Align hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate RR42_RS00955 RR42_RS00955 hydroxymethylglutaryl-CoA lyase
Query= BRENDA::P97519 (325 letters) >lcl|FitnessBrowser__Cup4G11:RR42_RS00955 RR42_RS00955 hydroxymethylglutaryl-CoA lyase Length = 311 Score = 364 bits (935), Expect = e-105 Identities = 178/294 (60%), Positives = 230/294 (78%) Query: 28 TLPKRVKIVEVGPRDGLQNEKSIVPTPVKIKLIDMLSEAGLPVIEATSFVSPKWVPQMAD 87 TLP VK+VEVGPRDGLQNEK++VPT VK+ LI+ LS+AG IEA SFVSPKWVPQMAD Sbjct: 2 TLPHYVKVVEVGPRDGLQNEKAMVPTEVKVDLINRLSDAGFVNIEAASFVSPKWVPQMAD 61 Query: 88 HSDVLKGIQKFPGINYPVLTPNMKGFEEAVAAGAKEVSIFGAASELFTRKNVNCSIEESF 147 +DV+ IQ+ PG Y VLTPNMKGFE AVAA A EV IFGAASE F++KN+NCSI ES Sbjct: 62 GADVMARIQRRPGTLYSVLTPNMKGFEGAVAASADEVVIFGAASEAFSQKNINCSIAESI 121 Query: 148 QRFDGVMQAARAASISVRGYVSCALGCPYEGKVSPAKVAEVAKKLYSMGCYEISLGDTIG 207 +RF V AA+ + +R +SCALGCPY+G+V V +V +++ +GC EI + DTIG Sbjct: 122 ERFAPVAAAAKEKGLRLRASISCALGCPYQGEVPVHAVVDVVRRMRDLGCDEIDIADTIG 181 Query: 208 VGTPGLMKDMLTAVLHEVPVAALAVHCHDTYGQALANTLVALQMGVSVVDSSVAGLGGCP 267 VGTPG +++++ AV E P+ L+ H HDTYGQAL+N L +LQ+G+S+ +SVAGLGGCP Sbjct: 182 VGTPGRVQEVMHAVAAEFPIDRLSGHFHDTYGQALSNILASLQVGISIFHASVAGLGGCP 241 Query: 268 YAKGASGNLATEDLVYMLTGLGIHTGVNLQKLLEAGDFICQALNRKTSSKVAQA 321 YAKGA+GN+ATED++YML G+GIHTGV+L++++ AGDFI Q++ R SS+V +A Sbjct: 242 YAKGATGNVATEDVLYMLHGMGIHTGVDLEQVVRAGDFISQSIGRANSSRVGRA 295 Lambda K H 0.318 0.133 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: 313 Number of extensions: 12 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: 325 Length of database: 311 Length adjustment: 27 Effective length of query: 298 Effective length of database: 284 Effective search space: 84632 Effective search space used: 84632 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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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