Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate H281DRAFT_04763 H281DRAFT_04763 hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= SwissProt::O34873 (299 letters) >FitnessBrowser__Burk376:H281DRAFT_04763 Length = 327 Score = 192 bits (487), Expect = 1e-53 Identities = 109/291 (37%), Positives = 162/291 (55%), Gaps = 7/291 (2%) Query: 5 KKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAID 64 ++V + EVG RDGLQ+ + TE K WI+ G+ ++E+ SFV K +P + DA + Sbjct: 6 ERVVVTEVGMRDGLQSIAQTMPTESKRRWIDAAYAAGVRHMEVASFVPAKLLPQMADADE 65 Query: 65 VAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHIL 124 V + + ALVPN +G + ALE G++ +S S H+ N+ K+ +E + + Sbjct: 66 VIAHALGYRDLIVTALVPNLKGAQRALEAGVHRIVAPISVSAAHSLANVRKTPAEMIDVF 125 Query: 125 KQVNN--DAQKANLTTR----AYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGD 178 + D A T R A LSTVFGC + VP E + ++ G ++LGD Sbjct: 126 AAMREAIDGAPAAGTRRVELIAGLSTVFGCTLQGAVPYEDIAAIARDAVRAGADVIALGD 185 Query: 179 TIGAANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLG 238 T G A P QV ++E + +LH HDTRG ALAN + LQ GI FD S GLG Sbjct: 186 TTGEATPRQVGEIIEVVRGVAGDKLRSLHLHDTRGLALANTLVGLQHGIREFDASLAGLG 245 Query: 239 GCPYAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLSAAKWIEEKM-GKPL 288 GCP+APG++GN TED+V+MLE M +T + L +L+++ + + + G+PL Sbjct: 246 GCPHAPGATGNVNTEDLVFMLESMGYETGIDLTRLIASRAVLADALPGEPL 296 Lambda K H 0.315 0.132 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: 217 Number of extensions: 11 Number of successful extensions: 3 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: 299 Length of database: 327 Length adjustment: 27 Effective length of query: 272 Effective length of database: 300 Effective search space: 81600 Effective search space used: 81600 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 (21.6 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