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 Ga0059261_3683 Ga0059261_3683 Enoyl-CoA hydratase/carnithine racemase
Query= SwissProt::Q5XIE6 (385 letters) >FitnessBrowser__Korea:Ga0059261_3683 Length = 345 Score = 258 bits (659), Expect = 2e-73 Identities = 140/347 (40%), Positives = 214/347 (61%), Gaps = 10/347 (2%) Query: 35 AEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAFC 94 ++VL+ G G I LNRPK ++AL+ M I L W D +++I A G+ FC Sbjct: 2 SDVLISVEGQVGRIRLNRPKAIHALNTGMCAAILDALISWRDDTAVEVVMIDHAEGRGFC 61 Query: 95 AGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVHGQ 154 AGGDI+ ++E+ + ++D FR EY +N+A+ + KP VA +DGITMGGGVG+S + Sbjct: 62 AGGDIRMIAESGAGDGSAARDFFRVEYRMNHALFTYAKPVVAFMDGITMGGGVGISQPAK 121 Query: 155 FRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGIATH 214 +RVATE + AMPETGIGLFPDVGGG++L RL G+ G +LALTG RL G + G+A+H Sbjct: 122 YRVATENTKLAMPETGIGLFPDVGGGWYLSRLAGRTGQYLALTGHRLDGAECLALGLASH 181 Query: 215 FVDSEKLHVLEEELLALKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCFSAN 274 ++ SE L + ++A P A D VL+ A S D I+ H I+ F+++ Sbjct: 182 YLHSEALEDAKARIIA--DPQAID--AVLD---ALSSPAPDARIL--AHRGAIDRLFASD 232 Query: 275 TVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEGST-KTLQEVLTMEYRLTQ 333 +E +L L DG +A +Q+ + SP ++K++L+ L++G T T ++ + E+ + Sbjct: 233 RLEDVLAALEADGGEWAAQQLATLRTKSPQTMKVSLKLLLDGKTMPTFEDEMRQEFAVGS 292 Query: 334 ACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSLGS 380 ++ HDF EGVRA++IDKD PKW PA++++V+D ++ F L + Sbjct: 293 HVVQRHDFIEGVRALIIDKDNAPKWNPANVEEVSDHLIDQIFAPLSA 339 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: 327 Number of extensions: 15 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: 345 Length adjustment: 29 Effective length of query: 356 Effective length of database: 316 Effective search space: 112496 Effective search space used: 112496 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