Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate H281DRAFT_01200 H281DRAFT_01200 short chain enoyl-CoA hydratase (EC 4.2.1.17)
Query= BRENDA::Q1D5Y4 (258 letters) >FitnessBrowser__Burk376:H281DRAFT_01200 Length = 278 Score = 154 bits (388), Expect = 2e-42 Identities = 94/231 (40%), Positives = 128/231 (55%), Gaps = 1/231 (0%) Query: 24 NAISRAMLKELGELVTRVSSSRDVRAVVITGAGDKAFCAGADLKERATMAEDEVRAFLDG 83 NA + L +L + V R++ VRA+VITG G K F AGADL A + R Sbjct: 23 NAFTPDGLLQLQQTVERLNGETRVRAIVITGEGPKFFSAGADLNAFADGNREVARVAAAR 82 Query: 84 LRRTFRAIEKSDCVFIAAINGAALGGGTELALACDLRVAAPAAELGLTEVKLGIIPGGGG 143 F A++ + V IAAING A+GGG E ALACD+R+A A + L E +G++P G G Sbjct: 83 FGAAFEALQNARPVVIAAINGFAMGGGLECALACDIRIAEQHAVMALPETAVGLLPCGCG 142 Query: 144 TQRLARLVGPGRAKDLILTARRINAAEAFSVGLANRLAPEGHLLAVAYGLAESVVENAPI 203 TQ L LVG G AK +ILT R++AA A +GL + +G A +A V +P Sbjct: 143 TQTLPWLVGEGWAKRMILTGERVDAATALRIGLVEEVVEKGAAREAALSMAARVATLSPQ 202 Query: 204 AVATAKHAIDEG-TGLELDDALALELRKYEEILKTEDRLEGLRAFAEKRAP 253 AV +K I +G G+ ALALE ++ ++ D+ EG+ AF EKR P Sbjct: 203 AVGFSKTLIHQGRNGVPRSAALALERERFVDLFDGADQREGVNAFLEKRTP 253 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: 125 Number of extensions: 2 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: 278 Length adjustment: 25 Effective length of query: 233 Effective length of database: 253 Effective search space: 58949 Effective search space used: 58949 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 Sep 17 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