Align 3-hydroxy-3-methylglutaryl-coenzyme A lyase/3-methylglutaconyl-coenzyme A hydratase; EC 4.1.3.4; EC 4.2.1.18 (characterized)
to candidate PP_3540 PP_3540 Hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__Putida:PP_3540 Length = 299 Score = 272 bits (696), Expect = 1e-77 Identities = 151/297 (50%), Positives = 189/297 (63%), Gaps = 6/297 (2%) Query: 6 KTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADAQV 65 K VR+VEVGPRDGLQN Q I K+ L+ L +AGL IE+ SFVSP+ +PQ+A + Sbjct: 5 KHVRLVEVGPRDGLQNEAQPISVADKVRLVNDLTEAGLAYIEVGSFVSPKWVPQMAGSAE 64 Query: 66 VVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTVDE 125 V A IQ+ P + L PNL+G E AL G+KEVAVF +A+E FS+ NINC++ E Sbjct: 65 VF--AGIQQ---RPGVTYAALAPNLRGFEDALAAGVKEVAVFAAASEAFSQRNINCSISE 119 Query: 126 GLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLGDT 185 L+R + A S G+ VRGYVSC+ PY+G V +AL D GCYEVSLGDT Sbjct: 120 SLKRFEPIMDAARSHGMRVRGYVSCVLGCPYEGKVSAEQVAPVARALHDMGCYEVSLGDT 179 Query: 186 LGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAGLG 245 +G GT D R L + VP E LAGHFHDTYG A+ANV+ + G+ +FDSSVAGLG Sbjct: 180 IGTGTAGDTRRLFEVVSAQ-VPREQLAGHFHDTYGQALANVYASLLEGISVFDSSVAGLG 238 Query: 246 GCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAA 302 GCP A GA GN+ASED+VY+ + GI TG+DL L+ G+ IS L SR A Sbjct: 239 GCPYAKGATGNIASEDVVYLLQGLGIETGIDLGLLIAAGQRISGVLGRDNGSRVARA 295 Lambda K H 0.318 0.134 0.389 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: 423 Number of extensions: 13 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: 599 Length of database: 299 Length adjustment: 32 Effective length of query: 567 Effective length of database: 267 Effective search space: 151389 Effective search space used: 151389 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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