Align 4-hydroxy-2-oxovalerate aldolase; HOA; EC 4.1.3.39; 4-hydroxy-2-keto-pentanoic acid aldolase; 4-hydroxy-2-oxopentanoate aldolase (uncharacterized)
to candidate WP_012102499.1 CKL_RS10580 2-isopropylmalate synthase
Query= curated2:A5D523 (339 letters) >NCBI__GCF_000016505.1:WP_012102499.1 Length = 514 Score = 74.3 bits (181), Expect = 6e-18 Identities = 79/259 (30%), Positives = 115/259 (44%), Gaps = 36/259 (13%) Query: 6 EIRIMDTTLRDGMHAMAHQFTPEQMAQVAAALDEAGVDVIEVTHGDGLAGSSFQYGFAAA 65 +I I DTTLRDG +A L + VDVIE GF A Sbjct: 4 KIYIFDTTLRDGEQTPKVSLNINDKITIAKQLQKLSVDVIEA-------------GFPKA 50 Query: 66 TDEEYLEAVAPVLKKAKLAALILPGIGTCRDMRMAVQA--GVKVFRIATHVTEADISEEH 123 + ++ EAV + + + ++ + D+ A +A G RI + +DI EH Sbjct: 51 SHGDF-EAVKAIAESIQGPVIVGLARASKEDIDCAWEALKGSLKPRIHIFLATSDIHMEH 109 Query: 124 MGLAK-----EMGAEVVGF---LMMSHTVGKEKIAEQA-----KLMESY---GADVVYMV 167 K + A++V + L S E K++E+ GADVV + Sbjct: 110 KLKMKPEEVLKRAADMVRYAKGLCPSIEFSPEDATRTRPEFLYKVLEAVIEAGADVVNIP 169 Query: 168 DSAGAMIPPEVTEKIGYLKE-VLNIP---VGFHAHNNLGLAVGNTLAAVAAGATAVDGTL 223 D+ G P E I +KE V NI + H HN+LGLAV N+LAA+ +GA V+ + Sbjct: 170 DTVGYTTPVEYGAFIRGIKENVKNIEDAIISVHCHNDLGLAVANSLAAIESGAEQVECAI 229 Query: 224 RGLGAGAGNTSTEVLVAAL 242 GLG AGN + E +V A+ Sbjct: 230 NGLGERAGNAALEEIVMAI 248 Lambda K H 0.319 0.134 0.373 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: 354 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: 339 Length of database: 514 Length adjustment: 31 Effective length of query: 308 Effective length of database: 483 Effective search space: 148764 Effective search space used: 148764 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: 50 (23.9 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