Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_041100391.1 SUTH_RS15075 enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_000828635.1:WP_041100391.1 Length = 258 Score = 149 bits (375), Expect = 7e-41 Identities = 91/251 (36%), Positives = 134/251 (53%), Gaps = 2/251 (0%) Query: 6 VDARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGAD 65 V+ RG + + T++ NA++ ++ E+G + +V +VITG+ +KAF AGAD Sbjct: 8 VETRGKVGLITLNRPKALNALNDTLIDEIGAAFDGFEADENVGCIVITGS-EKAFAAGAD 66 Query: 66 LKERATMAEDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPA 125 + A +V + + R + I + IAA+ G ALGGG ELA+ CD+ AA Sbjct: 67 IGAMAGWNFMDVYK-ANYISRNWDRIPRCRKPVIAAVAGFALGGGCELAMMCDMIYAADT 125 Query: 126 AELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGH 185 A+ G E+KLGI+PG GGTQRL R VG +A D+ LTAR I+A EA GL R+ P Sbjct: 126 AKFGQPEIKLGILPGAGGTQRLPRAVGKAKAMDMCLTARFIDAQEAERAGLVARIIPADK 185 Query: 186 LLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLEGLR 245 LL AE++ + V K +++ L + L E R + D+ EG+ Sbjct: 186 LLEETLAAAETIAGFSLPVVMMIKESVNRAYESSLQEGLLFERRTFHSAFALADQKEGMA 245 Query: 246 AFAEKRAPVYK 256 AF EKR P ++ Sbjct: 246 AFVEKRKPAFR 256 Lambda K H 0.319 0.136 0.380 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: 147 Number of extensions: 8 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: 258 Length of database: 258 Length adjustment: 24 Effective length of query: 234 Effective length of database: 234 Effective search space: 54756 Effective search space used: 54756 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 (21.7 bits) S2: 47 (22.7 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