Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Echvi_1276 Echvi_1276 Dihydrodipicolinate synthase/N-acetylneuraminate lyase
Query= SwissProt::Q57695 (289 letters) >FitnessBrowser__Cola:Echvi_1276 Length = 308 Score = 152 bits (385), Expect = 7e-42 Identities = 91/295 (30%), Positives = 165/295 (55%), Gaps = 11/295 (3%) Query: 2 FKGVYPAIITPFKNK-EVDFDGLEENINFLIENGVSGIVAVGTTGESPTLSHEEHKKVIE 60 F+G+ P +ITP ++ ++D GLE IN +I GV G+ +GTTGES +LS++ ++++ Sbjct: 11 FRGIVPPMITPLADENQLDIPGLERLINHIIAGGVHGLFILGTTGESTSLSYDIRHELVK 70 Query: 61 KVVDVVNGRVQVIAGAGSNCTEEAIELSVFAEDVGADAVLSITPYYNKPTQEGLRKHFGK 120 + +VNGRV V+ G E++ L+ A GA AV++ PYY Q L +++ Sbjct: 71 RTCAIVNGRVPVLVGITDTAATESLRLADTAAKEGAAAVVAAPPYYFSLGQPELIEYYEY 130 Query: 121 VAESINLPIVLYNVPSRTAVNLEPKTVKLLAEEYSNISAVKEANPNLSQVSELIHDAK-- 178 + E ++LP+ LYN+PS T + +EP TVK L+ +Y NI +K+++ N + ++++ K Sbjct: 131 LVERLSLPLFLYNMPSHTKIVIEPDTVKTLS-QYDNIVGLKDSSANNAYFNKVMAKMKDR 189 Query: 179 --ITVLSGNDELTLPIIALGGKGVISVVANIVPKEFVEMVNYALEGDFEKAREIHYKLFP 236 ++ G +E+ + LG G ++ AN+ P+ +V++ A GD E + +H + Sbjct: 190 QDFSLFVGPEEIMAETVLLGAHGGVNGGANMFPELYVKLYAAAESGDLETVKRLHAIVMQ 249 Query: 237 LMKAM-----FIETNPIPVKTALNMMGRPAGELRLPLCEMSEEHKKILENVLKDL 286 + M F + +K AL+++G + + PL E+ ++IL LK++ Sbjct: 250 ISTKMYSLGQFGSSYLKGIKGALSLLGICSDYMASPLHRFREKEREILAEQLKEI 304 Lambda K H 0.315 0.135 0.374 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: 199 Number of extensions: 5 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: 289 Length of database: 308 Length adjustment: 27 Effective length of query: 262 Effective length of database: 281 Effective search space: 73622 Effective search space used: 73622 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: 42 (22.0 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