Align 3-Hydroxy-3-isohexenylglutaryl-CoA lyase (EC 4.1.3.26) (characterized)
to candidate PP_3540 PP_3540 Hydroxymethylglutaryl-CoA lyase
Query= BRENDA::Q9I2A0 (300 letters) >FitnessBrowser__Putida:PP_3540 Length = 299 Score = 474 bits (1220), Expect = e-138 Identities = 235/299 (78%), Positives = 264/299 (88%) Query: 1 MNLPKKVRLVEVGPRDGLQNEKQPIEVADKIRLVDDLSAAGLDYIEVGSFVSPKWVPQMA 60 M+LPK VRLVEVGPRDGLQNE QPI VADK+RLV+DL+ AGL YIEVGSFVSPKWVPQMA Sbjct: 1 MSLPKHVRLVEVGPRDGLQNEAQPISVADKVRLVNDLTEAGLAYIEVGSFVSPKWVPQMA 60 Query: 61 GSAEVFAGIRQRPGVTYAALAPNLKGFEAALESGVKEVAVFAAASEAFSQRNINCSIKDS 120 GSAEVFAGI+QRPGVTYAALAPNL+GFE AL +GVKEVAVFAAASEAFSQRNINCSI +S Sbjct: 61 GSAEVFAGIQQRPGVTYAALAPNLRGFEDALAAGVKEVAVFAAASEAFSQRNINCSISES 120 Query: 121 LERFVPVLEAARQHQVRVRGYISCVLGCPYDGDVDPRQVAWVARELQQMGCYEVSLGDTI 180 L+RF P+++AAR H +RVRGY+SCVLGCPY+G V QVA VAR L MGCYEVSLGDTI Sbjct: 121 LKRFEPIMDAARSHGMRVRGYVSCVLGCPYEGKVSAEQVAPVARALHDMGCYEVSLGDTI 180 Query: 181 GVGTAGATRRLIEAVASEVPRERLAGHFHDTYGQALANIYASLLEGIAVFDSSVAGLGGC 240 G GTAG TRRL E V+++VPRE+LAGHFHDTYGQALAN+YASLLEGI+VFDSSVAGLGGC Sbjct: 181 GTGTAGDTRRLFEVVSAQVPREQLAGHFHDTYGQALANVYASLLEGISVFDSSVAGLGGC 240 Query: 241 PYAKGATGNVASEDVLYLLNGLEIHTGVDMHALVDAGQRICAVLGKSNGSRAAKALLAK 299 PYAKGATGN+ASEDV+YLL GL I TG+D+ L+ AGQRI VLG+ NGSR A+A A+ Sbjct: 241 PYAKGATGNIASEDVVYLLQGLGIETGIDLGLLIAAGQRISGVLGRDNGSRVARACSAQ 299 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: 368 Number of extensions: 15 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