Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_057507779.1 ABB28_RS05820 enoyl-CoA hydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >NCBI__GCF_001431535.1:WP_057507779.1 Length = 259 Score = 102 bits (255), Expect = 8e-27 Identities = 77/214 (35%), Positives = 104/214 (48%), Gaps = 26/214 (12%) Query: 19 LTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYD-SF 77 +T+ RP LNA+ + +R+L + AQDP V V+L GAG KAF AG DI + S Sbjct: 16 VTVQRPEKLNALNGETLRALAAAFEQAAQDPAVRVVILTGAGPKAFVAGADISEMNTLSA 75 Query: 78 KSGDTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTERSRLAM 137 G DF + L I KPV+A ++GF LGGG+ L LR+ + +RL Sbjct: 76 VEG----RDFSLLGQRLMRQIERMPKPVIARVNGFALGGGLELAMACHLRIAVDTARLGQ 131 Query: 138 PEVAIGYFPDVGGSHFLPRVPGE-LGIYLGVSGVQIRAADALYCGLADWYLESNKLGTLD 196 PE+ +G P GGS L R+ G + L + G I AA AL GL N++ + D Sbjct: 132 PEITLGLIPGFGGSQRLLRLCGRAAALELCLLGTPIDAARALQLGLV------NEVASAD 185 Query: 197 EQLDQLQWHETPLKDLQGLLAKLAVQQLPAAPLA 230 DL +A LA + AAPLA Sbjct: 186 --------------DLDARVAGLAERLANAAPLA 205 Lambda K H 0.322 0.138 0.422 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: 189 Number of extensions: 14 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 356 Length of database: 259 Length adjustment: 27 Effective length of query: 329 Effective length of database: 232 Effective search space: 76328 Effective search space used: 76328 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