Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_082699858.1 V474_RS17855 3-hydroxybutyryl-CoA dehydrogenase
Query= BRENDA::C4IEM5 (282 letters) >NCBI__GCF_001046635.1:WP_082699858.1 Length = 289 Score = 295 bits (755), Expect = 8e-85 Identities = 149/281 (53%), Positives = 191/281 (67%) Query: 1 MKKVFVLGAGTMGAGIVQAFAAKGCEVIVRDIKEEFVDRGIATITKSLSKLVAKEKITEA 60 M+ V ++GAG MGAGI Q A+KG +V++ D+ E ++G A I KSL+KLV KEKIT+A Sbjct: 1 MQTVGIIGAGIMGAGIAQTVASKGMDVVLTDVSLENAEKGKAGIAKSLAKLVTKEKITQA 60 Query: 61 DKEEILSRISGTTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPETILASNTSSLS 120 D + +L+RI+ D + DL++EAA E IK +IF + +I+ASNTSS+ Sbjct: 61 DADALLARITPAADYSAMSGADLIIEAATEREDIKHKIFEAAGKVLGANSIMASNTSSIP 120 Query: 121 ITEVASATKRADKVIGMHFFNPAPVMKLVEVIRGAATSQETFDAVKEMSESIGKTPVEVA 180 IT +A+++ A + G+HFFNP PVM LVEVI G ATSQ+T D +K E +GKT V Sbjct: 121 ITRMAASSPDAARFCGLHFFNPVPVMGLVEVIPGLATSQDTIDRMKAFGEKLGKTVVLAG 180 Query: 181 EAPGFVVNRILIPMINEATFILQEGVAKEEDIDAAMKLGANHPMGPLALGDLIGLDVCLA 240 + PGFVVNRIL PM+NEA F+L G+ EDIDA K+G NHPMGPL L D +GLD Sbjct: 181 DEPGFVVNRILCPMLNEAIFVLGAGIGSVEDIDAGCKIGLNHPMGPLTLADFVGLDTLYE 240 Query: 241 IMDVLYNETGDTKYRASSLLRKYVRAGWLGRKTGKGFYDYS 281 IM V TGD KYR + LL+KYV AGW GRK+GKGFYDYS Sbjct: 241 IMKVFQATTGDPKYRPAPLLQKYVEAGWYGRKSGKGFYDYS 281 Lambda K H 0.317 0.134 0.369 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: 270 Number of extensions: 8 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: 289 Length adjustment: 26 Effective length of query: 256 Effective length of database: 263 Effective search space: 67328 Effective search space used: 67328 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