Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate RR42_RS25280 RR42_RS25280 3-hydroxy-3-methylglutaryl-CoA lyase
Query= SwissProt::O34873 (299 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS25280 RR42_RS25280 3-hydroxy-3-methylglutaryl-CoA lyase Length = 323 Score = 193 bits (490), Expect = 5e-54 Identities = 107/275 (38%), Positives = 153/275 (55%), Gaps = 2/275 (0%) Query: 3 YPKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDA 62 +P + I+EVG RDGLQ+ + TE K WI GL +E+ SFV + +P L D Sbjct: 5 FPHRAVIREVGLRDGLQSIQTILPTERKKEWIRAAYDAGLRELEVGSFVPARLLPQLADT 64 Query: 63 IDVAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLH 122 ++ G+ + LVPN RG E+A+ G + V +SAS H+ N+ K+ E + Sbjct: 65 AEIVAFARTFPGLFVSVLVPNLRGAEDAIASGADLMIVPLSASHAHSLANLRKTPDEVVA 124 Query: 123 ILKQVN--NDAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTI 180 + ++ DA + + T FGC + +V I +V+RL +ALF+ G + L DT+ Sbjct: 125 DVGRIRAARDAAGSKTVIEGGVGTAFGCTIQGEVKIAEVLRLMQALFDAGADRVCLADTV 184 Query: 181 GAANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLGGC 240 G A+P V + E A HFHDTRG LAN+ ALQ G+T FD G+GGC Sbjct: 185 GYADPLMVLDLFERARAVAGDKLWCGHFHDTRGLGLANVFAALQTGVTRFDACLTGIGGC 244 Query: 241 PYAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLS 275 P+APG+SGN A+ED+ YMLE M I+T V + LL+ Sbjct: 245 PHAPGASGNVASEDLAYMLESMGIQTGVDIPALLT 279 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: 218 Number of extensions: 8 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: 323 Length adjustment: 27 Effective length of query: 272 Effective length of database: 296 Effective search space: 80512 Effective search space used: 80512 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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