Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_017867317.1 LACPOB_RS0102810 3-oxoacyl-[acyl-carrier-protein] reductase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >NCBI__GCF_000349725.1:WP_017867317.1 Length = 243 Score = 94.7 bits (234), Expect = 2e-24 Identities = 77/255 (30%), Positives = 125/255 (49%), Gaps = 24/255 (9%) Query: 12 GLRVFVSAGAAGIGLAIAEAFIEAQAEVYIC---DVNQAAIDEATSRFPKLHAGIADVSK 68 G F++ + GIG IA AF +A+A V + +V +E S + + D+S+ Sbjct: 5 GKTAFITGSSRGIGKQIALAFAQAKANVILNARKEVPAQLEEEIKSYGVQCVTILGDISR 64 Query: 69 QAQVDQIIDDARRKLGGLDVLVNNAGIAGPT---GAVEELDPAQWESTVSTNLNSQFYFL 125 V +++ +A +DVLVNNAGI G EE + S + NL Y + Sbjct: 65 ADDVKRMVKEAYGSFPQIDVLVNNAGITNDKLLIGMKEE----DFRSVIDVNLVGT-YSM 119 Query: 126 RKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVN 185 +A+ II ++SV G G + YA++K ++GL K++A E N+R N Sbjct: 120 TRAILKKMNKKRTGVIINLASVVGLHGNVGQANYAASKAGVIGLTKTVAKEGALRNIRCN 179 Query: 186 AILPGVVEGERMDRVISARADALGIPFNAMREEYLKKISLRRMVTVDDIAAMALFLASPA 245 AI PG++E + D V+S + ++ + + I L+R +++A A+FLA Sbjct: 180 AIAPGMIESDMTD-VLS----------DKVKNQLMAGIPLKRFGDSNEVAKTAVFLAQ-- 226 Query: 246 GSNVTGQAISVDGNV 260 +TGQ ISVDG + Sbjct: 227 NDYITGQVISVDGGM 241 Lambda K H 0.318 0.134 0.375 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: 134 Number of extensions: 8 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: 263 Length of database: 243 Length adjustment: 24 Effective length of query: 239 Effective length of database: 219 Effective search space: 52341 Effective search space used: 52341 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: 41 (21.7 bits) S2: 46 (22.3 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