Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_047093910.1 AAV99_RS08330 3-hydroxybutyrate dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_001013305.1:WP_047093910.1 Length = 251 Score = 129 bits (324), Expect = 6e-35 Identities = 86/250 (34%), Positives = 123/250 (49%), Gaps = 7/250 (2%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIATDISKTHLEELASIA---GVETHLLDVT 64 L GK L+T + GIG A + A EGA V+ +E+A I G ++ Sbjct: 3 LEGKRALVTGSTSGIGLAIAKALAAEGASVVINGFGDA--DEIAGICAEIGATHSGANLM 60 Query: 65 DDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAVLPGM 124 D I+ ++A+ G +D+L N AG + E + W LN A+FHT R +P M Sbjct: 61 DVGEIETMMAEAGPLDILVNNAGMQHVCPVEEFPVEKWHQVIALNLTAVFHTTRLAVPAM 120 Query: 125 LAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAICPGTI 184 K G I+N ASA S + AY ASK V G TK+VA + G+ N I PG + Sbjct: 121 REKGWGRIINTASAHSKTAS-PFKSAYNASKHGVDGFTKTVALELAETGVTANCISPGYV 179 Query: 185 ESPSLNQRISTQAKETGKSEDEV-RAAFVARQPMGRIGKAEEVAALALYLASDESNFTTG 243 +P + +I K G +E++V +A+QP + + EEV ALA +L E TG Sbjct: 180 WTPLIEGQIPDTMKARGLTEEQVINDVLLAKQPTKKFVQVEEVGALATFLCRTEMGNVTG 239 Query: 244 SIHMIDGGWS 253 + IDGGW+ Sbjct: 240 ANWSIDGGWT 249 Lambda K H 0.316 0.129 0.359 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: 137 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: 254 Length of database: 251 Length adjustment: 24 Effective length of query: 230 Effective length of database: 227 Effective search space: 52210 Effective search space used: 52210 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