKDKVALITGASRGIGRAIALKFAQNGANVV---INYSSSQSQAENLKEEIEKIGTKTMI 60 Query: 56 WPTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKM 115 D+S+ EV + + FGR+D LVNNAG+ L++ +NE F+K+ Sbjct: 61 IKCDVSNPDEVSHMFSQVEKEFGRLDILVNNAGITKDGLIL---------RMNEEDFDKV 111 Query: 116 VNINQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWS 175 + IN KG FL ++A A+ MVKQR G I+N+SS G+ G+ GQ+ YAA+KA + T+S + Sbjct: 112 IAINLKGAFLCARAAAKMMVKQRFGNIINISSVVGIAGNVGQANYAASKAGIIGLTKSLA 171 Query: 176 KELGKHGIRVVGVAPGIL--EKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRSG 233 KEL IRV +APG + + T + + + +EA+ +SIPLGR G Sbjct: 172 KELASRNIRVNAIAPGFIKTDMTEVLSDKVKEAML----------------SSIPLGRFG 215 Query: 234 RLTEVADFVCYLLSERASYMTGVTTNIAGG 263 E+A+ +L S +SY+TG + GG Sbjct: 216 EADEIANVALFLASSLSSYITGQVIVVDGG 245 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: 167 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: 248 Length adjustment: 24 Effective length of query: 243 Effective length of database: 224 Effective search space: 54432 Effective search space used: 54432 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