Align malyl-CoA lyase (EC 4.1.3.24); (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate WP_043745375.1 AMB_RS20125 CoA ester lyase
Query= BRENDA::S5N020 (348 letters) >NCBI__GCF_000009985.1:WP_043745375.1 Length = 349 Score = 518 bits (1334), Expect = e-152 Identities = 247/346 (71%), Positives = 285/346 (82%) Query: 3 KLAHNFYKPLAIGAPEPIRELPVRPERVVHFFPPHVEKIRARIPEVAKQVDVLCGNLEDA 62 K F++PLAIGAP P RELPVR ER++HFFPPH EK+RA+ E+ K VDVL GNLEDA Sbjct: 4 KPPRKFFEPLAIGAPAPYRELPVRLERMIHFFPPHNEKMRAKAAEMGKNVDVLLGNLEDA 63 Query: 63 IPMDAKEAARNGFIEVVKATDFGDTALWVRVNALNSPWVLDDIAEIVAAVGNKLDVIMIP 122 IP DAK+AAR GF+EV KA D +T LW RVN LNSPW LDD+ IV GNK+DV+M+P Sbjct: 64 IPADAKDAARAGFVEVAKAWDNPNTGLWTRVNCLNSPWFLDDMNAIVGEAGNKVDVVMLP 123 Query: 123 KVEGPWDIHFVDQYLALLEARHQIKKPILIHALLETAQGMVNLEEIAGASPRMHGFSLGP 182 KVEGPWDIH++DQ LA LEA+H +K+PI+IHA+LETA G+ N+ I ASPRMHG SLGP Sbjct: 124 KVEGPWDIHYLDQLLAQLEAKHGVKRPIMIHAILETALGVENVAAICQASPRMHGISLGP 183 Query: 183 ADLAASRGMKTTRVGGGHPFYGVLADPQEGQAERPFYQQDLWHYTIARMVDVAVAHGLRA 242 ADLAASRGMKTTRVGGGHPFYGVL D EG+A R +QQDLWHYT+A+MVD + G++A Sbjct: 184 ADLAASRGMKTTRVGGGHPFYGVLEDAAEGKAGRTLFQQDLWHYTVAKMVDACQSAGIKA 243 Query: 243 FYGPFGDIKDEAACEAQFRNAFLLGCTGAWSLAPNQIPIAKRVFSPDVNEVLFAKRILEA 302 FYGPFGD D+AACEAQFRNAFLLGC G WSL P QI IAK+VFSPDV EVLFAK+ILEA Sbjct: 244 FYGPFGDFSDDAACEAQFRNAFLLGCAGGWSLHPKQIDIAKKVFSPDVAEVLFAKKILEA 303 Query: 303 MPDGSGVAMIDGKMQDDATWKQAKVIVDLARMIAKKDPDLAQAYGL 348 MPDG+G MIDGKMQDDATWKQAKV+VDLA+ +A KDP +AQAYGL Sbjct: 304 MPDGTGAVMIDGKMQDDATWKQAKVMVDLAKAVAAKDPAMAQAYGL 349 Lambda K H 0.322 0.139 0.425 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: 506 Number of extensions: 18 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: 348 Length of database: 349 Length adjustment: 29 Effective length of query: 319 Effective length of database: 320 Effective search space: 102080 Effective search space used: 102080 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 (21.9 bits) S2: 49 (23.5 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