Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate RR42_RS24325 RR42_RS24325 citryl-CoA lyase
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Cup4G11:RR42_RS24325 Length = 307 Score = 233 bits (593), Expect = 6e-66 Identities = 126/307 (41%), Positives = 183/307 (59%), Gaps = 11/307 (3%) Query: 10 PARPNRCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWG 69 P R R QL PGS + EK A+S AD + LDLED+VAP+ K AR II+A+N LDW Sbjct: 8 PTRRRRVQLATPGSSEKMMEKAASSNADHVFLDLEDAVAPNQKVAARKKIIDALNHLDWQ 67 Query: 70 RKYLSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKG 129 K VRIN L T + Y D+++++E AG LD IM+ KV ADV D L++ +E+ Sbjct: 68 GKVRCVRINDLSTEYAYEDIIEIVEGAGHNLDTIMMTKVNGPADVLFADRLLSMMEKKLR 127 Query: 130 RTKPLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYM 189 + + E +IE G+ +VE IA S+ RL+ + G DF+A+MG+ IG T Sbjct: 128 LPRRIGLEALIEEVPGLQNVEAIAQSTERLECLIFGMGDFSAAMGVNLESIGNT------ 181 Query: 190 LHDGQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKW 249 + D WH+A+ ++ ACR I PVDGP+ +F D EG+R + RR+ TLG VGKW Sbjct: 182 ----GGYPGDIWHYARFRLIMACRAADIDPVDGPWAEFRDSEGYRNECRRAGTLGCVGKW 237 Query: 250 AIHPKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIK-QAEV 308 AIHP Q+ +A F+P V +AR++ +A A+A G GA G +VD+A+++ Sbjct: 238 AIHPSQIEIALAEFSPDPAKVAQARKLESAYVQAEAEGLGAINVDGVMVDVATMRLLRNT 297 Query: 309 IVRQAEM 315 ++++A+M Sbjct: 298 VLKKAQM 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: 246 Number of extensions: 13 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: 318 Length of database: 307 Length adjustment: 27 Effective length of query: 291 Effective length of database: 280 Effective search space: 81480 Effective search space used: 81480 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