Align 3-Hydroxy-3-isohexenylglutaryl-CoA lyase (EC 4.1.3.26) (characterized)
to candidate Ac3H11_3018 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= BRENDA::Q9I2A0 (300 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3018 Length = 304 Score = 342 bits (876), Expect = 8e-99 Identities = 173/298 (58%), Positives = 217/298 (72%) Query: 2 NLPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMAG 61 ++P +VRL++VGPRDGLQNEK P+ A KI LV L AGL IEV S+VSPKWVPQMA Sbjct: 4 SIPSRVRLIDVGPRDGLQNEKTPVPAAVKIELVHRLQQAGLKEIEVTSYVSPKWVPQMAD 63 Query: 62 SAEVFAGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDSL 121 + EV AGI ++ GV Y+ L PNLKGFEAA+ E+ VF +ASEAFSQRNINCSI +S+ Sbjct: 64 NHEVMAGITRQSGVAYSVLTPNLKGFEAAVLDKPDEIVVFGSASEAFSQRNINCSIVESI 123 Query: 122 ERFVPVLEAARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTIG 181 ERF PV++AA +RVRG +SC +GCPY+GD+ P +VA++A L+ +G V + DTIG Sbjct: 124 ERFAPVVQAALAAGIRVRGAMSCTVGCPYEGDIAPERVAYLAGLLKGIGVQRVDVADTIG 183 Query: 182 VGTAGATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLLEGIAVFDSSVAGLGGCP 241 VGT +R IEA + ++GHFHDTYGQAL+N A+L G+ + SSVAGLGGCP Sbjct: 184 VGTPRKVQRAIEATLQHFGIDEVSGHFHDTYGQALSNTLAALELGVWNYQSSVAGLGGCP 243 Query: 242 YAKGATGNVASEDVLYLLNGLEIHTGVDMHALVDAGQRICAVLGKSNGSRAAKALLAK 299 YAKGATGNVA+EDV+Y+L G+ I TGVD+ L+DAG I LG+ SRAA ALL K Sbjct: 244 YAKGATGNVATEDVVYMLQGMGIETGVDLDKLIDAGAYISDFLGRKPNSRAANALLTK 301 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: 306 Number of extensions: 11 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: 304 Length adjustment: 27 Effective length of query: 273 Effective length of database: 277 Effective search space: 75621 Effective search space used: 75621 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