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_011841500.1 RSPH17029_RS10985 homocitrate synthase
Query= curated2:A5D523 (339 letters) >NCBI__GCF_000015985.1:WP_011841500.1 Length = 391 Score = 96.3 bits (238), Expect = 1e-24 Identities = 100/331 (30%), Positives = 145/331 (43%), Gaps = 53/331 (16%) Query: 7 IRIMDTTLRDGMHAMAHQFTPEQMAQVAAALDEAGVDVIEVTHGDGLAGSSFQYGFAAAT 66 + + DTTLRDG FT + +A AL AGV +EV G A Sbjct: 19 VALCDTTLRDGEQTAGVAFTRAEKRAIAEALQAAGVAEVEV-------------GVPAMG 65 Query: 67 DEEY--LEAVAPVLKKAKLAALILPGIGTCR----DMRMAVQAGVKVFRIATHVTEADIS 120 +EE + AVA VLK A + CR D+ A + GV I V+E IS Sbjct: 66 EEERADIRAVAAVLKTAA-------PVVWCRLRAEDLAAAQRTGVVRLHIGVPVSERQIS 118 Query: 121 EEHMGLAKEMGAEVVGFLMMSHT-------VGKEK--------IAEQAKLMESYGADVVY 165 + +G + V L+ + + VG E +AE A + GA Sbjct: 119 AK-LGKDAAWVRDKVEKLVRAASWAGHKVSVGAEDASRADPFFLAEIAHVAAEAGAIRFR 177 Query: 166 MVDSAGAMIPPEVTEKIGYLKEVLNIPVGFHAHNNLGLAVGNTLAAVAAGATAVDGTLRG 225 + D+ G + P E +G + +PV FH HN+LG+A N+LAA AGA+ + T+ G Sbjct: 178 ISDTLGVLDPFAAHELVGRVVTRCPLPVEFHGHNDLGMATANSLAAARAGASHLSVTVNG 237 Query: 226 LGAGAGNTSTEVLVAALKKAGYQVGVDLYKIMDAATVLEPMMRRP----QVIDNASIILG 281 LG AGN + E + AAL+ AG GV L ++ + ++ RP + I + Sbjct: 238 LGERAGNAALEEVAAALEAAGRATGVALGQLCALSELVARASGRPLSPQKPIVGEGVFTH 297 Query: 282 YAGVYSSFLLH---TYRAA----ERFGLDPR 305 G++ L+ TY +A ERFG R Sbjct: 298 ECGIHVDGLMKDRATYESADLRPERFGRSHR 328 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: 259 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: 391 Length adjustment: 29 Effective length of query: 310 Effective length of database: 362 Effective search space: 112220 Effective search space used: 112220 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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