Align hydroxymethylglutaryl-CoA lyase; EC 4.1.3.4 (characterized)
to candidate AO356_24105 AO356_24105 hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_018268 (301 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24105 Length = 306 Score = 376 bits (966), Expect = e-109 Identities = 192/298 (64%), Positives = 221/298 (74%) Query: 3 AVKVFEVGPRDGLQNERQPLSVAARVGLIGELAGTGLRHIEAGAFVSPRWVPQMAGSDEV 62 +V++ EVG RDGLQNE + L+ A RV L+ +LA GLR +EAGAFVS RWVP MAGS +V Sbjct: 8 SVRLVEVGARDGLQNENRTLAPAIRVELLKKLANAGLRTLEAGAFVSERWVPHMAGSGDV 67 Query: 63 LRQLPSNDGVSYTALVPNRQGFEAAQRAGCREVAVFAAASEAFSRNNINCSIDESFERFT 122 + LP V++TALVPN +G E A AGCREVAVFAAASEAFS+ NINCSI ES ERF Sbjct: 68 FKALPDLPDVTWTALVPNARGLEEALAAGCREVAVFAAASEAFSQKNINCSIAESLERFE 127 Query: 123 PVLRAANEASIRVRGYVSCVLGCPFSGAVAPEAVAKVARRLYELGCYEISLGDTIGAGRP 182 V+ A +A +RVRGYVSCV+GCPF+G V PE VA V+ LY +GCYEISLGDTIG G P Sbjct: 128 AVMVRARDADVRVRGYVSCVMGCPFTGHVKPETVAAVSAALYGMGCYEISLGDTIGTGTP 187 Query: 183 DETAQLFELCARQLPVAALAGHFHDTWGMAIANVHAALAQGVRTFDSSVAGLGGCPYSPG 242 T L + C R +PV ALAGHFHDT+GMAIAN+H AL GVR FDSSVAGLGGCPYSPG Sbjct: 188 AATKALLDACTRVVPVNALAGHFHDTYGMAIANIHTALGMGVRVFDSSVAGLGGCPYSPG 247 Query: 243 ASGNVATEDLLYLLHGLGYSTGVDLEAVAQVGVRISAQLGTANRSRAGLALAARSARE 300 A+GNVATED+LYLL GLG GVDL+AV G I A LG SR AL A+ RE Sbjct: 248 ATGNVATEDVLYLLDGLGIKHGVDLDAVVDAGEFIDAHLGRETASRVARALLAKRRRE 305 Lambda K H 0.319 0.134 0.395 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: 315 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: 301 Length of database: 306 Length adjustment: 27 Effective length of query: 274 Effective length of database: 279 Effective search space: 76446 Effective search space used: 76446 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 (21.8 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