Align SDR family oxidoreductase (characterized, see rationale)
to candidate WP_011841012.1 RSPH17029_RS07260 3-hydroxybutyrate dehydrogenase
Query= uniprot:A0A4P7ABK7 (254 letters) >NCBI__GCF_000015985.1:WP_011841012.1 Length = 257 Score = 135 bits (341), Expect = 6e-37 Identities = 87/254 (34%), Positives = 128/254 (50%), Gaps = 9/254 (3%) Query: 8 LAGKTVLITAAAQGIGRASTELFAREGARVIA---TDISKTHL--EELASIAGVETHLL- 61 L GK ++T + GIG E AR GA ++ TD + H E++ GV + Sbjct: 3 LNGKRAIVTGSNSGIGLGCAEELARAGAEIVINSFTDRDEDHALAEKIGREHGVSCRYIA 62 Query: 62 -DVTDDDAIKALVAKVGTVDVLFNCAGYVAAGNILECDDKAWDFSFNLNAKAMFHTIRAV 120 D++D +A +AL+ G D+L N AG +I E + W+ +N + FHT A Sbjct: 63 ADMSDGEACRALIETAGGCDILVNNAGIQHVSSIEEFPVEKWNAILAINLSSAFHTTAAA 122 Query: 121 LPGMLAKKAGSIVNIASAASSVKGVANRFAYGASKAAVVGLTKSVAADFVSQGIRCNAIC 180 LPGM AK G IVNIAS A + + AY A+K VVG TK A + +GI CNAIC Sbjct: 123 LPGMRAKGWGRIVNIAS-AHGLTASPYKSAYVAAKHGVVGFTKVTALETAGKGITCNAIC 181 Query: 181 PGTIESPSLNQRISTQAKETGKS-EDEVRAAFVARQPMGRIGKAEEVAALALYLASDESN 239 PG + +P + +I Q K E +R + RQP + ++ ++L S ++ Sbjct: 182 PGYVLTPLVEAQIPDQMKAHDMDRETVIREVMLDRQPSRQFATTGQIGGTVVFLCSGAAD 241 Query: 240 FTTGSIHMIDGGWS 253 TG+ +DGGW+ Sbjct: 242 QITGTTISVDGGWT 255 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: 158 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: 254 Length of database: 257 Length adjustment: 24 Effective length of query: 230 Effective length of database: 233 Effective search space: 53590 Effective search space used: 53590 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 Apr 10 2024. 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