Align 3-Hydroxy-3-isohexenylglutaryl-CoA lyase (EC 4.1.3.26) (characterized)
to candidate H281DRAFT_02101 H281DRAFT_02101 hydroxymethylglutaryl-CoA lyase
Query= BRENDA::Q9I2A0 (300 letters) >FitnessBrowser__Burk376:H281DRAFT_02101 Length = 308 Score = 376 bits (965), Expect = e-109 Identities = 183/300 (61%), Positives = 226/300 (75%) Query: 1 MNLPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMA 60 M +PK+V++VEVGPRDGLQNEK+ + A KI L++ LSAAG +E SFVSPKWVPQMA Sbjct: 1 MAVPKQVKIVEVGPRDGLQNEKEFVPTATKIELINRLSAAGFRNVEAASFVSPKWVPQMA 60 Query: 61 GSAEVFAGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDS 120 AEV +GI +RPG Y+ L PNL+GFE AL + E+ +F AASEAFSQ+NINCSI +S Sbjct: 61 DGAEVMSGIERRPGTIYSVLTPNLRGFEGALAARADEIVIFGAASEAFSQKNINCSIAES 120 Query: 121 LERFVPVLEAARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTI 180 +ERF PV +AA++H +R+RG +SC LGCPY G+V V V + +GC E+ + DTI Sbjct: 121 IERFAPVAQAAKEHGLRIRGSVSCALGCPYQGEVPVASVVDVVQRFAALGCDEIDIADTI 180 Query: 181 GVGTAGATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLLEGIAVFDSSVAGLGGC 240 GVGT TR + EAV PRERL+GHFHDTYGQALANIYA+L EGI ++ +SVAGLGGC Sbjct: 181 GVGTPKRTREVFEAVTQVFPRERLSGHFHDTYGQALANIYAALQEGIEIYHASVAGLGGC 240 Query: 241 PYAKGATGNVASEDVLYLLNGLEIHTGVDMHALVDAGQRICAVLGKSNGSRAAKALLAKA 300 PYAKGATGNVA+EDVLYL+NGL I TG+D+ +V G I +G+ N SRA KALLAKA Sbjct: 241 PYAKGATGNVATEDVLYLMNGLGIETGIDLAQVVAIGDFISTSIGRPNVSRAGKALLAKA 300 Lambda K H 0.318 0.135 0.392 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: 333 Number of extensions: 12 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: 300 Length of database: 308 Length adjustment: 27 Effective length of query: 273 Effective length of database: 281 Effective search space: 76713 Effective search space used: 76713 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: 48 (23.1 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