Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate WP_051402380.1 N177_RS12700 3-hydroxybutyryl-CoA dehydrogenase
Query= CharProtDB::CH_091789 (282 letters) >NCBI__GCF_000496075.1:WP_051402380.1 Length = 278 Score = 278 bits (712), Expect = 7e-80 Identities = 142/269 (52%), Positives = 183/269 (68%) Query: 12 MGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEATKVEILTRISG 71 MGSGIA A G+EV L D+ E + GL IN NL++ V GKI E + L IS Sbjct: 1 MGSGIAHVCALAGYEVKLNDVSVERCEAGLATINGNLARQVSSGKIGEEARQSALRLISA 60 Query: 72 TVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLSITEVASATKRP 131 L +D DLVIE+A+E ++K++I +L P+ I+A+NTSS+SIT +AS + RP Sbjct: 61 AASLEEMSDVDLVIESAIENEEVKRKILRELCPHLSPDAIVATNTSSISITRLASVSDRP 120 Query: 132 DKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVAEAPGFVVNRIL 191 ++ IG+HF NP PVM+LVE++RGIAT TF+ + ++GK + P F+VNRIL Sbjct: 121 ERFIGIHFMNPVPVMELVELVRGIATEDVTFETARAFVTSLGKTIAVSEDFPAFMVNRIL 180 Query: 192 IPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLAIMDVLYSETGD 251 +PMINEA+ L EG+ +VE ID AM+LGA HPMGPLEL DFIGLD CL+IM +LY D Sbjct: 181 LPMINEAIYTLYEGVGTVEAIDTAMRLGARHPMGPLELADFIGLDTCLSIMQMLYEGLAD 240 Query: 252 SKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280 SKYRP LL KYV AGWLGRK+ +GFYDY Sbjct: 241 SKYRPCPLLVKYVEAGWLGRKAQRGFYDY 269 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: 207 Number of extensions: 1 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: 278 Length adjustment: 26 Effective length of query: 256 Effective length of database: 252 Effective search space: 64512 Effective search space used: 64512 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 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