Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_157035422.1 PING_RS03450 2,3-dehydroadipyl-CoA hydratase
Query= BRENDA::A4YI89 (259 letters) >NCBI__GCF_000015285.1:WP_157035422.1 Length = 244 Score = 167 bits (424), Expect = 1e-46 Identities = 94/237 (39%), Positives = 142/237 (59%), Gaps = 4/237 (1%) Query: 23 DKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPAEAWKFS 82 +K NAL+ L EL + +AE I +++TG + F AGAD+ + + W Sbjct: 10 EKRNALSNDCLNELAGVLDKAEQQNHIAAVVLTGGQRCFAAGADLNELATQGAIDTWLNP 69 Query: 83 KKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEINLGIYPGY 142 + E+ ++ SKP +A +NGYALG GLEL L CDI I+ ++A GLPEI LG+ PG Sbjct: 70 RP--ELWARLNKFSKPLLAAVNGYALGAGLELVLLCDIAISGQKALFGLPEITLGLIPGA 127 Query: 143 GGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVV-PLANLEQETRKLAEKIAKK 201 GGTQRL R +GK +M++TG I + A + GL++ VV P LE+ T +AE IAK+ Sbjct: 128 GGTQRLARTVGKSLTNQMVLTGLPITAERALQAGLISEVVIPELTLER-TIIIAETIAKR 186 Query: 202 SPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKREPTFKG 258 +P+++ K+ + + +S L GL E + + ++ D+KEG+ AF KR+PT+KG Sbjct: 187 APLAIKAAKQSLQQVPNSSLDQGLKFERQLFVTLAASNDRKEGIDAFFNKRQPTYKG 243 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: 147 Number of extensions: 5 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: 244 Length adjustment: 24 Effective length of query: 235 Effective length of database: 220 Effective search space: 51700 Effective search space used: 51700 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: 46 (22.3 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