Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AO353_25675 AO353_25675 enoyl-CoA hydratase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2986 (356 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25675 Length = 257 Score = 96.7 bits (239), Expect = 6e-25 Identities = 61/196 (31%), Positives = 104/196 (53%), Gaps = 15/196 (7%) Query: 8 VLAEVRNHIGHLTLNRPAGLNALTLDMVRNLHRQLDAWAQDSQVHAVVLRGAGEKAFCAG 67 +L EV+ +G +TLNRP LNAL +V L+ LD + ++ +VL G+ +KAF AG Sbjct: 6 ILLEVQGRVGLITLNRPQALNALNAQIVSELNHALDGLEANPEIGCIVLTGS-KKAFVAG 64 Query: 68 GDIRSLHDSFKSGDTLHEDFFVEEYALDL-AIHHYRKPVLALMDGFVLGGGMGLVQGADL 126 DI+ + + + ++++ D + + RKPV+A + GF LGGG L D Sbjct: 65 ADIKEM------AELTYPQIYLDDLFSDSDRVANRRKPVIAAVAGFALGGGCELALMCDF 118 Query: 127 RVVTEKSRLAMPEVGIGYFPDVGGSYFLSRIPGEL-GIYLGVSGVQIRAADALYCGLADW 185 + + ++ PE+ +G P +GG+ L+R G+ + + +SG I A +A CG+ Sbjct: 119 ILAGDNAKFGQPEINLGVLPGMGGTQRLTRAVGKAKAMEMCLSGRLIDAVEAERCGIV-- 176 Query: 186 YLESGKLGVLDEKLDQ 201 ++ +DE LD+ Sbjct: 177 ----ARIVPVDELLDE 188 Lambda K H 0.322 0.139 0.419 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: 187 Number of extensions: 13 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: 257 Length adjustment: 27 Effective length of query: 329 Effective length of database: 230 Effective search space: 75670 Effective search space used: 75670 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 17 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