Align Enoyl-CoA hydratase [valine degradation] (EC 4.2.1.17) (characterized)
to candidate WP_090274896.1 BLU11_RS15435 enoyl-CoA hydratase/isomerase family protein
Query= reanno::psRCH2:GFF2389 (257 letters) >NCBI__GCF_900105005.1:WP_090274896.1 Length = 270 Score = 167 bits (422), Expect = 3e-46 Identities = 105/247 (42%), Positives = 141/247 (57%), Gaps = 6/247 (2%) Query: 14 VALITLNRPQALNALNGQLISELNQALGQLEADPQIGCIVLTGS-AKAFAAGADIKEMAE 72 V + L RP +NA+N + + AL +LE DP+I IV+ G A+ F AGADIKE Sbjct: 23 VGWVVLTRPGQINAINDAIREGVPAALERLENDPRIHVIVIRGEGARGFCAGADIKEKRG 82 Query: 73 LTYPQIYLDDFFADA---DRIATRRKPLIAAVAGYALGGGCELALLCDMIFAADNARFGQ 129 + I + A + I KP+I A+ GY +GGG ELAL CD+ FA+ NA Sbjct: 83 VE-TSIQVRKRMEGARWIEAIDAVSKPVIVAIQGYCMGGGLELALACDIRFASPNAVLAL 141 Query: 130 PEVNLGVLPGIGGTQRLTRAVGKAKAMDMCLTGRQMDAAEAERAGLVARVF-PAESLLEE 188 PE LG++PG GGTQRL R V A+D+ LTG ++DA A + GLV+RV AE+LLEE Sbjct: 142 PETGLGLIPGGGGTQRLCRVVAPGYALDLLLTGERLDAERARQIGLVSRVAKTAETLLEE 201 Query: 189 TLKAARVIAEKSLPATMMIKESVNRAFETTLAEGIRFERRVFHAVFATADQKEGMAAFSE 248 A IA KS A++ K + A E L +G+ E +F + T D KE AF+E Sbjct: 202 VSALALQIAGKSPMASVYAKRAARAASEVDLKKGLDLELDLFSLLATTKDAKEAALAFAE 261 Query: 249 KRKPEFT 255 +R P+FT Sbjct: 262 RRAPQFT 268 Lambda K H 0.321 0.135 0.375 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: 155 Number of extensions: 11 Number of successful extensions: 4 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: 257 Length of database: 270 Length adjustment: 25 Effective length of query: 232 Effective length of database: 245 Effective search space: 56840 Effective search space used: 56840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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