Align 3-hydroxybutyryl-CoA dehydrogenase subunit (EC 1.1.1.35) (characterized)
to candidate WP_084055931.1 B9A12_RS02385 3-hydroxybutyryl-CoA dehydrogenase
Query= metacyc::MONOMER-11936 (282 letters) >NCBI__GCF_900176285.1:WP_084055931.1 Length = 283 Score = 324 bits (830), Expect = 2e-93 Identities = 164/281 (58%), Positives = 200/281 (71%) Query: 1 MKKIFVLGAGTMGAGIVQAFAQKGCEVIVRDIKEEFVDRGIAGITKGLEKQVAKGKMSEE 60 +K V+GAG MG GI Q A G +VI+ DIK+EFV RG+ I K L + V KGKMS+E Sbjct: 3 VKTFGVIGAGQMGNGIAQVAAMSGLQVIMNDIKDEFVQRGLNNIKKILARNVDKGKMSQE 62 Query: 61 DKEAILSRISGTTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPEAILASNTSSLS 120 + +A+L RI + D+K A D VVEAA EN IK +IF +LD IC AILA+NTSS+ Sbjct: 63 EMDAVLGRIKTSVDLKDMAAADYVVEAATENEPIKFQIFRDLDAICPEHAILATNTSSIP 122 Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEIIKGIATSQETFDAVKELSVAIGKEPVEVA 180 I +AS TKRP+KVIGMHF NP PVMKLVE+I+G+ATS ETF L+ GK P E Sbjct: 123 IGRIASQTKRPEKVIGMHFMNPVPVMKLVEVIRGLATSDETFKITWGLAEKFGKTPAEAQ 182 Query: 181 EAPGFVVNGILIPMINEASFILQEGIASVEDIDTAMKYGANHPMGPLALGDLIGLDVCLA 240 + PGF+ N IL+PMINEA + L G+ + EDIDT MK G NHPMGPLAL DLIGLD CLA Sbjct: 183 DYPGFIANRILMPMINEAVYCLYHGVGTREDIDTVMKLGMNHPMGPLALADLIGLDTCLA 242 Query: 241 IMDVLFTETGDNKYRASSILRKYVRAGWLGRKSGKGFYDYS 281 IM+ L+ D+KYR +LRKYV AGWLGRK+G+GFY+YS Sbjct: 243 IMETLYQGFCDSKYRPCPLLRKYVEAGWLGRKTGRGFYEYS 283 Lambda K H 0.318 0.136 0.378 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: 262 Number of extensions: 5 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: 283 Length adjustment: 26 Effective length of query: 256 Effective length of database: 257 Effective search space: 65792 Effective search space used: 65792 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 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