Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_073037062.1 BUB04_RS03725 enoyl-CoA hydratase-related protein
Query= reanno::Cup4G11:RR42_RS28545 (384 letters) >NCBI__GCF_900129305.1:WP_073037062.1 Length = 263 Score = 90.5 bits (223), Expect = 5e-23 Identities = 80/273 (29%), Positives = 121/273 (44%), Gaps = 24/273 (8%) Query: 23 VRFDEINGIGLITLNRPRQLNALSYPMIGLLDAQLAAWAARDDIAAVVLRGAGPKAFCAG 82 + F+ +G+ LIT NRP+ LNAL+ + L +AA D + VVL GAG KAF AG Sbjct: 6 ILFEVRDGVALITFNRPKALNALNPQTLEELARAVAAARDDDAVRVVVLTGAGDKAFVAG 65 Query: 83 GDIRALYDSFHAGTALHRQFFVDEYQ-LDYRLHCYPKPVVALMDGIVMGGGMGLAQAAHL 141 DI L L + F + Q + + L PKPV+A ++G +GGG LA + Sbjct: 66 ADITELQKM----NPLEARLFAQKGQDVFFSLEDLPKPVIACVNGFALGGGCELAMSCDF 121 Query: 142 RVLTERSRVAMPETGIGLVPDVGASHFLSKL-PLALALYVGLTGVTLGAADTLLCKLADI 200 +++++ PE +G++P G + L++L A A + +TG + A L Sbjct: 122 IYASDKAKFGQPEINLGIIPGFGGTQRLARLVGRAKAKELCMTGEMIDAQQAKELGLVAK 181 Query: 201 AVPAASLEHFEQTLAAINRTGDVLADLRAALQATPDAGEQAAPLQSVLPAVLRHFRADAS 260 P +L E+TL A AT A + L+++ V R AD Sbjct: 182 VFPHEAL--LEETLKA----------------ATAMAAKSCTALRAIKHVVDRGMDADLK 223 Query: 261 VAGLLDSLAAESDPAYADWAARTLDILRGRSPL 293 L++ A A D T L R P+ Sbjct: 224 TGCALEAEAFGVCFAGQDAKEGTTAFLEKRKPV 256 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: 165 Number of extensions: 7 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: 263 Length adjustment: 27 Effective length of query: 357 Effective length of database: 236 Effective search space: 84252 Effective search space used: 84252 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 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