Align Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate SM_b21125 SM_b21125 hydroxymethylglutaryl-CoA lyase
Query= reanno::Smeli:SM_b21125 (289 letters) >FitnessBrowser__Smeli:SM_b21125 Length = 289 Score = 563 bits (1451), Expect = e-165 Identities = 289/289 (100%), Positives = 289/289 (100%) Query: 1 MTSPAKERVTIVEVAPRDGLQNESRLVATEDKIRLVDLLADCGYERIEVTSFVSPRWVPQ 60 MTSPAKERVTIVEVAPRDGLQNESRLVATEDKIRLVDLLADCGYERIEVTSFVSPRWVPQ Sbjct: 1 MTSPAKERVTIVEVAPRDGLQNESRLVATEDKIRLVDLLADCGYERIEVTSFVSPRWVPQ 60 Query: 61 LADAPAVMAGIVRRPGTRYAALTPNMRGFEAALAAGADEVAIFASASESFSERNINCSIA 120 LADAPAVMAGIVRRPGTRYAALTPNMRGFEAALAAGADEVAIFASASESFSERNINCSIA Sbjct: 61 LADAPAVMAGIVRRPGTRYAALTPNMRGFEAALAAGADEVAIFASASESFSERNINCSIA 120 Query: 121 ESIERFRPVAEASRHRGVPLRGYVSCVVECPYEGAIVPAETARVARLLADLGCYEISLGD 180 ESIERFRPVAEASRHRGVPLRGYVSCVVECPYEGAIVPAETARVARLLADLGCYEISLGD Sbjct: 121 ESIERFRPVAEASRHRGVPLRGYVSCVVECPYEGAIVPAETARVARLLADLGCYEISLGD 180 Query: 181 TIGRGTPEAVDAMLAAALREIDAPKLAGHFHDTSGRALENIAVALERGIRVFDASAGGLG 240 TIGRGTPEAVDAMLAAALREIDAPKLAGHFHDTSGRALENIAVALERGIRVFDASAGGLG Sbjct: 181 TIGRGTPEAVDAMLAAALREIDAPKLAGHFHDTSGRALENIAVALERGIRVFDASAGGLG 240 Query: 241 GCPYAPGAAGNVDTLAVNAFLEAQSFATGLDSEKLDRAAAFARSLRSTA 289 GCPYAPGAAGNVDTLAVNAFLEAQSFATGLDSEKLDRAAAFARSLRSTA Sbjct: 241 GCPYAPGAAGNVDTLAVNAFLEAQSFATGLDSEKLDRAAAFARSLRSTA 289 Lambda K H 0.319 0.133 0.382 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: 400 Number of extensions: 3 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: 289 Length of database: 289 Length adjustment: 26 Effective length of query: 263 Effective length of database: 263 Effective search space: 69169 Effective search space used: 69169 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 (21.8 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