Align 3-hydroxybutyryl-CoA dehydrogenase subunit (EC 1.1.1.35) (characterized)
to candidate WP_013076501.1 BTUS_RS12845 3-hydroxyacyl-CoA dehydrogenase family protein
Query= metacyc::MONOMER-11936 (282 letters) >NCBI__GCF_000092905.1:WP_013076501.1 Length = 288 Score = 226 bits (575), Expect = 6e-64 Identities = 124/282 (43%), Positives = 172/282 (60%), Gaps = 2/282 (0%) Query: 1 MKKIFVLGAGTMGAGIVQAFAQKGCEVIVRDIKEEFVDRGIAGITKGLEKQVAKGKMSEE 60 +K+I V+G+G MG I A G V V+DI E ++R +T+ LEK+V KGK+S E Sbjct: 6 VKRIGVVGSGAMGTQIAAVCALAGYPVKVQDIATESLERARQVLTEQLEKRVQKGKLSRE 65 Query: 61 DKEAILSRISGTTDMKLAA-DCDLVVEAAIENMKIKKEIFAELDGICKPEAILASNTSSL 119 + SR+S TTD+ A D D V+EA +E + K+E+FA LD + AILA+N+S++ Sbjct: 66 QVDGAWSRLSWTTDLGEAVRDADYVIEAIVEKLDAKRELFARLDELAPAHAILATNSSTI 125 Query: 120 SITEVASATKRPDKVIGMHFFNPAPVMKLVEIIKGIATSQETFDAVKELSVAIGKEPVEV 179 +++A AT+RP+ V MHFFNP VM+LVE++ TS++T D EL IGK P+ + Sbjct: 126 VSSKIADATRRPENVCNMHFFNPVLVMELVEVVMNPQTSEDTADTAVELCRRIGKTPILL 185 Query: 180 -AEAPGFVVNGILIPMINEASFILQEGIASVEDIDTAMKYGANHPMGPLALGDLIGLDVC 238 E GFV N +L+ + EA ++ ++GIA +DID A NHPMGP L D GLDV Sbjct: 186 KKEISGFVANRLLMALFKEAMYLYEQGIADFKDIDLAATKALNHPMGPFTLMDFTGLDVN 245 Query: 239 LAIMDVLFTETGDNKYRASSILRKYVRAGWLGRKSGKGFYDY 280 +M + ETGD + ILR+ G GRKSGKGFY Y Sbjct: 246 YYVMQQQYAETGDPAMKPPEILREKFERGEFGRKSGKGFYTY 287 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: 201 Number of extensions: 9 Number of successful extensions: 3 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: 288 Length adjustment: 26 Effective length of query: 256 Effective length of database: 262 Effective search space: 67072 Effective search space used: 67072 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