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 WP_057508571.1 ABB28_RS10470 hydroxymethylglutaryl-CoA lyase
Query= CharProtDB::CH_122457 (599 letters) >NCBI__GCF_001431535.1:WP_057508571.1 Length = 310 Score = 171 bits (432), Expect = 5e-47 Identities = 107/282 (37%), Positives = 153/282 (54%), Gaps = 13/282 (4%) Query: 3 NSTKTVRIVEVGPRDGLQNIPQSIDSTIKLDLIRRLRDAGLQTIELTSFVSPRAIPQLAD 62 N+ + + + EV RDGLQ P + + K+ L G IE++SFVSP+A+P LAD Sbjct: 2 NTVRPLIVQEVCLRDGLQIEPVFVATADKIRLADAFSALGFARIEVSSFVSPKAVPALAD 61 Query: 63 AQVVVQNADIQKLLKNPKLRLPVLVPNLKGLERALHNGIKEVAVFISATEGFSRANINCT 122 A V + + P LVPNLKG ERAL G E+ + +SA + + AN+ T Sbjct: 62 AAEVFAG-----MQRAPGTVYVALVPNLKGAERALAAGAGELNLVMSAGQTHNLANMRMT 116 Query: 123 VDEGLERARQVASRAASAGLSVRGYVSCIFADPYDGPTRPSSVLRCTKALLDAGCYEVSL 182 DE E ++A+ + + G V+ F P++G + VL + LD GC ++L Sbjct: 117 TDESFEGFARIAA-LPRGNVLLNGSVATAFGCPFEGAQPVAKVLDLVRRYLDLGCTGITL 175 Query: 183 GDTLGIGTPADVRWLITYLQDNGVPL---EMLAGHFHDTYGGAVANVWEAYKCGLRMFDS 239 DT G+ P V L+ + +PL + L HFH+T G +ANV AY G + FD+ Sbjct: 176 ADTTGMANPRQVAALV----EQALPLVGADALTLHFHNTRGLGLANVVAAYDAGAQRFDA 231 Query: 240 SVAGLGGCPXALGAKGNVASEDLVYMFERSGIHTGVDLSKLV 281 ++ GLGGCP A GA GN+ +EDLV M E GI TG+DL L+ Sbjct: 232 ALGGLGGCPFAPGASGNICTEDLVAMCEEMGIPTGLDLPALI 273 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: 417 Number of extensions: 24 Number of successful extensions: 4 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: 310 Length adjustment: 32 Effective length of query: 567 Effective length of database: 278 Effective search space: 157626 Effective search space used: 157626 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 Apr 09 2024. 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