Align hydroxymethylglutaryl-CoA lyase; EC 4.1.3.4 (characterized)
to candidate GFF2664 HP15_2608 hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_018268 (301 letters) >FitnessBrowser__Marino:GFF2664 Length = 307 Score = 250 bits (639), Expect = 3e-71 Identities = 122/263 (46%), Positives = 178/263 (67%) Query: 4 VKVFEVGPRDGLQNERQPLSVAARVGLIGELAGTGLRHIEAGAFVSPRWVPQMAGSDEVL 63 V+V +VGPRDGLQ++ + LSV AR LI L G GLR+IEAG+FVSP+ VPQMAG+DE+ Sbjct: 3 VRVNDVGPRDGLQSQGKTLSVDARAQLIEALVGAGLRNIEAGSFVSPKAVPQMAGTDELF 62 Query: 64 RQLPSNDGVSYTALVPNRQGFEAAQRAGCREVAVFAAASEAFSRNNINCSIDESFERFTP 123 +LP++D V Y LVPN +G++ A AG + V V + ++ ++ NI S+DE+ + Sbjct: 63 SRLPASDKVRYAGLVPNMKGYQLATAAGAKVVNVVLSVTDTMNQKNIRMSLDETADVCKA 122 Query: 124 VLRAANEASIRVRGYVSCVLGCPFSGAVAPEAVAKVARRLYELGCYEISLGDTIGAGRPD 183 ++ + + V+ Y++ CPF G V PE VA+ AR ++ G +I + DTIGA P Sbjct: 123 IVERGHLEGVEVQAYLAVAFECPFEGLVDPEVVARYARLMHSAGAAKIIIADTIGAANPT 182 Query: 184 ETAQLFELCARQLPVAALAGHFHDTWGMAIANVHAALAQGVRTFDSSVAGLGGCPYSPGA 243 + Q+ +L ++ L+ HFHDT GMA+AN+ A+ +GV FDSS+ GLGGCP+SPGA Sbjct: 183 QVRQVLDLVVPEVGADRLSCHFHDTRGMALANITVAVDRGVCEFDSSIGGLGGCPFSPGA 242 Query: 244 SGNVATEDLLYLLHGLGYSTGVD 266 +GNVATED++ LL+ +G+ TG+D Sbjct: 243 TGNVATEDVVLLLNSMGHDTGID 265 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: 268 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: 307 Length adjustment: 27 Effective length of query: 274 Effective length of database: 280 Effective search space: 76720 Effective search space used: 76720 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