Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate WP_010630985.1 RH97_RS03700 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >NCBI__GCF_000246965.1:WP_010630985.1 Length = 248 Score = 124 bits (312), Expect = 1e-33 Identities = 86/271 (31%), Positives = 141/271 (52%), Gaps = 39/271 (14%) Query: 5 LNLKEKIITVTGGASGIGLAIVDELLAQGANVQMIDIHGGDKHQSSGNYN---------- 54 + LK K VTG + GIG AI +GA+V + + G+K ++ Sbjct: 1 MGLKGKAALVTGASRGIGKAIALAFAREGASV--VVNYAGNKARAEETAAEIRELGQEAL 58 Query: 55 FWPTDISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEK 114 + D++S +V + + + ++FG +D +VNNAG+ LL+ + EA ++ Sbjct: 59 VYQCDVTSEPDVQEMIKTVSKKFGHLDIVVNNAGITRDGLLM---------RIKEADWDA 109 Query: 115 MVNINQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSW 174 ++N N KGVFL+++A R M++QRSG I+N++S G+ G+ GQ+ Y+A KA + T++ Sbjct: 110 VLNTNLKGVFLVTKAALRPMMRQRSGKIINIASVVGILGNAGQANYSAAKAGVIGLTKTT 169 Query: 175 SKELGKHGIRVVGVAPG--ILEKTGLRTPEYEEALAWTRNITVEQLREGYSKNSIPLGRS 232 ++E+ GI V VAPG I E T + +E + K IPL R Sbjct: 170 AREVASRGITVNAVAPGFIITEMTAELPDQVKEQM----------------KAQIPLQRL 213 Query: 233 GRLTEVADFVCYLLSERASYMTGVTTNIAGG 263 G +VA V +L S+ ++YMTG ++ GG Sbjct: 214 GTPEDVASVVRFLASDDSNYMTGQILSVDGG 244 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: 160 Number of extensions: 5 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