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_011423940.1 RHE_RS02885 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q5XIE6 (385 letters) >NCBI__GCF_000092045.1:WP_011423940.1 Length = 350 Score = 254 bits (648), Expect = 3e-72 Identities = 147/346 (42%), Positives = 208/346 (60%), Gaps = 7/346 (2%) Query: 33 ETAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKA 92 + +EV++ERRG AG+I LNRP+ LN+L+L MIR I L + RD + ++ G G + Sbjct: 2 QDSEVIIERRGTAGIIRLNRPRALNSLTLAMIRTITEALDGFARDAEVATVVATGEGERG 61 Query: 93 FCAGGDIKALSEAKKAGQTLSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVH 152 FCAGGDI+AL E+ +AG L+ +REE+ LN+ IA KPYVAL+DGITMGGGVGLS H Sbjct: 62 FCAGGDIRALHESARAGDGLAGTFWREEFRLNHMIAVYPKPYVALMDGITMGGGVGLSSH 121 Query: 153 GQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGIA 212 G+ R+ TER+ AMPETGIG PDVG + LP+ G+ G +L LTG + D A +A Sbjct: 122 GRHRIVTERTRLAMPETGIGYVPDVGATWLLPKAPGEAGTWLGLTGLDIAAADAIYAHLA 181 Query: 213 THFVDSEKLHVLEEELLAL-KSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCF 271 + S +L + E L L + S+ DV GVL+ Y G+ + + I+ F Sbjct: 182 DLQIASSRLAEVIETLSGLPRGSSSGDVDGVLQVY--AEPPGESR---LRHNSTMIDRAF 236 Query: 272 SANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEG-STKTLQEVLTMEYR 330 ++VE+IL L + FA E +V+ SPTSLK+ L+ L G + +L E L E Sbjct: 237 RFDSVEEILAALAGEDGEFAAETRRVLLTRSPTSLKLALQLLRAGRRSGSLAECLGRELG 296 Query: 331 LTQACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFK 376 ++ DF EG+RA +IDKD+ PKW PA ++ V + + ++ K Sbjct: 297 ACLQMLDNPDFFEGIRAAVIDKDRNPKWSPASVEAVKAQTVENFLK 342 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: 291 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: 350 Length adjustment: 30 Effective length of query: 355 Effective length of database: 320 Effective search space: 113600 Effective search space used: 113600 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 Apr 09 2024. 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