Align NAD(P)-dependent dehydrogenase (Short-subunit alcohol dehydrogenase family) (characterized, see rationale)
to candidate WP_085218348.1 B9N75_RS08190 3-hydroxybutyrate dehydrogenase
Query= uniprot:A0A4R8NY47 (263 letters) >NCBI__GCF_900177405.1:WP_085218348.1 Length = 261 Score = 114 bits (285), Expect = 2e-30 Identities = 80/257 (31%), Positives = 118/257 (45%), Gaps = 12/257 (4%) Query: 16 SLAGKRVVITGGGSGIGAALVEAFVGQGAQVCFLDIATEPSEALVASLKDAAVAPR--FF 73 SL GK +ITG SGIG A + G GA + + A + + R + Sbjct: 2 SLKGKAALITGSTSGIGLAYAKTLAGAGAHIMLNGFGDRDAIAKIQREIEGLSGARTDYS 61 Query: 74 PCNLMNLEALRATFTEIETVMGGVDILINNAANDDRHKSEDVTPAYWDERLAVNLRHQFF 133 +L N A+ A + ++ +GGVDILINNA ++ W+ +A+NL F Sbjct: 62 DADLTNPAAIEAMIGQAKSSLGGVDILINNAGMQHVAPVDEFPIDKWNAIIALNLSAAFH 121 Query: 134 CAQAVLPGMRERKGGVILNFGSISWHLGLPDLTLYMTAKAGIEGMTHGMARDFGRDGVRV 193 + +P M+E+K G I++ S + P+ + Y+ AK GI G+T +A + G+ V Sbjct: 122 AIRLAVPHMKEKKWGRIISTASAHSLVASPNKSAYVAAKHGIAGLTKTVALEVATHGITV 181 Query: 194 NAIIPGAI----------RTPRQTLLWHTPEEEAKILAAQCLPVRVDPHDVAALALFLSS 243 N I PG + T + L +LAAQ V P VA+LAL+L S Sbjct: 182 NCISPGYVWTQLVEDQIPDTMKSRGLTREQVMNDVLLAAQPTKQFVTPEQVASLALYLCS 241 Query: 244 DSGAKCTGREYYVDAGW 260 D A TG +D GW Sbjct: 242 DDAAAITGANLSMDGGW 258 Lambda K H 0.322 0.137 0.417 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: 9 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: 261 Length adjustment: 25 Effective length of query: 238 Effective length of database: 236 Effective search space: 56168 Effective search space used: 56168 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 (21.9 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