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_011383077.1 AMB_RS03265 enoyl-CoA hydratase
Query= SwissProt::Q5XIE6 (385 letters) >NCBI__GCF_000009985.1:WP_011383077.1 Length = 258 Score = 96.7 bits (239), Expect = 7e-25 Identities = 74/242 (30%), Positives = 116/242 (47%), Gaps = 17/242 (7%) Query: 37 VLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAFCAG 96 + +E RG GVI LNRPK +NAL +I ++ L +E D +++ G+ KAF AG Sbjct: 6 ITVETRGNVGVIALNRPKAMNALCAALISELGQALDAFEADDSIGAVVLTGSE-KAFAAG 64 Query: 97 GDIKALSEAKKAGQTLSQDLFREEYILNN--AIASCQKPYVALIDGITMGGGVGLSVHGQ 154 DIK ++ D++ +I + + C+KP VA + G +GGG +++ Sbjct: 65 ADIKEMASKSY------MDVYLANFITDGWERVTKCRKPIVAAVAGFALGGGCEMAMMCD 118 Query: 155 FRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGK-LGYFLALTGFRLKGRDVHRAGIAT 213 F +A + + F PE IG P GG L R GK + LTG + + RAG+ + Sbjct: 119 FIIAGDNAKFGQPEITIGTIPGAGGTQRLTRAVGKSKAMEMCLTGRMMDAAEAERAGLVS 178 Query: 214 HFVDSEKLHVLEEELLA---LKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSC 270 V +L L+E + A + S S V ES +A + + + FE + +S Sbjct: 179 RIVPVAEL--LDEAVKAAGKIASLSRPIVMLCKESVNAAFETTLAQGVTFERRL--FHST 234 Query: 271 FS 272 FS Sbjct: 235 FS 236 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: 152 Number of extensions: 5 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: 258 Length adjustment: 27 Effective length of query: 358 Effective length of database: 231 Effective search space: 82698 Effective search space used: 82698 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