Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_110206127.1 DNK54_RS06420 enoyl-CoA hydratase/isomerase family protein
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_003194585.1:WP_110206127.1 Length = 262 Score = 180 bits (457), Expect = 2e-50 Identities = 88/261 (33%), Positives = 155/261 (59%), Gaps = 2/261 (0%) Query: 1 MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60 M + ++ +++G++ + +NRP+K N+L A + LD +++ E+D IRV++I G+ + Sbjct: 2 MAEDDLQAERDGHVMRVWINRPEKRNSLTAGIFSALDSLIAEVENDQRIRVMVIRGREQM 61 Query: 61 FCAGADITQF--NQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALAC 118 C+G D+ + L+ + W + + ++ A+ KPTI ++ G+A GG EL L+C Sbjct: 62 LCSGFDLDELAGTVLSGSYGWDGAAIAAPVFARLHAMKKPTICVVEGFATAGGFELMLSC 121 Query: 119 DIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLV 178 D +A E A++G I ++ G G RL R++G RA E+++TG + G AE++GLV Sbjct: 122 DFAVADENARIGDLHIRRALHGGAGPIYRLPRIVGLRRAKEIVLTGKMVTGSQAERWGLV 181 Query: 179 NRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFST 238 N P L+ +++A KSP+ + L K +N+G ++ + +ALE V + V + Sbjct: 182 NEAHPADQLDVAVEGWVDQLADKSPLQMQLSKLTLNQGFEASAEALMALERVAFAVTMQS 241 Query: 239 EDKKEGVSAFLEKREPTFKGK 259 +D KEGV+AFLEKR+P + G+ Sbjct: 242 QDAKEGVAAFLEKRDPQWSGR 262 Lambda K H 0.315 0.135 0.382 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: 143 Number of extensions: 6 Number of successful extensions: 2 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: 259 Length of database: 262 Length adjustment: 25 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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: 42 (22.0 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