Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate 3609102 Dshi_2490 Citryl-CoA lyase (RefSeq)
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Dino:3609102 Length = 310 Score = 281 bits (720), Expect = 1e-80 Identities = 146/309 (47%), Positives = 200/309 (64%), Gaps = 11/309 (3%) Query: 12 RPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRK 71 R R +L P S P + +K A SAAD + LDLED+VAP +K QAR N I+A+N +DW K Sbjct: 5 RLQRSELAVPASNPTMIDKAAESAADFVFLDLEDAVAPPEKVQARKNAIQALNDIDWAAK 64 Query: 72 --YLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKG 129 +SVRINGLDT + YRDVVD++EQAGDR+ +++PKVG AD+Y V+A+V E A G Sbjct: 65 GKTVSVRINGLDTHYMYRDVVDIMEQAGDRVHTLLVPKVGVTADLYMVEAMVNQAEMACG 124 Query: 130 RTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYM 189 + E +IE+A G+A+VE IA RL+A+ G AD+AASM +T IGG +Y Sbjct: 125 LETRVGLEALIETALGMANVEAIAQFGGRLEALHFGVADYAASMRARTVNIGGLNPDYP- 183 Query: 190 LHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKW 249 D WH + +V ACR +G+ +DGPFGDFSD +G+ A ARR+A LG GKW Sbjct: 184 --------GDQWHASITRMVIACRAYGLRAIDGPFGDFSDPDGYMAGARRAAALGCEGKW 235 Query: 250 AIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEVI 309 AIHP Q+ +AN+VF+P E V++A I+ + A+A G+GA G+++D AS K A + Sbjct: 236 AIHPSQIEMANDVFSPPEAEVSKAHRIIEELRNAEAAGKGAASLDGKMIDAASEKMARNV 295 Query: 310 VRQAEMISA 318 + A I+A Sbjct: 296 IDTANAIAA 304 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: 271 Number of extensions: 8 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: 310 Length adjustment: 27 Effective length of query: 291 Effective length of database: 283 Effective search space: 82353 Effective search space used: 82353 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