Align 3-hydroxybutyryl-CoA dehydrogenase subunit (EC 1.1.1.35) (characterized)
to candidate WP_041700899.1 CKL_RS02265 3-hydroxybutyryl-CoA dehydrogenase
Query= metacyc::MONOMER-11936 (282 letters) >NCBI__GCF_000016505.1:WP_041700899.1 Length = 280 Score = 394 bits (1013), Expect = e-115 Identities = 195/280 (69%), Positives = 235/280 (83%) Query: 1 MKKIFVLGAGTMGAGIVQAFAQKGCEVIVRDIKEEFVDRGIAGITKGLEKQVAKGKMSEE 60 MK + VLG+GTM GIVQAFA+ G +VI+R E + +G+A + K +K+V+KGK+S+E Sbjct: 1 MKSVAVLGSGTMSRGIVQAFAEAGIDVIIRGRTEGSIGKGLAAVKKAYDKKVSKGKISQE 60 Query: 61 DKEAILSRISGTTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPEAILASNTSSLS 120 D + I+ R+S TT+++ ADCDL++EAA E+M IKK+ F +L+ ICKPE I A+NTSSLS Sbjct: 61 DADKIVGRVSTTTELEKLADCDLIIEAASEDMNIKKDYFGKLEEICKPETIFATNTSSLS 120 Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEIIKGIATSQETFDAVKELSVAIGKEPVEVA 180 ITEVA+ATKRPDK IGMHFFNPA VMKLVEII+G+ TSQETFD +KE S+ IGK PVEVA Sbjct: 121 ITEVATATKRPDKFIGMHFFNPANVMKLVEIIRGMNTSQETFDIIKEASIKIGKTPVEVA 180 Query: 181 EAPGFVVNGILIPMINEASFILQEGIASVEDIDTAMKYGANHPMGPLALGDLIGLDVCLA 240 EAPGFVVN IL+PMINEA IL EGIAS EDIDTAMK GANHPMGPLALGDLIGLDV LA Sbjct: 181 EAPGFVVNKILVPMINEAVGILAEGIASAEDIDTAMKLGANHPMGPLALGDLIGLDVVLA 240 Query: 241 IMDVLFTETGDNKYRASSILRKYVRAGWLGRKSGKGFYDY 280 +MDVL++ETGD+KYRA ++LRKYVRAGWLGRKSGKGF+ Y Sbjct: 241 VMDVLYSETGDSKYRAHTLLRKYVRAGWLGRKSGKGFFAY 280 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: 316 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: 280 Length adjustment: 26 Effective length of query: 256 Effective length of database: 254 Effective search space: 65024 Effective search space used: 65024 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