Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate H281DRAFT_02940 H281DRAFT_02940 beta-methylmalyl-CoA/L-malyl-CoA lyase (EC 4.1.3.24)
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Burk376:H281DRAFT_02940 Length = 310 Score = 180 bits (457), Expect = 3e-50 Identities = 112/307 (36%), Positives = 164/307 (53%), Gaps = 8/307 (2%) Query: 12 RPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRK 71 R R L P + + E A S+AD + LDLED+V K A + AIN LDWG K Sbjct: 2 RVTRTFLAVPAHQRRMVESAARSSADAVFLDLEDAVPQAQKETALLGAVAAINELDWGHK 61 Query: 72 YLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRT 131 +SVR+N + +V LL A RLD +++PKV C ADV V L+ ++ R Sbjct: 62 AVSVRVNVPASATIETEVARLLTDA-PRLDTLLVPKVECTADVDRVVGLIKL--HSQRRR 118 Query: 132 KPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYML- 190 P+ EV+IE+A G+ + E+IAA S ++++ G DF+AS+G + IG + Y + Sbjct: 119 TPIGLEVMIETALGLVNCEQIAAHSELIESLHFGVGDFSASIGAKGVDIGLSHPGYRLTA 178 Query: 191 HDGQKHWS----DPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMV 246 Q +S D W + I+ A R H + +DGP G F D + A A ++AT+G Sbjct: 179 RSAQGDYSSTALDMWAYPMMRILVAARAHRLRAIDGPCGAFHDSDLTSALAVKAATMGFD 238 Query: 247 GKWAIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQA 306 GK IHP Q+ F P+ + EA+ ++AAM A+ G GA G+LVD A+I+ A Sbjct: 239 GKQVIHPCQIDTTLRAFVPTADELCEAQRVIAAMTEAEREGRGAVQVDGKLVDYANIRMA 298 Query: 307 EVIVRQA 313 + +V A Sbjct: 299 QRVVAMA 305 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: 204 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: 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