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_043745113.1 AMB_RS18135 enoyl-CoA hydratase/isomerase family protein
Query= SwissProt::Q5XIE6 (385 letters) >NCBI__GCF_000009985.1:WP_043745113.1 Length = 344 Score = 292 bits (747), Expect = 1e-83 Identities = 163/354 (46%), Positives = 215/354 (60%), Gaps = 13/354 (3%) Query: 34 TAEVLLERRGCAGVITLNRPKLLNALSLNMIRQIYPQLKKWERDPDTFLIIIKGAGGKAF 93 +AE+ +R G G ITL+RPK LNAL+L+ + ++P+L +W D D I I+GAG KAF Sbjct: 2 SAEIHFDRTGHLGRITLDRPKALNALTLDQVHAMHPRLDQWAADADVACITIEGAGEKAF 61 Query: 94 CAGGDIKALSEAKKAGQT-LSQDLFREEYILNNAIASCQKPYVALIDGITMGGGVGLSVH 152 CAGGDIK L EA KAG + +R+EY LN I + KPYVALIDGI MGGGVG+SVH Sbjct: 62 CAGGDIKQLYEACKAGDLEFAAAFYRDEYRLNRRIHTSPKPYVALIDGIVMGGGVGVSVH 121 Query: 153 GQFRVATERSLFAMPETGIGLFPDVGGGYFLPRLQGKLGYFLALTGFRLKGRDVHRAGIA 212 G +RVATER+LFAMPETGIG FPDVGG YFLPRL G +G +L LTG RLK D G+A Sbjct: 122 GLYRVATERTLFAMPETGIGFFPDVGGSYFLPRLPGSIGMYLGLTGARLKAADTLHVGVA 181 Query: 213 THFVDSEKLHVLEEELLALKSPSAEDVAGVLESYHAKSKMGQDKSIIFEEHMDKINSCFS 272 THFV+S +L L E L A D A V S + +I + + I+ CF Sbjct: 182 THFVESAQLPALIEAL-----SEARDAAEVKASLDGFASDPGPAAI--DARRELIDRCFG 234 Query: 273 ANTVEQILENLRQDGSPFAMEQIKVINKMSPTSLKITLRQLMEGSTKTLQEVLTMEYRLT 332 ++ ++ L + PFA E + I SP + ++ + G+T + + + ME+RL Sbjct: 235 KASLAEVFAALEGESDPFAAETLATIRAKSPHLVAVSFEMIRRGATLSFDDCMKMEFRLA 294 Query: 333 QACMEGHDFHEGVRAVLIDKDQTPKWKPADLKDVTDEDLNSYFKSL-GSRDLKF 385 A HDF EGVRA+LID+D P W PA T+ + ++F ++ G DL F Sbjct: 295 MALAPAHDFVEGVRALLIDRDNKPAWNPAG----TEGQVLAHFDAVPGCGDLTF 344 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: 324 Number of extensions: 18 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: 344 Length adjustment: 29 Effective length of query: 356 Effective length of database: 315 Effective search space: 112140 Effective search space used: 112140 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