Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate BPHYT_RS03930 BPHYT_RS03930 3-hydroxy-3-methylglutaryl-CoA lyase
Query= SwissProt::O34873 (299 letters) >FitnessBrowser__BFirm:BPHYT_RS03930 Length = 325 Score = 190 bits (482), Expect = 4e-53 Identities = 107/291 (36%), Positives = 165/291 (56%), Gaps = 7/291 (2%) Query: 5 KKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAID 64 ++V + EVG RDGLQ+ + TE K WI+ G+ ++E+ SFV K +P + DA + Sbjct: 6 ERVVVTEVGMRDGLQSIARTMPTEFKRRWIDAAYAAGVRHMEVASFVPAKLLPQMADADE 65 Query: 65 VAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHI- 123 V + ALVPN +G + ALE G++ +S S H+ N+ ++ +E + Sbjct: 66 VIAHALTYDDLMVTALVPNLKGAQRALEAGVHRIVAPISVSSAHSLANVRRTPAEMIEAF 125 Query: 124 --LKQVNNDAQKAN---LTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGD 178 +++ + KA + A LSTVFGC + VP + ++ A + G ++LGD Sbjct: 126 AAMRESIDGTSKAGGRRVELIAGLSTVFGCTLQGAVPYADIAAIARAAVQAGADVIALGD 185 Query: 179 TIGAANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLG 238 T G A P QV ++E + +LHFHDTRG LAN + ALQ GI FD S GLG Sbjct: 186 TTGEATPRQVGEIIELVRDVVGGKLHSLHFHDTRGLGLANTLVALQHGIREFDASLAGLG 245 Query: 239 GCPYAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLSAAKWIEEKM-GKPL 288 GCP+APG++GN TED+V+ML+ M +T + L++LL++ + + + G+PL Sbjct: 246 GCPHAPGATGNVNTEDLVFMLDSMGYETGIDLDRLLASRAVLADALPGEPL 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: 206 Number of extensions: 8 Number of successful extensions: 2 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: 325 Length adjustment: 27 Effective length of query: 272 Effective length of database: 298 Effective search space: 81056 Effective search space used: 81056 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