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 WP_011384942.1 AMB_RS12890 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q5XIE6 (385 letters) >NCBI__GCF_000009985.1:WP_011384942.1 Length = 352 Score = 276 bits (705), Expect = 8e-79 Identities = 156/351 (44%), Positives = 213/351 (60%), Gaps = 8/351 (2%) Query: 36 EVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAFCA 95 E L+ G G I LNRPK+LNALS I L WE DPD +I+I+G G +AFCA Sbjct: 4 ETLISSGGRLGRIVLNRPKVLNALSARQYHDITACLVSWESDPDVAVILIEGEGERAFCA 63 Query: 96 GGDIKALSEAKKAGQT-LSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVHGQ 154 GGDI+ + +A + G + S D+FR EY LN I + KPYV+++DGI MGGG LSV+G+ Sbjct: 64 GGDIRMVWDAARRGDSEFSHDVFRTEYRLNRRIHAYPKPYVSVLDGICMGGGARLSVNGR 123 Query: 155 FRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGIATH 214 FRVATER+ FAMPETGIG FPDVG +FL R G LG +L LTG +L D AGIATH Sbjct: 124 FRVATERTRFAMPETGIGFFPDVGATHFLNRCPGDLGLYLGLTGKQLGPADCLWAGIATH 183 Query: 215 FVDSEKLHVLEEEL-LALKSPSAED-VAGVLESYHAKSKMGQDKSIIFEEHMDKINSCFS 272 FV + ++ L L +A +S ED V VL +H G HM+ + CF+ Sbjct: 184 FVPAARVDDLRAGLRVAAQSADPEDAVEDVLARFHQPVADGP-----LVRHMEALERCFA 238 Query: 273 ANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEGSTKTLQEVLTMEYRLT 332 ++ ++E LR DG +A + I ++ +P SL +TLRQL EG + + E+RLT Sbjct: 239 PRRLDDMIEALRLDGGQWAWDTIWELSGRAPFSLAVTLRQLREGRGMGFDDAIRREFRLT 298 Query: 333 QACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSLGSRDL 383 + G DF EG+RA ++DKD+ P W P+ L +V + + + F++LG +L Sbjct: 299 WRFLLGQDFLEGIRAQVVDKDRRPNWSPSSLAEVDELAVAACFQTLGDDEL 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: 341 Number of extensions: 12 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: 352 Length adjustment: 30 Effective length of query: 355 Effective length of database: 322 Effective search space: 114310 Effective search space used: 114310 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