Align Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized)
to candidate N515DRAFT_1006 N515DRAFT_1006 3-oxoacyl-[acyl-carrier protein] reductase
Query= reanno::Koxy:BWI76_RS01745 (267 letters) >FitnessBrowser__Dyella79:N515DRAFT_1006 Length = 248 Score = 103 bits (256), Expect = 5e-27 Identities = 86/271 (31%), Positives = 127/271 (46%), Gaps = 42/271 (15%) Query: 7 LKEKIITVTGGASGIGLAIVDELLAQGANVQM---IDIHGGDK-----HQSSGNYNFWPT 58 LK K+ VTG + GIG I L A+GA V + G D ++ G Sbjct: 4 LKGKVALVTGASKGIGAGIAKALAAEGAAVVVNYASSKAGADAVVDAITKAGGKAVAVKG 63 Query: 59 DISSASEVHKTVDHIIQRFGRIDGLVNNAGVNFPRLLVDEKAPSGRYELNEAAFEKMVNI 118 D++ A++ D ++ FGR+D LVNN+GV E AP ++ E F K N+ Sbjct: 64 DVAQAADAQAIADAAVKEFGRLDILVNNSGVY-------EFAPLE--QITEDHFHKQFNV 114 Query: 119 NQKGVFLMSQAVARQMVKQRSGVIVNVSSESGLEGSEGQSCYAATKAALNSFTRSWSKEL 178 N G+ L +QA A+ M + G I+N+ S G S Y ATK A+++ T S+EL Sbjct: 115 NVLGLLLTTQAAAKHMGE--GGSIINIGSLVTRIVPPGGSVYTATKGAVDAITGVLSREL 172 Query: 179 GKHGIRVVGVAPGILEKTGLRTPEY------EEALAWTRNITVEQLREGYSKNSIPLGRS 232 G IRV + PG++E G T + +EA+A T PLGR Sbjct: 173 GPRKIRVNALNPGMVETEGTVTAGFIGSDFHQEAIAHT-----------------PLGRI 215 Query: 233 GRLTEVADFVCYLLSERASYMTGVTTNIAGG 263 G+ ++A +L S+ + ++TG AGG Sbjct: 216 GQPQDIATIAVFLASDDSYWLTGEKLYAAGG 246 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: 171 Number of extensions: 11 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: 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 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