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_012113349.1 XAUT_RS06660 2-isopropylmalate synthase
Query= curated2:B1VRH5 (340 letters) >NCBI__GCF_000017645.1:WP_012113349.1 Length = 527 Score = 65.1 bits (157), Expect = 4e-15 Identities = 74/286 (25%), Positives = 113/286 (39%), Gaps = 45/286 (15%) Query: 3 QVVIHDPTLRDGQHAVHHRLGLTELRRYAEAADAARVPVVEVGHGNGLGASSLQVGLAAA 62 +VVI D TLRDG+ + E A D V V+E G +A+ Sbjct: 19 RVVIFDTTLRDGEQCPGASMTFEEKLEVAALLDEMGVDVIEAGFP-----------IASI 67 Query: 63 TDDAMLSTVREALRHSRLGTFMLPGWGTSDDLRRAISHGVDVFRVGVHATEASLAEHHLG 122 D ++ + +++ + D A+ H R G T S + H+ Sbjct: 68 GDFESVAEIARRTQNATVAGLSRAALNDIDRCAEAVKHA----RRGRIHTFLSTSPVHMK 123 Query: 123 FLRDAGAEAHCVLMM---------SHMASPGELAEQAAR------------AVGYGAQAV 161 + + H VL M +H+ +E R A+ GA + Sbjct: 124 YKLQK--QPHEVLEMVVASVTRARNHVEDVEWSSEDGTRTEIDFLCRCVEAAIKAGATTI 181 Query: 162 GIMDSAGHFLPPDVTARIGAIVEAV-GTVPVIF--HGHNNLGMAVANSVAAAEAGARIID 218 I D+ G+ P + A ++E V + IF H H++LGMAVANS+A GAR I+ Sbjct: 182 NIPDTVGYTTPAEYEALFRTVIERVPNSDKAIFSVHCHDDLGMAVANSLAGLAGGARQIE 241 Query: 219 GCARGFGAGAGNTQLEVLVPVLERSG----FATGIDLYALLDAADL 260 G G AGN LE +V +E + +GI+ L A+ L Sbjct: 242 CTVNGIGERAGNAALEEVVMAIETRSDVLPYRSGINTKMLTRASKL 287 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: 320 Number of extensions: 10 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: 2 Length of query: 340 Length of database: 527 Length adjustment: 32 Effective length of query: 308 Effective length of database: 495 Effective search space: 152460 Effective search space used: 152460 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 Apr 09 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