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) >FitnessBrowser__Cup4G11:RR42_RS25280 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:
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