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 GFF1023 Psest_1056 2-isopropylmalate synthase, bacterial type
Query= curated2:B8G187 (333 letters) >FitnessBrowser__psRCH2:GFF1023 Length = 514 Score = 73.9 bits (180), Expect = 8e-18 Identities = 74/254 (29%), Positives = 101/254 (39%), Gaps = 15/254 (5%) Query: 3 KVKIFDLTLRDGSHAKSHQFTPEQMAVLAEQIDSTGVAAIEFGHGNGLGGSALQYGFAAA 62 +V IFD TLRDG + T E+ +A ++ V IE G G A Sbjct: 6 RVIIFDTTLRDGEQSPGASMTAEEKLRIARALERLKVDVIEAGFAIASPGDFAAVKLVAD 65 Query: 63 TDREYMEAVAPVVKNADL--SIIILPGV--GTRHELHLAKEFGAKYARMCTQITEVDIAE 118 ++ +AD+ + L G G H +Y V+ A Sbjct: 66 NIKDSTVCSLARAVDADIERAAEALAGANSGRIHTFIATSPIHMQYKLRMQPDQVVEQAV 125 Query: 119 QHIKMAKQLGMIPIAVLPCAGIIPVKDTVRYTQMAESYGAEVIYLLDGGGYQLPEQ---- 174 + +K A+ L AG + R + A GA I + D GY +P Q Sbjct: 126 RAVKKARSLCADVEFSCEDAGRSEIDFLCRIIKAAIDAGARTINIPDTVGYAIPHQYADT 185 Query: 175 ---TYERIAAMKKAVDVPIGFHGHNNLQLAVANSKAAVEAGAEYIDCCLKGFGAGAGNCP 231 ERI KAV H HN+L LAVANS AAV AGA ++C + G G AGN Sbjct: 186 IRQLLERIPNADKAV---FSVHCHNDLGLAVANSLAAVVAGARQVECTINGLGERAGNAA 242 Query: 232 -TEIFAAVMDRMEI 244 EI A+ R ++ Sbjct: 243 LEEIVMAIKTRQDL 256 Lambda K H 0.322 0.137 0.404 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: 344 Number of extensions: 20 Number of successful extensions: 3 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: 333 Length of database: 514 Length adjustment: 31 Effective length of query: 302 Effective length of database: 483 Effective search space: 145866 Effective search space used: 145866 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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