Align 3-Hydroxy-3-isohexenylglutaryl-CoA lyase (EC 4.1.3.26) (characterized)
to candidate GFF3323 PS417_17005 hydroxymethylglutaryl-CoA lyase
Query= BRENDA::Q9I2A0 (300 letters) >FitnessBrowser__WCS417:GFF3323 Length = 299 Score = 468 bits (1204), Expect = e-137 Identities = 229/295 (77%), Positives = 262/295 (88%) Query: 1 MNLPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMA 60 M+LP VRLVEVGPRDGLQNE QPI V+DK+RLVD LSAAGL YIEVGSFVSPKWVPQMA Sbjct: 1 MSLPSHVRLVEVGPRDGLQNEAQPISVSDKVRLVDALSAAGLSYIEVGSFVSPKWVPQMA 60 Query: 61 GSAEVFAGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDS 120 GSAEVFA I+++PGVTY ALAPNL+GFE A+ +GVKEVAVFAAASEAFSQRNINCSI +S Sbjct: 61 GSAEVFAQIQRKPGVTYGALAPNLRGFEDAVSAGVKEVAVFAAASEAFSQRNINCSISES 120 Query: 121 LERFVPVLEAARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTI 180 LERF P++ AA+Q+ V VRGY+SCVLGCPY+G + P QVA VAREL MGCYEVSLGDTI Sbjct: 121 LERFAPIMAAAKQNGVSVRGYVSCVLGCPYEGQIAPEQVAAVARELYAMGCYEVSLGDTI 180 Query: 181 GVGTAGATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLLEGIAVFDSSVAGLGGC 240 G GTAGATRRL E V ++VPR++LAGHFHDTYGQA+ANIYASLLEGI+VFDSS+AGLGGC Sbjct: 181 GTGTAGATRRLFEVVGAQVPRDKLAGHFHDTYGQAIANIYASLLEGISVFDSSIAGLGGC 240 Query: 241 PYAKGATGNVASEDVLYLLNGLEIHTGVDMHALVDAGQRICAVLGKSNGSRAAKA 295 PYAKGA+GNVA+EDV+YLLNGL I TG+D+ AL+ AGQ+I +VLG+ GSR AKA Sbjct: 241 PYAKGASGNVATEDVVYLLNGLGIETGIDLEALIGAGQQISSVLGRPTGSRVAKA 295 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: 355 Number of extensions: 9 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: 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