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_073040916.1 BUB04_RS14925 2-isopropylmalate synthase
Query= curated2:Q764S0 (337 letters) >NCBI__GCF_900129305.1:WP_073040916.1 Length = 520 Score = 98.6 bits (244), Expect = 3e-25 Identities = 87/277 (31%), Positives = 127/277 (45%), Gaps = 39/277 (14%) Query: 5 AIRIMDTTLRDGSHAIRHRFTKENVRQIVQALDEAGVPVIEVSHGDGLGGSSLQYGMSLV 64 AIRI DTTLRDG + + E ++ + L GV V+E + + Sbjct: 3 AIRIFDTTLRDGEKSPGTVLSVEEKLRLARQLARLGVDVLEAG-----------FPAASE 51 Query: 65 EEMELIEEAAKTSRRAKIAALLLPGIGTKKELQQAKDC--GIQMVRIATQCSEADVSEQH 122 + E + A+ + IAAL P ++ Q A D G RI T + +H Sbjct: 52 RQFEAVRRIAEEVQGPVIAALARPT--HPRDFQAAADALAGAARRRIHTFVPVSPSYRRH 109 Query: 123 F---GLAKELGL------------ETVGFLMMAHMLSP-EELAQQAKLMESYGADIVYIV 166 F L + LGL E V F ++ + +P +++ A+ GA I+ I Sbjct: 110 FLQMDLGEALGLAAKGVELAREKVEDVEFSLVDALRAPLDDVTAMARAAAEAGARIINIA 169 Query: 167 DSAGTMLPQDVIDRVIALKKVLN----VPIGFHAHNNLGLAIGNSLAAIQAGATNIDAST 222 D+ G P +V V A+ KVL+ V + H HN+LGLA+ NSLAA++AGA I + Sbjct: 170 DTVGYATPSEVERLVEAVAKVLDSFDDVHLSIHCHNDLGLAVANSLAAVRAGARQIHCTV 229 Query: 223 RGLGAGSGNTQTEVLVAVL----SRMGIETGIDLFQI 255 G+G +GN E + A+L G ETGI L QI Sbjct: 230 NGIGERAGNAALEEVAAILKARRDHFGCETGIHLDQI 266 Lambda K H 0.318 0.134 0.375 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: 399 Number of extensions: 21 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: 337 Length of database: 520 Length adjustment: 32 Effective length of query: 305 Effective length of database: 488 Effective search space: 148840 Effective search space used: 148840 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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