Align 3-Hydroxy-3-isohexenylglutaryl-CoA lyase (EC 4.1.3.26) (characterized)
to candidate CCNA_00500 CCNA_00500 hydroxymethylglutaryl-CoA lyase
Query= BRENDA::Q9I2A0 (300 letters) >FitnessBrowser__Caulo:CCNA_00500 Length = 299 Score = 221 bits (563), Expect = 2e-62 Identities = 120/290 (41%), Positives = 169/290 (58%), Gaps = 1/290 (0%) Query: 7 VRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMAGSAEVF 66 +++VEVGPRDGLQNEK + V +K+ L+ L AAG EV SFV+P VPQMAG+ E+ Sbjct: 5 IQIVEVGPRDGLQNEKTVLSVEEKLDLIAKLEAAGARRTEVVSFVNPSRVPQMAGAEEIM 64 Query: 67 AGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDSLERFVP 126 A + + L N++G+E + +G E V AS+ F+ RN + + +E Sbjct: 65 AALPADLVHSRIGLVLNMRGWERCVSTGCDEANVVVCASDGFATRNQGSTTQQQVETLAA 124 Query: 127 VLEA-ARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTIGVGTA 185 ++E A + + IS GCP+DG+V QV + RE +G E+++ DTIGV Sbjct: 125 IVERQAAEGGPPITATISVAFGCPFDGEVSQDQVVAIVREAAALGVPEIAIADTIGVADP 184 Query: 186 GATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLLEGIAVFDSSVAGLGGCPYAKG 245 RR IEAV + P RL HFHDT LAN +AS+ G+ V D+SV GLGGCP+A Sbjct: 185 WTVRRRIEAVRAAAPDTRLRMHFHDTRNTGLANAFASVEAGVDVLDASVGGLGGCPFAPN 244 Query: 246 ATGNVASEDVLYLLNGLEIHTGVDMHALVDAGQRICAVLGKSNGSRAAKA 295 ATGN+ +ED++Y+L TG D+ AL+ G+ I LGK+ S A+A Sbjct: 245 ATGNIGTEDLVYMLERAGFETGYDLAALIQIGRDISQRLGKAPASSLARA 294 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: 224 Number of extensions: 6 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: 300 Length of database: 299 Length adjustment: 27 Effective length of query: 273 Effective length of database: 272 Effective search space: 74256 Effective search space used: 74256 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