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 GFF2597 HP15_2541 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q5XIE6 (385 letters) >FitnessBrowser__Marino:GFF2597 Length = 273 Score = 95.9 bits (237), Expect = 1e-24 Identities = 65/196 (33%), Positives = 98/196 (50%), Gaps = 12/196 (6%) Query: 31 HTETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGG 90 H ET +LLE++G IT+NRP + NA+SL M+ ++ + E D ++I+GAGG Sbjct: 6 HCET--LLLEKQGPTLFITINRPDVRNAMSLEMVAELSAVFTQIENDLHIRAVVIRGAGG 63 Query: 91 KAFCAGGDIKALSEAKKAGQTLSQDLFREEYILNNA-------IASCQKPYVALIDGITM 143 FCAGGDIK ++ A+ GQ ++ Y LN A + K +A+ +G M Sbjct: 64 H-FCAGGDIKDMAGAR--GQKAAEGEADPFYRLNRAFGQMIQQVNESSKVVIAITEGAVM 120 Query: 144 GGGVGLSVHGQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKG 203 GGG GL+ +A + F MPET +G+ P + + R+ LAL G R+ Sbjct: 121 GGGFGLACVSDVAIAGPSAKFGMPETSLGVIPAQIAPFVVERIGLTQARRLALLGLRIDA 180 Query: 204 RDVHRAGIATHFVDSE 219 + GI S+ Sbjct: 181 NEACSLGIVHQAASSD 196 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: 186 Number of extensions: 6 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: 273 Length adjustment: 28 Effective length of query: 357 Effective length of database: 245 Effective search space: 87465 Effective search space used: 87465 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