Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Echvi_3953 Echvi_3953 Dihydrodipicolinate synthase/N-acetylneuraminate lyase
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__Cola:Echvi_3953 Length = 303 Score = 138 bits (348), Expect = 1e-37 Identities = 88/290 (30%), Positives = 150/290 (51%), Gaps = 4/290 (1%) Query: 1 MKFEGIYTPAITPLGHDGEIDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDL 60 M + G++ T DG ID D F LE+ ++A V G+I+GG+ GE +E+ +L Sbjct: 1 MNWNGVFPAVTTKFHGDGSIDYDTFFLNLEAQIDAGVSGVILGGTLGESSVLEDEEKIEL 60 Query: 61 AAYARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTE-RENAVH 119 ++ I R+P+V+ T +I +AK A+E+G DA+++ PP P++ RE + Sbjct: 61 TKKTKEKIAGRVPVVLNIAEGSTAKAIYWAKKAEELGLDALMLL-PPMRYPSDHRETVTY 119 Query: 120 ALAVDRAANLPIMLYNYPARMGVVMGEEYFSRVGKSKNVVAIKESSGDMGNLHLLARKF- 178 V +A +LPIM+YN P + E F + + +N+ A+KES+ D+ N+ + +F Sbjct: 120 FKTVAQATHLPIMIYNNPVDYKTYVTLEMFDELMECENIQAVKESTRDVSNVTRMKTRFG 179 Query: 179 PQIALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAML 238 + + CG D +E GA V P+E V L++ C E+ ++ I L Sbjct: 180 DRYKILCGVDTLTMESVLMGADGLVAGLVCAFPKETVVLFDLC-KERRIEEALPIYQWFL 238 Query: 239 PLMDFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTT 288 PL++ K VQ IK ++ G+ +VRAP L +E+ ++ ++ T Sbjct: 239 PLLELDIHPKLVQYIKLAEQMAGIGTENVRAPRLTLIGEERARVEKLIQT 288 Lambda K H 0.320 0.135 0.397 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: 203 Number of extensions: 12 Number of successful extensions: 3 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: 303 Length of database: 303 Length adjustment: 27 Effective length of query: 276 Effective length of database: 276 Effective search space: 76176 Effective search space used: 76176 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: 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