Align hydroxymethylglutaryl-CoA lyase (EC 4.1.3.4) (characterized)
to candidate 7024490 Shewana3_1668 hydroxymethylglutaryl-CoA lyase (RefSeq)
Query= BRENDA::P97519 (325 letters) >FitnessBrowser__ANA3:7024490 Length = 310 Score = 358 bits (920), Expect = e-104 Identities = 184/304 (60%), Positives = 229/304 (75%), Gaps = 1/304 (0%) Query: 18 LRAASTSSMGTLPKRVKIVEVGPRDGLQNEKSIVPTPVKIKLIDMLSEAGLPVIEATSFV 77 + A S++ RV + E+GPRDGLQNE + VPT K+ LI+ L++AG+ IEA SFV Sbjct: 1 MSALDLSTLSASSDRVSLFEMGPRDGLQNEAA-VPTQAKVALIESLADAGVKRIEAGSFV 59 Query: 78 SPKWVPQMADHSDVLKGIQKFPGINYPVLTPNMKGFEEAVAAGAKEVSIFGAASELFTRK 137 SPKWVPQMAD DVL+ I++ G+ Y LTPN+KG E A+ A A EV+IFGAAS+ F+++ Sbjct: 60 SPKWVPQMADSGDVLRQIRRQAGVVYSALTPNVKGLELALDAKASEVAIFGAASQSFSQR 119 Query: 138 NVNCSIEESFQRFDGVMQAARAASISVRGYVSCALGCPYEGKVSPAKVAEVAKKLYSMGC 197 N+NCSIEES +RF +M A+AA+I VRGYVSC LGCPYEG+++ ++VA V++ LY MGC Sbjct: 120 NINCSIEESIERFIPLMDMAKAANIPVRGYVSCVLGCPYEGEIAASEVARVSEILYKMGC 179 Query: 198 YEISLGDTIGVGTPGLMKDMLTAVLHEVPVAALAVHCHDTYGQALANTLVALQMGVSVVD 257 YEISLGDTIGVGTP + ML AV+ VPV LA+H HDTYGQALAN L +GV D Sbjct: 180 YEISLGDTIGVGTPLKARKMLQAVMERVPVEMLALHFHDTYGQALANITACLDLGVRSFD 239 Query: 258 SSVAGLGGCPYAKGASGNLATEDLVYMLTGLGIHTGVNLQKLLEAGDFICQALNRKTSSK 317 +SVAGLGGCPYAKGASGNLA+EDLVYML GLG+ TG++L+KL AG I + LNR SK Sbjct: 240 ASVAGLGGCPYAKGASGNLASEDLVYMLHGLGLKTGIDLEKLALAGFGISKQLNRLNGSK 299 Query: 318 VAQA 321 VA A Sbjct: 300 VANA 303 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: 303 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: 310 Length adjustment: 27 Effective length of query: 298 Effective length of database: 283 Effective search space: 84334 Effective search space used: 84334 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