Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate Ga0059261_0570 Ga0059261_0570 Citrate lyase beta subunit
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Korea:Ga0059261_0570 Length = 273 Score = 130 bits (326), Expect = 5e-35 Identities = 101/302 (33%), Positives = 147/302 (48%), Gaps = 41/302 (13%) Query: 15 RCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANII-----EAINGLDWG 69 R +LF P SRP F+K ASAAD ++ DLEDSV D KA ARA + +A+ G Sbjct: 2 RSKLFVPCSRPEFFDKALASAADALSFDLEDSVPADGKAAARARLAAFLASDAVRGTP-- 59 Query: 70 RKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKG 129 K + VR+N P + D+ + R+D I +PK+ A V A A Sbjct: 60 -KRIIVRVNDPAGPDFTADIEAI---RNCRIDLINLPKIEDAPGVIAA---------ANA 106 Query: 130 RTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYM 189 + + V IE+ + IA + PR+ + +G D A++G Sbjct: 107 TGRAIGLLVNIETPHALMRAAAIANAHPRVAGLQVGLNDLFATLGADR------------ 154 Query: 190 LHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKW 249 D + + W A A GI DG + D +D+ GFRA+A + LG +GK Sbjct: 155 -RDPRAVHAALWQIRLGAAAA-----GIFAYDGAWPDLADEAGFRAEAGMAQALGYMGKS 208 Query: 250 AIHPKQVALANEVFTPS-ETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEV 308 IHP+Q+A ANEVF + + AV AR ++AA AA G GA +++GR+VD I QA+ Sbjct: 209 CIHPRQIAAANEVFDHTLDRAV--ARRLVAAAQAAALDGRGAFLFEGRMVDRPMIAQAQA 266 Query: 309 IV 310 ++ Sbjct: 267 LL 268 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: 209 Number of extensions: 10 Number of successful extensions: 3 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: 273 Length adjustment: 26 Effective length of query: 292 Effective length of database: 247 Effective search space: 72124 Effective search space used: 72124 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