Align Hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate GFF1017 PGA1_c10340 hydroxymethylglutaryl-CoA lyase MvaB
Query= reanno::Smeli:SM_b21125 (289 letters) >FitnessBrowser__Phaeo:GFF1017 Length = 283 Score = 335 bits (859), Expect = 7e-97 Identities = 166/280 (59%), Positives = 204/280 (72%) Query: 7 ERVTIVEVAPRDGLQNESRLVATEDKIRLVDLLADCGYERIEVTSFVSPRWVPQLADAPA 66 E V I EV PRDGLQNE R + +KI L+D L D G+ RIEV SFVSPRWVPQ+A + Sbjct: 3 ESVEIFEVGPRDGLQNEKRDIPVAEKIALIDRLTDAGFRRIEVASFVSPRWVPQMAGSGE 62 Query: 67 VMAGIVRRPGTRYAALTPNMRGFEAALAAGADEVAIFASASESFSERNINCSIAESIERF 126 V+AGI R RYAALTPNMRG+E AL A ADE+AIFASASE FS+ NIN S+AESIERF Sbjct: 63 VLAGIRRNSDVRYAALTPNMRGYEDALTAKADEIAIFASASEGFSKANINASVAESIERF 122 Query: 127 RPVAEASRHRGVPLRGYVSCVVECPYEGAIVPAETARVARLLADLGCYEISLGDTIGRGT 186 P+ EA+RH +P+RGY+SCV ECP++G P A +A L +GCYEISLGDTIG+ T Sbjct: 123 TPIIEAARHIDMPVRGYISCVTECPFDGPTDPDAVAALADRLFSMGCYEISLGDTIGQAT 182 Query: 187 PEAVDAMLAAALREIDAPKLAGHFHDTSGRALENIAVALERGIRVFDASAGGLGGCPYAP 246 P+++ ML A + +LAGH+HDT+GRA++NI +L G+RVFDA+ GGLGGCPYAP Sbjct: 183 PDSIARMLLAVRERVPVTRLAGHYHDTAGRAIDNIDASLSLGVRVFDAAVGGLGGCPYAP 242 Query: 247 GAAGNVDTLAVNAFLEAQSFATGLDSEKLDRAAAFARSLR 286 GAAGNV T AV+ L + TGL + L AAA AR++R Sbjct: 243 GAAGNVATEAVHEHLTRLGYETGLKGDVLTDAAAMARAMR 282 Lambda K H 0.319 0.133 0.382 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: 278 Number of extensions: 8 Number of successful extensions: 1 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: 289 Length of database: 283 Length adjustment: 26 Effective length of query: 263 Effective length of database: 257 Effective search space: 67591 Effective search space used: 67591 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 (21.8 bits) S2: 47 (22.7 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