Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_041097743.1 SUTH_RS05635 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >NCBI__GCF_000828635.1:WP_041097743.1 Length = 697 Score = 72.8 bits (177), Expect = 3e-17 Identities = 61/203 (30%), Positives = 99/203 (48%), Gaps = 17/203 (8%) Query: 19 LTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYDSFK 78 +TL+ P +N + D+ + +D DP V AVVL G+ ++AF G DIR + S K Sbjct: 15 ITLDNPP-VNGLGYDLRCGIVAGIDQATADPAVKAVVLIGS-DRAFSGGADIRE-FGSPK 71 Query: 79 SGDTLHEDFFVEEYALDLA--IHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTERSRLA 136 S + E L + + KPV+A + G +GGG+ L G RV + +A Sbjct: 72 S--------YAEPNLLTVIRIVEACPKPVVAAIGGVCMGGGLELTLGCHFRVAIAGASIA 123 Query: 137 MPEVAIGYFPDVGGSHFLPRVPG-ELGIYLGVSGVQIRAADALYCGLADWYLESNKLGTL 195 +PE+ +G P GG+ +PR+ G E + L +SG + + L D ++E N L Sbjct: 124 LPEIKLGLLPGAGGTQRMPRIVGVEAALNLILSGNPVPSEKFKGTPLFDEFIEGNGGDLL 183 Query: 196 DEQL---DQLQWHETPLKDLQGL 215 L D++ + PLK ++ + Sbjct: 184 KGALAFADKVVAEKRPLKRIRDI 206 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: 571 Number of extensions: 35 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: 697 Length adjustment: 34 Effective length of query: 322 Effective length of database: 663 Effective search space: 213486 Effective search space used: 213486 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: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. 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