Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate 17296 b3225 N-acetylneuraminate lyase (NCBI)
Query= BRENDA::Q6G468 (294 letters) >FitnessBrowser__Keio:17296 Length = 297 Score = 99.8 bits (247), Expect = 7e-26 Identities = 62/205 (30%), Positives = 113/205 (55%), Gaps = 6/205 (2%) Query: 2 LKGAVTALITPFDDNGAIDEKAFCNFVEWQITQGINGVSPVGTTGESPTLTHEEHKRIIE 61 L+G + AL+TPFD A+D+ + V++ I QGI+G+ G+TGE+ + E ++++E Sbjct: 5 LRGVMAALLTPFDQQQALDKASLRRLVQFNIQQGIDGLYVGGSTGEAFVQSLSEREQVLE 64 Query: 62 LCVEQVAKRVPVVAGAGSNSTSEAVELAKHAEKAGADAVLVVTPYYNRPNQRGLYTHFSS 121 + E+ ++ ++A G ST+E+ +LA A++ G DAV VTP+Y + H+ + Sbjct: 65 IVAEEAKGKIKLIAHVGCVSTAESQQLAASAKRYGFDAVSAVTPFYYPFSFEEHCDHYRA 124 Query: 122 IA-KAISIPIIIYNIPSRSVIDMAVETMRDLCRDFKNIIGVKDATGKIERASEQREKCGK 180 I A +P+++YNIP+ S + + ++ + L + +K +G + + EQ + Sbjct: 125 IIDSADGLPMVVYNIPALSGVKLTLDQINTLV-TLPGVGALKQTSGDLYQ-MEQIRREHP 182 Query: 181 DFVQLSGDD---CTALGFNAHGGVG 202 D V +G D + L A GG+G Sbjct: 183 DLVLYNGYDEIFASGLLAGADGGIG 207 Lambda K H 0.318 0.134 0.394 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: 175 Number of extensions: 7 Number of successful extensions: 1 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: 294 Length of database: 297 Length adjustment: 26 Effective length of query: 268 Effective length of database: 271 Effective search space: 72628 Effective search space used: 72628 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: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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