Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_086511176.1 BZY95_RS17490 enoyl-CoA hydratase
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >NCBI__GCF_002151265.1:WP_086511176.1 Length = 257 Score = 96.3 bits (238), Expect = 9e-25 Identities = 69/212 (32%), Positives = 107/212 (50%), Gaps = 5/212 (2%) Query: 30 GIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAGGDIRALY 89 G+ +T+NRP+ LNAL+ ++ L+A L R D+ A+++ GAG KAF AG DI + Sbjct: 13 GVVRLTINRPKALNALNSAVLTELEALLTELEKRSDLRALLITGAGEKAFVAGADITEMR 72 Query: 90 DSFHAGTALHRQFFVDEYQLDYRLHCYPKPVVALMDGIVMGGGMGLAQAAHLRVLTERSR 149 R F + RL P PVVAL++G +GGG LA A V ++ + Sbjct: 73 TKTPEEA---RAFASQALRTIKRLETLPVPVVALVNGFCLGGGCELALACDWAVASDNAI 129 Query: 150 VAMPETGIGLVPDVGASHFL-SKLPLALALYVGLTGVTLGAADTLLCKLADIAVPAASLE 208 PE +G++P G + L ++ A+AL + TG + A + L L + +P A LE Sbjct: 130 FGQPEVLLGVIPGFGGTQRLPRRVGPAMALDLVTTGRKIDAQEALRIGLVNRVMPQAELE 189 Query: 209 HFEQTLAAINRTGDVLADLRAALQATPDAGEQ 240 + + L G+ +R+A QA D +Q Sbjct: 190 AYAEELTK-QLAGNGPLAVRSAKQAVHDGMDQ 220 Lambda K H 0.322 0.137 0.405 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: 186 Number of extensions: 11 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: 384 Length of database: 257 Length adjustment: 27 Effective length of query: 357 Effective length of database: 230 Effective search space: 82110 Effective search space used: 82110 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: 48 (23.1 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