Align 3-hydroxyisobutyryl-CoA hydrolase, mitochondrial; 3-hydroxyisobutyryl-coenzyme A hydrolase; HIB-CoA hydrolase; HIBYL-CoA-H; EC 3.1.2.4 (characterized)
to candidate Dsui_0981 Dsui_0981 enoyl-CoA hydratase/carnithine racemase
Query= SwissProt::Q5XIE6 (385 letters) >FitnessBrowser__PS:Dsui_0981 Length = 263 Score = 87.8 bits (216), Expect = 3e-22 Identities = 61/188 (32%), Positives = 94/188 (50%), Gaps = 5/188 (2%) Query: 35 AEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAFC 94 + +L+E G G++TLN+P NA ++ +I LK+ E DP ++++ A GK+FC Sbjct: 4 SSILIEVDGPVGILTLNKPDRHNAFDETLMAEITAGLKQLEADPAVRVVVLS-ATGKSFC 62 Query: 95 AGGDIKALSEAKKAGQTLSQDLFREEYI--LNNAIASCQKPYVALIDGITMGGGVGLSVH 152 AG D+ + A AG T Q+L + L + + KP VA + G GGGVGL Sbjct: 63 AGADLNWMKRA--AGYTPEQNLADAGNLAELLRTLNTLAKPTVARVQGPAYGGGVGLVAA 120 Query: 153 GQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGIA 212 VA+ ++FA+ E +GL P V Y + L + LT R + +R G+ Sbjct: 121 CDVAVASYDAMFALTEVKLGLIPAVISPYVIAALGERQCRRYFLTAERFSAAEGYRLGLL 180 Query: 213 THFVDSEK 220 V SE+ Sbjct: 181 HEIVPSEE 188 Lambda K H 0.320 0.136 0.394 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: 173 Number of extensions: 3 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: 385 Length of database: 263 Length adjustment: 27 Effective length of query: 358 Effective length of database: 236 Effective search space: 84488 Effective search space used: 84488 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 (21.8 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