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 SM_b20752 SM_b20752 3-hydroxyisobutyryl-CoA hydrolase
Query= SwissProt::Q5XIE6 (385 letters) >FitnessBrowser__Smeli:SM_b20752 Length = 356 Score = 256 bits (654), Expect = 7e-73 Identities = 145/355 (40%), Positives = 211/355 (59%), Gaps = 8/355 (2%) Query: 28 MSKHTETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKG 87 M T EV++ER+G G + LNRP+ LN+L+ MIR I L ++ER+P+ +++ G Sbjct: 1 MEMQTTLPEVIVERQGAIGRLRLNRPRALNSLNRTMIRAIAAALTEFERNPEIAAVLVTG 60 Query: 88 AGGKAFCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGV 147 G + CAGGDI+ + E+ + +REE+I+N+ I++ KPY+A++DGI MGGGV Sbjct: 61 EGERGLCAGGDIRMIYESGRERPGEGAQFWREEFIVNSRISAYSKPYIAIMDGIVMGGGV 120 Query: 148 GLSVHGQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVH 207 G+S HG RV TER+ FAMPETGIG F DVG + LPR G+ G +L LTG + V Sbjct: 121 GVSSHGSHRVVTERTRFAMPETGIGYFTDVGATWLLPRAPGEFGTYLGLTGRDIGAAAVI 180 Query: 208 RAGIATHFVDSEKLHVLEEELLALK-SPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDK 266 A +A FV SE + L L +L S +A+DV+ + ++ + + +H+ Sbjct: 181 HARLADSFVPSEMIGELLGALSSLSGSATADDVSAAI-----RAVSSEPPASALLDHLSV 235 Query: 267 INSCFSANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEG-STKTLQEVL 325 I+ CF+ N VE+I L +D S FA E ++++ S SLK+TL L EG S+ TL E L Sbjct: 236 IDRCFAFNAVEEIFAALEKDESDFARETLELLKTRSAISLKLTLSLLREGRSSATLNECL 295 Query: 326 TMEYRLTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSLGS 380 EY T + DF+EGVRA +IDKD+ PKW L + T E L + ++ G+ Sbjct: 296 EREYAATLGMLSNPDFYEGVRAAVIDKDRNPKWS-VGLSEATPELLARFGRNDGA 349 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: 299 Number of extensions: 9 Number of successful extensions: 3 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: 356 Length adjustment: 30 Effective length of query: 355 Effective length of database: 326 Effective search space: 115730 Effective search space used: 115730 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: 49 (23.5 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