Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_041098452.1 SUTH_RS08215 enoyl-CoA hydratase-related protein
Query= BRENDA::Q1D5Y4 (258 letters) >NCBI__GCF_000828635.1:WP_041098452.1 Length = 261 Score = 137 bits (345), Expect = 2e-37 Identities = 85/236 (36%), Positives = 129/236 (54%), Gaps = 5/236 (2%) Query: 24 NAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAEDEVRAFLDG 83 N + M++E+ + ++ DV+ ++ITGAG+KAF AG ++ + D+V ++ Sbjct: 30 NVLDIPMMEEINVALDACLAANDVKLLLITGAGEKAFSAGVEVADHTP---DKVDRMIEV 86 Query: 84 LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKLGIIPGGGG 143 FR + + +AA+NGAALGGG ELA+ACD+ VAA A+ G E+KL + P Sbjct: 87 FHGIFRRLNRMPMPTLAAVNGAALGGGMELAIACDMLVAAAGAKFGQPEIKLAVFPPIAA 146 Query: 144 TQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAESVVENAPI 203 L RLV P RA +L+L I+A EA +GL NR+ + A + + + Sbjct: 147 V-LLPRLVPPARAMELLLGGNNIDADEALRIGLVNRVFAKESFAADLKAFVDPYLALSRA 205 Query: 204 AVATAKHAIDEGTGLELDDAL-ALELRKYEEILKTEDRLEGLRAFAEKRAPVYKGR 258 A+ + + AI + D AL A E +E++ TED EGL AF EKR PV++ R Sbjct: 206 ALLSTRKAIRAASDKPFDAALDAAEEIYLKELMATEDAKEGLAAFLEKRKPVWRDR 261 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: 145 Number of extensions: 8 Number of successful extensions: 4 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: 261 Length adjustment: 24 Effective length of query: 234 Effective length of database: 237 Effective search space: 55458 Effective search space used: 55458 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