Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_010631287.1 RH97_RS05205 3-hydroxyacyl-CoA dehydrogenase family protein
Query= CharProtDB::CH_091789 (282 letters) >NCBI__GCF_000246965.1:WP_010631287.1 Length = 312 Score = 189 bits (481), Expect = 5e-53 Identities = 110/285 (38%), Positives = 166/285 (58%), Gaps = 6/285 (2%) Query: 2 KKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEAT 61 K + VIG+G MGSGIAQ+FA G+ V++ DIK EF+D+ I++NL+ LV G + EA Sbjct: 3 KTISVIGSGVMGSGIAQSFAVGGYSVIVNDIKQEFLDKAKKNIHENLNLLVGSGDLTEAD 62 Query: 62 KVEILTRISGTVDLNMAA-DCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120 + L RI T DL AA + DL+IEA E +D+K ++ DL KP+ +++SNTS+ Sbjct: 63 RNAALGRIRFTTDLKEAAGEADLIIEAIPEVIDLKWNLYDDLATYKKPDAVVSSNTSTFP 122 Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEV- 179 IT++ + K I HFFNPA ++ LVE+++ T +VK ++IGK PV + Sbjct: 123 ITKLTARESFDGKFIITHFFNPANLVPLVEIVKKKDTDLNLVQSVKNLLLSIGKTPVVLK 182 Query: 180 AEAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHP---MGPLELGDFIGLD 236 E GF+ NR+ ++ EA ++ +G+A +D+DKA+ G +GP + DF GLD Sbjct: 183 KEINGFIANRLQTALMREAFSLVGQGVADADDVDKAITAGPGFRWAFVGPTRIADFGGLD 242 Query: 237 ICLAIMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDYS 281 + D + + S+ P L+ K V LG K+G+G Y YS Sbjct: 243 TWKRVFDNIAPDLDKSEGAPE-LINKLVSTHKLGTKTGEGLYKYS 286 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: 251 Number of extensions: 14 Number of successful extensions: 5 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: 312 Length adjustment: 26 Effective length of query: 256 Effective length of database: 286 Effective search space: 73216 Effective search space used: 73216 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: 48 (23.1 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