Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate 3607636 Dshi_1045 HpcH/HpaI aldolase (RefSeq)
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Dino:3607636 Length = 281 Score = 137 bits (345), Expect = 3e-37 Identities = 105/297 (35%), Positives = 142/297 (47%), Gaps = 33/297 (11%) Query: 12 RPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIE-AINGLDWGR 70 R R LF P +RPA+F+K S AD + LDLED+V PD KA ARA +E + D G Sbjct: 5 RALRSFLFAPANRPAIFDKARGSGADAVCLDLEDAVPPDQKATARAPALEWLVQAADPG- 63 Query: 71 KYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGR 130 VRINGL TP D+ L A +++PKVG AA+V A E + Sbjct: 64 --CGVRINGLRTPEGLADIAALC-AARPGPGFVLLPKVGAAAEVQ------IAAEALEAA 114 Query: 131 TKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYML 190 LS +IE+A G+ V IA +S RL + GA D AA +G+ Sbjct: 115 GSDLSLGALIETAEGLEAVARIARASDRLSFLLFGAVDLAADLGV--------------- 159 Query: 191 HDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWA 250 DG +A+ +V A R G +D P DF D A R+ G GK A Sbjct: 160 -DGS---DAALAYARGRVVHAGRAAGRPVLDVPALDFRDLAAVGQAAARAKAHGFSGKAA 215 Query: 251 IHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAE 307 IHP +A+ N+ FTP + EA+E+LA +A+ G V G+L++ I+ E Sbjct: 216 IHPSNIAVINDAFTPGAEEIAEAQEVLALYEASP---NGLAVRNGKLIEKPVIRAME 269 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: 234 Number of extensions: 10 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: 281 Length adjustment: 27 Effective length of query: 291 Effective length of database: 254 Effective search space: 73914 Effective search space used: 73914 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