Align Hydroxymethylglutaryl-CoA lyase, mitochondrial; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate 201055 SO1893 hydroxymethylglutaryl-CoA lyase (NCBI ptt file)
Query= SwissProt::P38060 (325 letters) >FitnessBrowser__MR1:201055 Length = 315 Score = 355 bits (911), Expect = e-103 Identities = 182/304 (59%), Positives = 227/304 (74%), Gaps = 1/304 (0%) Query: 18 LRAVSTSSMGTLPKQVKIVEVGPRDGLQNEKSIVPTPVKIRLIDMLSEAGLPVIEATSFV 77 L +S +S+ V + E+GPRDGLQNE + VPT K+ LI+ L+ AG+ IEA SFV Sbjct: 6 LSNLSATSLSATSDSVSLFEMGPRDGLQNEAA-VPTQAKVALIEALANAGVKRIEAGSFV 64 Query: 78 SPKWVPQMADHSDVLKGIQKFPGINYPVLTPNMKGFEEAVAAGAKEVSVFGAVSELFTRK 137 SPKWVPQMAD +VL+ I++ G+ Y LTPN+KG E A+ A A EV++FGA S+ F+++ Sbjct: 65 SPKWVPQMADSGEVLRQIRRQAGVVYSALTPNVKGLELALDAKASEVAIFGAASQSFSQR 124 Query: 138 NANCSIEESFQRFAGVMQAAQAASISVRGYVSCALGCPYEGKVSPAKVAEVAKKLYSMGC 197 N NCSIEES +RF +M A+AA+I VRGYVSC LGCPYEG+++ ++VA V++ LY MGC Sbjct: 125 NINCSIEESIERFIPLMDMAKAANIPVRGYVSCVLGCPYEGEIAASEVARVSEILYKMGC 184 Query: 198 YEISLGDTIGVGTPGLMKDMLTAVMHEVPVTALAVHCHDTYGQALANTLVALQMGVSVVD 257 YEISLGDTIGVGTP + ML AVM VPV LA+H HDTYGQALAN L +GV D Sbjct: 185 YEISLGDTIGVGTPLKARKMLQAVMERVPVEKLALHFHDTYGQALANITACLDLGVRSFD 244 Query: 258 SSVAGLGGCPYAKGASGNLATEDLVYMLNGLGIHTGVNLQKLLEAGDFICQALNRKTSSK 317 +SVAGLGGCPYAKGASGNLA+EDLVYML+GLG+ TG++L+KL AG I + LNR SK Sbjct: 245 ASVAGLGGCPYAKGASGNLASEDLVYMLHGLGLKTGIDLEKLALAGFGISKQLNRLNGSK 304 Query: 318 VAQA 321 VA A Sbjct: 305 VANA 308 Lambda K H 0.317 0.132 0.379 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: 295 Number of extensions: 14 Number of successful extensions: 2 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: 315 Length adjustment: 28 Effective length of query: 297 Effective length of database: 287 Effective search space: 85239 Effective search space used: 85239 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