Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_011842533.1 RSPH17029_RS18450 3-hydroxybutyryl-CoA dehydrogenase
Query= CharProtDB::CH_091789 (282 letters) >NCBI__GCF_000015985.1:WP_011842533.1 Length = 294 Score = 292 bits (747), Expect = 7e-84 Identities = 150/277 (54%), Positives = 186/277 (67%) Query: 4 VCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEATKV 63 V VIGAG MG+GIAQ FA G+EV L D+ +D I + + V KG + + Sbjct: 7 VGVIGAGQMGAGIAQVFAQAGYEVRLSDLSPSQLDAARSRIAGSTGRAVAKGTLSAEERD 66 Query: 64 EILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLSITE 123 +L R+ T L DLVIE A E ++KK+I DL + T+L +NTSSLSIT Sbjct: 67 RVLDRVQVTTALEPIGGADLVIECATENEEVKKRILRDLTPLLADRTVLTTNTSSLSITR 126 Query: 124 VASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVAEAP 183 +A+ T RP + +G+HF NP PVMKLVE+IRGIAT Q TF +V+ +GK + P Sbjct: 127 LAAVTDRPQRFMGLHFMNPVPVMKLVELIRGIATDQATFASVEAVVATLGKTATTSEDYP 186 Query: 184 GFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLAIMD 243 F+VNR+L+PMINEAV L EG+ +V ID AM+LGANHPMGPLELGDFIGLD CLAIM+ Sbjct: 187 AFIVNRLLVPMINEAVYALYEGVGNVASIDAAMRLGANHPMGPLELGDFIGLDTCLAIMN 246 Query: 244 VLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280 VL+ GDSKYRP LL K+V AGWLGRKSG+GFYDY Sbjct: 247 VLHDGLGDSKYRPCPLLVKFVEAGWLGRKSGRGFYDY 283 Lambda K H 0.319 0.137 0.386 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: 235 Number of extensions: 3 Number of successful extensions: 1 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: 282 Length of database: 294 Length adjustment: 26 Effective length of query: 256 Effective length of database: 268 Effective search space: 68608 Effective search space used: 68608 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 (21.7 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