Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_012383370.1 BIND_RS01815 3-oxoacyl-ACP reductase
Query= reanno::BFirm:BPHYT_RS04775 (263 letters) >NCBI__GCF_000019845.1:WP_012383370.1 Length = 259 Score = 129 bits (325), Expect = 5e-35 Identities = 86/258 (33%), Positives = 127/258 (49%), Gaps = 11/258 (4%) Query: 12 GLRVLISGAAAGIGAAIAQAFLDVGANVYICDVDPAAIDRARTAHPQLHA-------GVA 64 G L++G GIG IA GAN+ I DV D+A+ ++ A +A Sbjct: 5 GKVALVTGGGQGIGRGIALRLAQEGANIAIADVKA---DKAKAVAEEIMALGRKATIFIA 61 Query: 65 DVSDCAQVDRIIDDARSKLGGLDLLINNAGIAGPTGAVEDLDPAEWERTIGTNLNSQFYF 124 D+SD AQ+ ID + LGG D+++NNAGIA + D+ E +R + NL + Sbjct: 62 DISDRAQIHAAIDHTEATLGGFDIIVNNAGIA-QVQPILDVTQEEVDRILKINLEGVLWG 120 Query: 125 LRKAVPLLKETSANPGIIAMASVAGRLGYAFRTPYAASKWAIVGMVKSLAIELGPNNVRV 184 ++ A K T II +S+AG G+A Y+A+K+ + + ++ A EL P + V Sbjct: 121 IQAAAKKFKATGRKGKIINASSIAGHDGFALLGVYSATKFGVRALTQAAAKELAPFGITV 180 Query: 185 NAILPGVVEGERMDRVISARAESLGIGFDQMKGEYLQKISLRRMVTVHDVAAMALFLASP 244 NA PG+V + + AE G +Y+ I+L R T DVAA+ FLA Sbjct: 181 NAYCPGIVGTDMWVEIDKRMAEVTGAEVGATYQKYVGGIALGRAETPDDVAALVAFLAGA 240 Query: 245 AGQNISGQAISVDGNVEY 262 I+GQAI DG + Y Sbjct: 241 DSDYITGQAIITDGGIVY 258 Lambda K H 0.320 0.136 0.391 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: 159 Number of extensions: 7 Number of successful extensions: 2 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: 259 Length adjustment: 25 Effective length of query: 238 Effective length of database: 234 Effective search space: 55692 Effective search space used: 55692 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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