Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate 14753 b0616 citrate lyase beta chain (acyl lyase subunit) (VIMSS)
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__Keio:14753 Length = 302 Score = 155 bits (393), Expect = 9e-43 Identities = 103/301 (34%), Positives = 162/301 (53%), Gaps = 18/301 (5%) Query: 8 RRALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGILE 67 RR++L++PG++ + S AD + +DLEDSV +K AR +V AL P I E Sbjct: 14 RRSMLFVPGANAAMVSNSFIYPADALMFDLEDSVALREKDTARRMVYHALQHPLYRDI-E 72 Query: 68 RAVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHTLSQLPLSQSA 127 VR+N++DS + DL V++ + +PK ++A D+ + I L + ++ Sbjct: 73 TIVRVNALDSEWGVNDLEAVVRG-GADVVRLPKTDTAQDVLDIEKEI------LRIEKAC 125 Query: 128 SRPPIS--LLALVESAKSLTNLSQICAASPLLQGLIFAAEDFALDLSLTRTPALTEFLFA 185 R P S LLA +ES +T +I AS L G+ AED+ +L R+P TE LFA Sbjct: 126 GREPGSTGLLAAIESPLGITRAVEIAHASERLIGIALGAEDYVRNLRTERSPEGTELLFA 185 Query: 186 RSAIATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHPSQV 245 R +I AAR+A + + D V + ++ G QE K LGF+GK I+P Q+ Sbjct: 186 RCSILQAARSAGIQA-FDTVYSDANNEAG-------FLQEAAHIKQLGFDGKSLINPRQI 237 Query: 246 STVQQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIVKKADAC 305 + ++ P +EV A RV A + A++ G G +L+GKM+D PV ++AR ++ +A+ Sbjct: 238 DLLHNLYAPTQKEVDHARRVVEAAEAAAREGLGVVSLNGKMVDGPVIDRARLVLSRAELS 297 Query: 306 G 306 G Sbjct: 298 G 298 Lambda K H 0.316 0.130 0.369 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: 198 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: 322 Length of database: 302 Length adjustment: 27 Effective length of query: 295 Effective length of database: 275 Effective search space: 81125 Effective search space used: 81125 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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