Align Hydroxymethylglutaryl-CoA lyase, mitochondrial; HL; HMG-CoA lyase; 3-hydroxy-3-methylglutarate-CoA lyase; EC 4.1.3.4 (characterized)
to candidate AZOBR_RS22280 AZOBR_RS22280 hydroxymethylglutaryl-CoA lyase
Query= SwissProt::P38060 (325 letters) >FitnessBrowser__azobra:AZOBR_RS22280 Length = 299 Score = 387 bits (994), Expect = e-112 Identities = 192/293 (65%), Positives = 231/293 (78%) Query: 29 LPKQVKIVEVGPRDGLQNEKSIVPTPVKIRLIDMLSEAGLPVIEATSFVSPKWVPQMADH 88 LPK V++VEVGPRDGLQNEK IVPT VKI L+D L++AGL IEA SFVSPKWVPQMAD Sbjct: 3 LPKSVRMVEVGPRDGLQNEKQIVPTAVKIGLVDRLTDAGLTAIEAGSFVSPKWVPQMADT 62 Query: 89 SDVLKGIQKFPGINYPVLTPNMKGFEEAVAAGAKEVSVFGAVSELFTRKNANCSIEESFQ 148 DV GI++ G+ Y LTPN KG E A+AA A EV+VF A SE F++KN NCSI ES Sbjct: 63 PDVFAGIRRKEGVRYVALTPNAKGLEGALAARADEVAVFAAASESFSQKNINCSIAESLD 122 Query: 149 RFAGVMQAAQAASISVRGYVSCALGCPYEGKVSPAKVAEVAKKLYSMGCYEISLGDTIGV 208 RF V++ A+A + VRGYVSC LGCPYEG+++PA VAEVA +L +MGCYE+SLGDTIG Sbjct: 123 RFVPVLEQAKAQGVPVRGYVSCVLGCPYEGEIAPAAVAEVAGRLLAMGCYEVSLGDTIGT 182 Query: 209 GTPGLMKDMLTAVMHEVPVTALAVHCHDTYGQALANTLVALQMGVSVVDSSVAGLGGCPY 268 GTP + M+ AV VP+ LAVH HDTYGQALAN L L+MGV+VVDSSVAGLGGCPY Sbjct: 183 GTPSKAQAMIAAVAKRVPMERLAVHFHDTYGQALANILATLEMGVAVVDSSVAGLGGCPY 242 Query: 269 AKGASGNLATEDLVYMLNGLGIHTGVNLQKLLEAGDFICQALNRKTSSKVAQA 321 AKGASGN+A+ED++YMLNGLG+ TGV+L +L+ AG +I A+ R T+SKVA+A Sbjct: 243 AKGASGNVASEDVLYMLNGLGVATGVDLDRLVAAGAYISDAIGRPTASKVARA 295 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: 328 Number of extensions: 14 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: 299 Length adjustment: 27 Effective length of query: 298 Effective length of database: 272 Effective search space: 81056 Effective search space used: 81056 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