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 AO356_24105 AO356_24105 hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_122457 (599 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_24105 Length = 306 Score = 271 bits (693), Expect = 3e-77 Identities = 146/306 (47%), Positives = 201/306 (65%), Gaps = 8/306 (2%) Query: 7 TVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLADAQVV 66 +VR+VEVG RDGLQN +++ I+++L+++L +AGL+T+E +FVS R +P +A + Sbjct: 8 SVRLVEVGARDGLQNENRTLAPAIRVELLKKLANAGLRTLEAGAFVSERWVPHMAGS--- 64 Query: 67 VQNADIQKLLKN-PKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCTVDE 125 D+ K L + P + LVPN +GLE AL G +EVAVF +A+E FS+ NINC++ E Sbjct: 65 ---GDVFKALPDLPDVTWTALVPNARGLEEALAAGCREVAVFAAASEAFSQKNINCSIAE 121 Query: 126 GLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSLGDT 185 LER V RA A + VRGYVSC+ P+ G +P +V + AL GCYE+SLGDT Sbjct: 122 SLERFEAVMVRARDADVRVRGYVSCVMGCPFTGHVKPETVAAVSAALYGMGCYEISLGDT 181 Query: 186 LGIGTPADVRWLITYLQDNGVPLEMLAGHFHDTYGGAVANVWEAYKCGLRMFDSSVAGLG 245 +G GTPA + L+ VP+ LAGHFHDTYG A+AN+ A G+R+FDSSVAGLG Sbjct: 182 IGTGTPAATKALLDAC-TRVVPVNALAGHFHDTYGMAIANIHTALGMGVRVFDSSVAGLG 240 Query: 246 GCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLVETGEWISRQLSIAISSRAGAALWA 305 GCP + GA GNVA+ED++Y+ + GI GVDL +V+ GE+I L +SR AL A Sbjct: 241 GCPYSPGATGNVATEDVLYLLDGLGIKHGVDLDAVVDAGEFIDAHLGRETASRVARALLA 300 Query: 306 MRKQTA 311 R++ A Sbjct: 301 KRRREA 306 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: 422 Number of extensions: 16 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: 306 Length adjustment: 32 Effective length of query: 567 Effective length of database: 274 Effective search space: 155358 Effective search space used: 155358 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: 51 (24.3 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