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_012407682.1 NPUN_RS04705 2-isopropylmalate synthase
Query= curated2:A5D523 (339 letters) >NCBI__GCF_000020025.1:WP_012407682.1 Length = 534 Score = 78.2 bits (191), Expect = 4e-19 Identities = 79/259 (30%), Positives = 115/259 (44%), Gaps = 35/259 (13%) Query: 7 IRIMDTTLRDGMHAMAHQFTPEQMAQVAAALDEAGVDVIEVTHGDGLAGSSFQYGFAAAT 66 I I DTTLRDG ++ +A L GVD+IE AG + FA+ Sbjct: 8 IIIFDTTLRDGEQCPGATLNIDEKLVIAKQLARLGVDIIE-------AG----FAFASPG 56 Query: 67 DEEYLEAVAPVLKKAKLAALILPGIGTCRDMRMAVQA---GVKVFRIATHVTEADISEEH 123 D E + +A ++ + D+ A +A VK RI T ++ +DI E+ Sbjct: 57 DFEAVSKIAQIVGTENGPVICSLARAIKADIEAAAEALKPAVKG-RIHTFISTSDIHLEY 115 Query: 124 ---------MGLAKEMGAEVVGFL-------MMSHTVGKEKIAEQAKLMESYGADVVYMV 167 + +A+EM A F+ M + E + + + + GA V + Sbjct: 116 QLRKSRAEVLAIAEEMVAYAKSFMTDVEFSPMDAARSDPEFLYQVLERTIAAGATTVNIP 175 Query: 168 DSAGAMIPPEVTEKI-GYLKEVLNIP---VGFHAHNNLGLAVGNTLAAVAAGATAVDGTL 223 D+ G P E I G ++ V NI + H HN+LGLAV N L AV GA ++ T+ Sbjct: 176 DTVGYTTPSEFGAIIKGIIENVPNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTI 235 Query: 224 RGLGAGAGNTSTEVLVAAL 242 G+G AGN S E LV AL Sbjct: 236 NGIGERAGNASLEELVMAL 254 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: 331 Number of extensions: 16 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: 339 Length of database: 534 Length adjustment: 32 Effective length of query: 307 Effective length of database: 502 Effective search space: 154114 Effective search space used: 154114 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: 51 (24.3 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