Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate CCNA_00752 CCNA_00752 3-hydroxybutyryl-CoA dehydrogenase
Query= CharProtDB::CH_091789 (282 letters) >FitnessBrowser__Caulo:CCNA_00752 Length = 292 Score = 300 bits (768), Expect = 2e-86 Identities = 153/280 (54%), Positives = 194/280 (69%) Query: 1 MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60 +K V VIGAG MGSGIA A G++V L D+ E +D G+ I KN+++ V +G I++A Sbjct: 4 IKTVGVIGAGQMGSGIAHVVALGGYDVRLHDVSRERIDAGIAVIEKNMARQVGRGIIDDA 63 Query: 61 TKVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120 L RI L DL IEAA E ++KK IF L KPET+LASNTSS+S Sbjct: 64 AMKAALARIQPAEGLEAIGATDLAIEAATENEEVKKSIFRSLQPYLKPETLLASNTSSIS 123 Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVA 180 IT +ASAT RP++ IG+HF NP P+MKLVE+IRGIAT T++ + ++GK Sbjct: 124 ITRLASATDRPERFIGLHFMNPVPLMKLVEIIRGIATDVPTYERAVTFAQSLGKITSNAE 183 Query: 181 EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLA 240 + P F+VNR+L+PMINEA+ L EG+ +V+ ID AMKLGANHPMGPLELGDFIGLD L+ Sbjct: 184 DFPAFIVNRVLVPMINEAIYTLYEGVGTVDAIDTAMKLGANHPMGPLELGDFIGLDTVLS 243 Query: 241 IMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280 IM+VL+ DSKYRP LL KYV AGWLG+K+G+GFYDY Sbjct: 244 IMNVLHEGLADSKYRPCPLLVKYVEAGWLGKKTGRGFYDY 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: 246 Number of extensions: 2 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: 292 Length adjustment: 26 Effective length of query: 256 Effective length of database: 266 Effective search space: 68096 Effective search space used: 68096 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 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