Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate GFF3794 PGA1_262p01980 putative enoyl-CoA hydratase
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Phaeo:GFF3794 Length = 263 Score = 146 bits (369), Expect = 4e-40 Identities = 84/255 (32%), Positives = 134/255 (52%), Gaps = 4/255 (1%) Query: 7 DARGPIEIWTIDGESRRNAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADL 66 + G + + T++ + NA++ A L L+ + +RA+++TGAG++AF AG D+ Sbjct: 8 ERNGAVAVLTLNRPEKLNALNYATNDCLLSLLNAIEIDPSIRAIILTGAGERAFSAGGDI 67 Query: 67 KERATMA----EDEVRAFLDGLRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVA 122 E ++ VR F + +E IAA+NG A GGG E+ A L VA Sbjct: 68 HEFTESVKAGVDEAVRDFCKRGQTMTARLEAFQKPIIAAVNGIAFGGGCEITEAVHLAVA 127 Query: 123 APAAELGLTEVKLGIIPGGGGTQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAP 182 + A E+ +GI P GGTQRL RL G RA +L+LT +A A +GL NR+ P Sbjct: 128 SERAMFAKPEINIGIPPTFGGTQRLPRLAGRKRALELLLTGDTFSAQRACEMGLVNRIVP 187 Query: 183 EGHLLAVAYGLAESVVENAPIAVATAKHAIDEGTGLELDDALALELRKYEEILKTEDRLE 242 L+ A+ LA+ ++ ++P+A + A+ G +D+ L +E ++ + T+D E Sbjct: 188 HDELMPAAFDLADRIIRHSPLAASRIITAVTRGINTTIDEGLLIEREQFARMAATKDVHE 247 Query: 243 GLRAFAEKRAPVYKG 257 GL A+ +R P Y G Sbjct: 248 GLGAWIARRTPEYVG 262 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: 151 Number of extensions: 4 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: 258 Length of database: 263 Length adjustment: 25 Effective length of query: 233 Effective length of database: 238 Effective search space: 55454 Effective search space used: 55454 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