Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate WP_020723626.1 C1M55_RS01960 enoyl-CoA hydratase
Query= BRENDA::Q9LKJ1 (378 letters) >NCBI__GCF_002893965.1:WP_020723626.1 Length = 263 Score = 88.2 bits (217), Expect = 2e-22 Identities = 63/202 (31%), Positives = 100/202 (49%), Gaps = 7/202 (3%) Query: 11 VLVEEKSSVRILTLNRPKQLNALSFHMISRLLQLFLAFEEDPSVKLVILKGHGRAFCAGG 70 V V+ S+ +T+++P NA + MI+ LL++ D +V+++++ G GR F AG Sbjct: 12 VTVDVTDSIATVTIDKPPA-NAFNPSMIAELLEILPVLASDQTVRVIVVTGTGRFFVAGA 70 Query: 71 DVAAVVRDINQGNWRLGANYFSSEYMLNYVMATYSKAQVSILNGIVMGGGAGVSVHGRFR 130 D+ V+R++ + R + + +L + K V+ +NG +GGGA +++ FR Sbjct: 71 DIT-VMRELTEETQRAMRPWVDVQRILE----SAPKPVVAKINGHALGGGAELTLACDFR 125 Query: 131 IATENTVFAMPETALGLFPDVGASYFLSRLPGFF-GEYVGLTGARLDGAEMLACGLATHF 189 I ++ PE LGLFP G S L RL G + + + G RL L GL Sbjct: 126 IMAQSATIGFPEIGLGLFPGAGGSQRLPRLIGAHRAKVLMIEGKRLSAEHALDIGLVDTV 185 Query: 190 VPSTRLTALEADLCRINSNDPT 211 V L A ADL R + PT Sbjct: 186 VADADLDAHCADLARELATKPT 207 Lambda K H 0.321 0.136 0.396 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: 178 Number of extensions: 8 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: 378 Length of database: 263 Length adjustment: 27 Effective length of query: 351 Effective length of database: 236 Effective search space: 82836 Effective search space used: 82836 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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