Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_092487896.1 BM299_RS18360 enoyl-CoA hydratase-related protein
Query= BRENDA::F4JML5 (301 letters) >NCBI__GCF_900115975.1:WP_092487896.1 Length = 260 Score = 189 bits (479), Expect = 8e-53 Identities = 102/255 (40%), Positives = 152/255 (59%) Query: 46 NRLSGSDSGIIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCA 105 N L ++GI + ++RP NA+N E L+ L A + + D+ RV+++ F A Sbjct: 5 NLLLEKEAGIAVLTINRPKVLNALNAETLQELDAAMDQLGNDDEVRVIILTGAGEKAFVA 64 Query: 106 GADLKERRTMSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRIC 165 GAD+ +T+ P E + + +FS IE L P IAAI G ALGGG E+++ACD+RI Sbjct: 65 GADIAFMQTLKPLEAKNFARLGQKVFSKIENLPKPVIAAINGFALGGGCELSMACDIRIA 124 Query: 166 GENAVFGLPETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVT 225 ENA G PE L +I G GGTQRL+RLV ++KE++FT DA A GLVN V Sbjct: 125 SENAKLGQPEVNLGLIAGFGGTQRLTRLVNPGLAKEILFTADMYDAEAAHRIGLVNHVVP 184 Query: 226 AGEAHEKAIEMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLE 285 AGE MA++I +GP+A++++K+A+++G+E ++ E + + T+DR E Sbjct: 185 AGELMNFCKNMAKRIAARGPVAVQLSKQAVNDGLEMDLEKAFVHEADLFGLVFATEDREE 244 Query: 286 GLAAFAEKRKPLYTG 300 G+AAF K+KP + G Sbjct: 245 GIAAFLGKKKPEFKG 259 Lambda K H 0.318 0.134 0.373 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: 166 Number of extensions: 2 Number of successful extensions: 1 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: 301 Length of database: 260 Length adjustment: 26 Effective length of query: 275 Effective length of database: 234 Effective search space: 64350 Effective search space used: 64350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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