Align malyl-CoA lyase (EC 4.1.3.24); (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate CCNA_03094 CCNA_03094 citrate lyase beta subunit
Query= BRENDA::S5N020 (348 letters) >FitnessBrowser__Caulo:CCNA_03094 Length = 352 Score = 473 bits (1216), Expect = e-138 Identities = 229/348 (65%), Positives = 268/348 (77%), Gaps = 2/348 (0%) Query: 3 KLAHNFYKPLAIGAPEPIRELPVRPERVVHFFPPHVEKIRARIPEVAKQVDVLCGNLEDA 62 K F+KPLAIGAP P RELP R ER++HF PPH+EK+RA++PE+A VDV+ NLEDA Sbjct: 5 KTPRGFFKPLAIGAPTPYRELPARVERMIHFVPPHLEKVRAKLPEIAPTVDVILANLEDA 64 Query: 63 IPMDAKEAARNGFIEVVKATDFG--DTALWVRVNALNSPWVLDDIAEIVAAVGNKLDVIM 120 IP DAK AA G + + + DF W R+N LNSPW LD+IA IV G+K+DVIM Sbjct: 65 IPADAKGAALAGLVAMSREVDFKALGVGFWTRINCLNSPWHLDEIATIVEKAGDKIDVIM 124 Query: 121 IPKVEGPWDIHFVDQYLALLEARHQIKKPILIHALLETAQGMVNLEEIAGASPRMHGFSL 180 +PKVEGPWDI ++DQ LA LEA+H + +PIL+HA+LETA+G++N+E IA ASPRM G SL Sbjct: 125 VPKVEGPWDIFYMDQLLASLEAKHGVTRPILLHAILETAEGVMNVEAIAAASPRMQGISL 184 Query: 181 GPADLAASRGMKTTRVGGGHPFYGVLADPQEGQAERPFYQQDLWHYTIARMVDVAVAHGL 240 GPADLAASR MKTTRVGGGHP Y V+ DP + R QQDLWHYT A+MVD AHG+ Sbjct: 185 GPADLAASRAMKTTRVGGGHPGYRVIEDPHADGSARVSVQQDLWHYTFAKMVDACAAHGI 244 Query: 241 RAFYGPFGDIKDEAACEAQFRNAFLLGCTGAWSLAPNQIPIAKRVFSPDVNEVLFAKRIL 300 + FYGPFG I D ACE QFRNAFL+GC GAWSL P+QI IAKRVFSPD EV FAK+IL Sbjct: 245 KPFYGPFGAIDDPVACEQQFRNAFLMGCAGAWSLHPSQIEIAKRVFSPDPAEVAFAKKIL 304 Query: 301 EAMPDGSGVAMIDGKMQDDATWKQAKVIVDLARMIAKKDPDLAQAYGL 348 EAMPDG+GVAMIDGKMQDDATWKQAKV+VD AR IA KD + A YGL Sbjct: 305 EAMPDGTGVAMIDGKMQDDATWKQAKVMVDCARQIAGKDAEYAGLYGL 352 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: 465 Number of extensions: 24 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: 348 Length of database: 352 Length adjustment: 29 Effective length of query: 319 Effective length of database: 323 Effective search space: 103037 Effective search space used: 103037 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