Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate WP_011427687.1 RHE_RS23145 CoA ester lyase
Query= BRENDA::Q9I562 (275 letters) >NCBI__GCF_000092045.1:WP_011427687.1 Length = 278 Score = 143 bits (361), Expect = 4e-39 Identities = 108/278 (38%), Positives = 140/278 (50%), Gaps = 14/278 (5%) Query: 6 VRSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTP-EARVL 64 +RS LFVP RPER KALASGAD VI+DLED+V K +AR ++ F+ P E ++L Sbjct: 3 LRSLLFVPGDRPERFAKALASGADAVILDLEDSVAPPNKPKARDSVHEFVQRRPGETKLL 62 Query: 65 VRINAAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAAVASGKPVWPIVESARGLA 124 +RIN P DLA GL+LPK E AA V A A + + + + Sbjct: 63 IRINPLASPEFEGDLAALSG-LQPFGLMLPKAEGAASVLKLASALAATILILPIATETPS 121 Query: 125 ALGEIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARY--------ALLLQTRLA 176 A+ EI + V G A DL G+ A + G RY +L L A Sbjct: 122 AIFEIGSYREVSDNLCGLTWGAEDLPAAIGATTARRTDG--RYTPPYELARSLTLFAAHA 179 Query: 177 GLAPPLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWAR 236 P +D VYP ++ GL V AR GF G++ IHPSQVE I+ P E+ WA Sbjct: 180 AAVPAIDTVYPDFRDLNGLRAYVGRARRDGFSGMMAIHPSQVETINHAFTPDAFEIAWAE 239 Query: 237 RVAEAGASG--AGVFVVDGEMVDAPVLGRARRLLERAG 272 +V A A+ AGV +DG M+D P L A R+L AG Sbjct: 240 KVTAAFAASPDAGVIQLDGRMLDLPHLKLAHRILASAG 277 Lambda K H 0.320 0.137 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: 174 Number of extensions: 11 Number of successful extensions: 5 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: 275 Length of database: 278 Length adjustment: 25 Effective length of query: 250 Effective length of database: 253 Effective search space: 63250 Effective search space used: 63250 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: 47 (22.7 bits)
This GapMind analysis is from Apr 09 2024. 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