Align 2-deoxy-D-ribonate 3-dehydrogenase (characterized)
to candidate WP_011385057.1 AMB_RS13470 3-hydroxybutyrate dehydrogenase
Query= reanno::Burk376:H281DRAFT_00644 (263 letters) >NCBI__GCF_000009985.1:WP_011385057.1 Length = 260 Score = 125 bits (315), Expect = 7e-34 Identities = 85/254 (33%), Positives = 132/254 (51%), Gaps = 9/254 (3%) Query: 12 GLRVFVSAGAAGIGLAIAEAFIEAQAEVYICDVNQAAIDEATSRFPKLHAGI------AD 65 G R V+ +GIGL IA A A V + A EA G+ AD Sbjct: 4 GKRALVTGSTSGIGLGIARALAAQGASVMLNGFGDGAEIEALRAGLAKEFGVTVLYNGAD 63 Query: 66 VSKQAQVDQIIDDARRKLGGLDVLVNNAGIAGPTGAVEELDPAQWESTVSTNLNSQFYFL 125 +SK ++ DA +LGG+D+LVNNAGI VEE +W++ ++ NL S F + Sbjct: 64 LSKPDGAGVLVRDAEARLGGVDILVNNAGIQH-VSPVEEFPLERWDAVIAINLTSVFQAI 122 Query: 126 RKAVPVLKETSDCASIIAMSSVAGRLGYPFRTPYASTKWAIVGLVKSLAAELGPSNVRVN 185 R A+P +K II ++S G + ++ Y ++K ++GL K + E ++V N Sbjct: 123 RAALPGMKARG-WGRIINVASAHGLVASVNKSAYVASKHGVLGLTKVVGLETAETDVTCN 181 Query: 186 AILPGVVEGERMDRVISARADALGIPF-NAMREEYLKKISLRRMVTVDDIAAMALFLASP 244 AI PG V + + I ARA+A G+P A R+ +K ++ T + I +A+FL S Sbjct: 182 AICPGWVLTPLVQKQIDARAEAQGVPVEQAGRDLLSEKQPSKKFTTPEQIGDLAVFLCSG 241 Query: 245 AGSNVTGQAISVDG 258 AG+N+TG ++++DG Sbjct: 242 AGANMTGTSLTMDG 255 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: 125 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: 263 Length of database: 260 Length adjustment: 25 Effective length of query: 238 Effective length of database: 235 Effective search space: 55930 Effective search space used: 55930 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: 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