Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate YP_004134379.1 Mesci_6210 citryl-CoA lyase
Query= BRENDA::Q9I562 (275 letters) >NCBI__GCF_000185905.1:YP_004134379.1 Length = 270 Score = 169 bits (428), Expect = 6e-47 Identities = 115/264 (43%), Positives = 149/264 (56%), Gaps = 9/264 (3%) Query: 10 LFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTPEARVLVRINA 69 LFVP +RPER KA SGAD VI+DLEDAV G K AR + + A ++VRINA Sbjct: 11 LFVPGSRPERFAKADNSGADAVILDLEDAVAPGDKDRAREVVVAYAAMLKSA-IVVRINA 69 Query: 70 AEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAA--VASGKPVWPIVESARGLAALG 127 A P H D+ R GV ++LPK E + A +A V +VESA GLA L Sbjct: 70 AGTPWHEADIDAVRRLEGV-SVMLPKAERPEDIADMAKHMARSVSVIALVESAVGLANLP 128 Query: 128 EIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTRLAGLAPPLDGVYP 187 I A +G+ ++FGS+D +LDL G L AR ++ ++R AG A P+DGV Sbjct: 129 AILATSGIVAVAFGSVDFSLDL----GCAHDRLTLLAARNEIVWRSRAAGRAAPIDGVTT 184 Query: 188 AIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWARRVAEAGASGAG 247 + + + R A MGFGG L IHP Q+EPI PS E+ WAR + A +SG Sbjct: 185 DLSSPEITEDDARHAMKMGFGGKLAIHPRQIEPIRVAFRPSDKEIIWARDIVGAASSGEA 244 Query: 248 VFVVDGEMVDAPVLGRARRLLERA 271 V V+GEMVD PV+ RAR++L RA Sbjct: 245 V-QVNGEMVDRPVIERARQVLRRA 267 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: 188 Number of extensions: 13 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: 275 Length of database: 270 Length adjustment: 25 Effective length of query: 250 Effective length of database: 245 Effective search space: 61250 Effective search space used: 61250 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 Sep 24 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