Align 4-hydroxy-tetrahydrodipicolinate synthase; HTPA synthase; EC 4.3.3.7 (characterized)
to candidate Echvi_4343 Echvi_4343 Dihydrodipicolinate synthase/N-acetylneuraminate lyase
Query= SwissProt::P9WP25 (300 letters) >FitnessBrowser__Cola:Echvi_4343 Length = 309 Score = 98.2 bits (243), Expect = 2e-25 Identities = 83/269 (30%), Positives = 115/269 (42%), Gaps = 6/269 (2%) Query: 15 LLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVL 74 L+ A TPF DGSLD LA L G G ++GTTGE T EKI LL A Sbjct: 9 LIAATFTPFCEDGSLDERKIPVLAQSLRANGMAGAFIAGTTGEGAAMTYDEKIRLLEAWA 68 Query: 75 EAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQ-RGLQAHFTAVA 133 +V+A G +I LA A G +G+ + PYY +P + L ++ ++A Sbjct: 69 PFSAAEFKVMAMLGGTSQKEAIALADRANALGIYGIAMTAPYYMRPNSVKQLVDYYESIA 128 Query: 134 DAT-ELPMLLYDIPGRSAVPIEP-DTIRALASH-PNIVGVKDAKADLHSGAQIMADTGLA 190 A + Y IP S V + D + + PN G+K DL + + G Sbjct: 129 AAAPDQAFYFYHIPLLSKVELPMLDFLEEVGERIPNFAGIKYTHNDLMEFNRCLRFQGGK 188 Query: 191 Y--YSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLC 248 Y G D L L+MGA G + + A + L+ AF D+ AR L Sbjct: 189 YDILWGWDETMLAGLSMGAKGAVGSTYNYAGPLYQNLMEAFQQQDMEAARHWQEKSIDLI 248 Query: 249 NAMSRLGGVTLSKAGLRLQGIDVGDPRLP 277 + GG KA ++L G+D G R P Sbjct: 249 SLFGHYGGAACGKAIMKLCGLDCGQFRYP 277 Lambda K H 0.318 0.133 0.382 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: 216 Number of extensions: 16 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: 300 Length of database: 309 Length adjustment: 27 Effective length of query: 273 Effective length of database: 282 Effective search space: 76986 Effective search space used: 76986 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