Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate AZOBR_RS14115 AZOBR_RS14115 (3S)-malyl-CoA thiolesterase
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__azobra:AZOBR_RS14115 Length = 291 Score = 157 bits (396), Expect = 4e-43 Identities = 107/311 (34%), Positives = 153/311 (49%), Gaps = 24/311 (7%) Query: 8 APPARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLD 67 A ARP R L+ PGS EK + AD + LDLED+VAPD KA+ARA I +I Sbjct: 2 AATARPRRSVLYMPGSNTRALEKGRSLPADGLILDLEDAVAPDAKAEARATIKASIAAGG 61 Query: 68 WGRKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERA 127 +G + L VR NGL+TP+ Y D+V A D +++PKV V +A++ RA Sbjct: 62 YGGRELVVRTNGLNTPWGYDDLV---MAASSGADAVLLPKVESPDMVRQAEAVL----RA 114 Query: 128 KGRTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENY 187 G + ++E+ G+ + +EIA +SP+L + +G +D A Sbjct: 115 NGSPDGQTIWCMMETPLGMLNTKEIAGASPKLGGLVMGTSDLAKD--------------- 159 Query: 188 YMLHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVG 247 LH P + + A R +G+ +DG D +DD GF + LG G Sbjct: 160 --LHAAHTRDRLPMLTSLGLCLLAARAYGLAILDGVHLDLNDDAGFGESCVQGRELGFDG 217 Query: 248 KWAIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAE 307 K IHPK +A N F PSE V +A I+ A A A+G+G + GRLV+ ++ A Sbjct: 218 KTLIHPKTIAACNAAFAPSEEEVAQAHRIIQAHAEAVAQGKGVVLVDGRLVENLHVENAR 277 Query: 308 VIVRQAEMISA 318 +V AE I A Sbjct: 278 RLVAMAEAIDA 288 Lambda K H 0.319 0.132 0.394 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: 215 Number of extensions: 11 Number of successful extensions: 4 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: 318 Length of database: 291 Length adjustment: 27 Effective length of query: 291 Effective length of database: 264 Effective search space: 76824 Effective search space used: 76824 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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