Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_011764415.1 AZO_RS03415 enoyl-CoA hydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >NCBI__GCF_000061505.1:WP_011764415.1 Length = 260 Score = 70.1 bits (170), Expect = 6e-17 Identities = 56/182 (30%), Positives = 89/182 (48%), Gaps = 11/182 (6%) Query: 7 EVLAEVRNHIGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCA 66 ++L + + + ++L+ P LNA+ M R L+ DP V +VLRGAG++AF A Sbjct: 4 QILVDRGDAVATVSLSNPGKLNAVNAGMWRQLRAAFAELGADPGVRCIVLRGAGDEAFAA 63 Query: 67 GGDIRSLYDSFKS-----GDTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLV 121 GGDI + F++ D LH + AL+ AI P +A + G +GGG+ + Sbjct: 64 GGDI----EEFRTVRATVDDALHYHEELVAAALN-AIRDCPVPTVAAIRGACVGGGLEIA 118 Query: 122 QGADLRVVTERSRLAMPEVAIGYFPDVGG-SHFLPRVPGELGIYLGVSGVQIRAADALYC 180 DLR+ SR P +G+ G + L V + + + + G + AA+AL Sbjct: 119 GCCDLRIAGASSRFGAPINKLGFSMYPGEMAGLLALVGPAVVLEILLEGRILDAAEALQK 178 Query: 181 GL 182 GL Sbjct: 179 GL 180 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: 210 Number of extensions: 8 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: 356 Length of database: 260 Length adjustment: 27 Effective length of query: 329 Effective length of database: 233 Effective search space: 76657 Effective search space used: 76657 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