Align hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate N515DRAFT_0926 N515DRAFT_0926 hydroxymethylglutaryl-CoA lyase
Query= BRENDA::P97519 (325 letters) >FitnessBrowser__Dyella79:N515DRAFT_0926 Length = 300 Score = 355 bits (912), Expect = e-103 Identities = 176/296 (59%), Positives = 225/296 (76%) Query: 26 MGTLPKRVKIVEVGPRDGLQNEKSIVPTPVKIKLIDMLSEAGLPVIEATSFVSPKWVPQM 85 M + V+IVEVG RDGLQNEK+++P VKI LID LS GL IEATSFVSPKWVPQ+ Sbjct: 1 MNSPDNHVRIVEVGARDGLQNEKTLLPADVKIALIDRLSSTGLSTIEATSFVSPKWVPQL 60 Query: 86 ADHSDVLKGIQKFPGINYPVLTPNMKGFEEAVAAGAKEVSIFGAASELFTRKNVNCSIEE 145 AD ++V +GI+K PG++YPVL PN +G+ A GA EV++F AASE F RKN+N I+E Sbjct: 61 ADAAEVFQGIRKVPGVSYPVLVPNEQGYRRARDVGATEVAVFTAASEAFNRKNINAGIDE 120 Query: 146 SFQRFDGVMQAARAASISVRGYVSCALGCPYEGKVSPAKVAEVAKKLYSMGCYEISLGDT 205 S +RF V++ ARA + VRGYVS LGCPY+G+V A V VA +L+ +GC+EISLGDT Sbjct: 121 SIERFRPVLELARADGVKVRGYVSTVLGCPYQGEVPVADVVRVAARLHQLGCHEISLGDT 180 Query: 206 IGVGTPGLMKDMLTAVLHEVPVAALAVHCHDTYGQALANTLVALQMGVSVVDSSVAGLGG 265 IGVGTP + ML AV EVP+AALAVH HDTYGQALAN L L+ GV VVDS+V+G GG Sbjct: 181 IGVGTPAKARAMLKAVAAEVPMAALAVHFHDTYGQALANILSCLEEGVRVVDSAVSGTGG 240 Query: 266 CPYAKGASGNLATEDLVYMLTGLGIHTGVNLQKLLEAGDFICQALNRKTSSKVAQA 321 CPYAKGA+GN+A+ED+VYML G+G+ TGV+L L+ G ++ L+++T+S+V +A Sbjct: 241 CPYAKGATGNVASEDVVYMLHGMGMQTGVDLDILVATGAWLAAQLHKETASRVTRA 296 Lambda K H 0.318 0.133 0.381 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: 293 Number of extensions: 7 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: 325 Length of database: 300 Length adjustment: 27 Effective length of query: 298 Effective length of database: 273 Effective search space: 81354 Effective search space used: 81354 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 Apr 09 2024. 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