Align Hydroxymethylglutaryl-CoA lyase YngG; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate Ac3H11_199 Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4)
Query= SwissProt::O34873 (299 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_199 Length = 349 Score = 198 bits (504), Expect = 1e-55 Identities = 107/274 (39%), Positives = 153/274 (55%), Gaps = 2/274 (0%) Query: 4 PKKVTIKEVGPRDGLQNEPVWIATEDKITWINQLSRTGLSYIEITSFVHPKWIPALRDAI 63 P + T++EVG RDGLQ+ ++T KI W+N G IE+ SFV + +P L D Sbjct: 38 PARATVREVGLRDGLQSIATVVSTAQKIEWLNAAYAAGQREIEVGSFVPARLLPQLADTA 97 Query: 64 DVAKGIDREKGVTYAALVPNQRGLENALEGGINEACVFMSASETHNRKNINKSTSESLHI 123 DV G+ + LVPN +G E ALE G + V +SAS H+ N+ K+ E + Sbjct: 98 DVLAHAKTLPGLVASVLVPNVKGAERALECGADLMVVPLSASHAHSLANLRKTPDEVVAE 157 Query: 124 LKQVN--NDAQKANLTTRAYLSTVFGCPYEKDVPIEQVIRLSEALFEFGISELSLGDTIG 181 + ++ DA + + T FGC + +V +V+RL +AL + G +SL DT+G Sbjct: 158 VARIRALRDASGRSTLIEGGVGTAFGCTLQGEVAESEVLRLMQALLDAGADHVSLADTVG 217 Query: 182 AANPAQVETVLEALLARFPANQIALHFHDTRGTALANMVTALQMGITVFDGSAGGLGGCP 241 A+PA V + + A HFHDTRG LAN+ A Q GIT FD G+GGCP Sbjct: 218 FADPASVARLFDKARALVGDRLACAHFHDTRGMGLANVYAAWQTGITRFDACLAGIGGCP 277 Query: 242 YAPGSSGNAATEDIVYMLEQMDIKTNVKLEKLLS 275 +APG+SGN TED+V+MLE+M + T + + LL+ Sbjct: 278 HAPGASGNVTTEDLVFMLERMGVATGIDVSALLA 311 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: 226 Number of extensions: 10 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: 349 Length adjustment: 28 Effective length of query: 271 Effective length of database: 321 Effective search space: 86991 Effective search space used: 86991 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