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 3607175 Dshi_0596 2-isopropylmalate synthase (RefSeq)
Query= curated2:B1VRH5 (340 letters) >FitnessBrowser__Dino:3607175 Length = 525 Score = 70.1 bits (170), Expect = 1e-16 Identities = 80/258 (31%), Positives = 110/258 (42%), Gaps = 34/258 (13%) Query: 3 QVVIHDPTLRDGQHAVHHRLGLTELRRYAEAADAARVPVVEVG-----HGNGLGAS---- 53 +V+I D TLRDG+ + + E A D V ++E G G+ S Sbjct: 9 RVLIFDTTLRDGEQSPGATMTHDEKLEIAALLDEMGVDIIEAGFPIASDGDFAAVSEIAK 68 Query: 54 ----SLQVGLAAAT---DDAMLSTVREALRHSRLGTFMLPGWGTSDDLRRAISH-GVDVF 105 S+ GLA A D VR A R R+ TF+ GTS L RAI + +D Sbjct: 69 NSVNSVICGLARANFKDIDRCWEAVRHA-RQPRIHTFI----GTS-PLHRAIPNLTMDEM 122 Query: 106 RVGVHATEASLAEHHLGFLRDAGAEAHCVLMMSHMASPGELAEQAARAVGYGAQAVGIMD 165 +H T + R+ M + L A+ GA + I D Sbjct: 123 ADRIHDT--------VTHARNLCDNVQWSPMDATRTEYDYLCRVIEIAIKAGATTINIPD 174 Query: 166 SAGHFLP---PDVTARIGAIVEAVGTVPVIFHGHNNLGMAVANSVAAAEAGARIIDGCAR 222 + G+ P D+ AR+ A V V H HN+LGMA AN++AA +AGAR ++ Sbjct: 175 TVGYTAPRESADLIARLIADVPGAEDVTFATHCHNDLGMATANALAAVDAGARQVECTIN 234 Query: 223 GFGAGAGNTQLEVLVPVL 240 G G AGNT LE +V L Sbjct: 235 GLGERAGNTALEEVVMAL 252 Lambda K H 0.320 0.135 0.393 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: 328 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 340 Length of database: 525 Length adjustment: 32 Effective length of query: 308 Effective length of database: 493 Effective search space: 151844 Effective search space used: 151844 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 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