Align hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate RR42_RS00955 RR42_RS00955 hydroxymethylglutaryl-CoA lyase
Query= BRENDA::P97519 (325 letters) >FitnessBrowser__Cup4G11:RR42_RS00955 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:
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