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 Dsui_1378 Dsui_1378 enoyl-CoA hydratase/carnithine racemase
Query= SwissProt::Q5XIE6 (385 letters) >FitnessBrowser__PS:Dsui_1378 Length = 258 Score = 110 bits (275), Expect = 4e-29 Identities = 84/263 (31%), Positives = 132/263 (50%), Gaps = 30/263 (11%) Query: 37 VLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAFCAG 96 ++ E +G G+ITLNRPK LNAL ++ ++ L ++E D + I+I G+ KAF AG Sbjct: 6 IIAEAKGRVGLITLNRPKALNALCDPLVDELGDALTEFEADENIGCIVITGSD-KAFAAG 64 Query: 97 GDIKALSEAKKAGQTLSQDLFREEYILNN--AIASCQKPYVALIDGITMGGGVGLSVHGQ 154 DI + + D ++ +YI N + +C+KP +A + G +GGG L++ Sbjct: 65 ADISMMKDFSY------MDAYKGDYITRNWEKVKTCRKPVIAAVAGYALGGGCELAMSCD 118 Query: 155 FRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKL-GYFLALTGFRLKGRDVHRAGIAT 213 F +A + + F PE +G+ P GG LPR GK L L+ + + RAG+ + Sbjct: 119 FIIAADSAQFGQPEVKLGILPGAGGTQRLPRAVGKAKAMDLCLSARMMDATEAERAGLVS 178 Query: 214 HFVDSEKLHVLEEELLALKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCFSA 273 V ++KL LEE L A AE +A SY M + +E+ +N F + Sbjct: 179 RIVPADKL--LEEALGA-----AEKIA----SYSLPVVM------MIKEN---VNRAFES 218 Query: 274 NTVEQILENLRQDGSPFAMEQIK 296 + E +L RQ + FA+E K Sbjct: 219 SLNEGLLFERRQFHAAFALEDQK 241 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: 186 Number of extensions: 6 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