Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate Pf6N2E2_3203 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3203 Length = 295 Score = 147 bits (371), Expect = 3e-40 Identities = 98/288 (34%), Positives = 148/288 (51%), Gaps = 4/288 (1%) Query: 5 GIYTPAITPLGHDGE-IDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLAAY 63 GI ITP DG+ +D DA ++ L+++ VH I GSTGE + E ++ + Sbjct: 8 GIIGYTITPFSTDGQGLDLDALGRSIDRLIDSGVHAIAPLGSTGEGAYLSDAEWDQVSEF 67 Query: 64 ARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHALAV 123 + + R+P VV T ++ A+ A+ GAD ++V Y +E E H A+ Sbjct: 68 SIARVAGRVPTVVSVSDLTTAKAVHRARFAQAKGADVVMVLPASYWKLSEAEILAHYQAI 127 Query: 124 DRAANLPIMLYNYPARMGVVMGEEYFSRVGKS-KNVVAIKESSGDMGNLHLLARKFP-QI 181 + +LPIMLYN PA G+ M E R+ + NV +KES+GD+ +H L Q+ Sbjct: 128 GASIDLPIMLYNNPATSGIDMSVELILRIFNTVDNVTMVKESTGDIQRMHKLQLLGEGQV 187 Query: 182 ALSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLM 241 G + ALE FA GAK W A N +P+ ++ LY A V+ + + RA+ LPL+ Sbjct: 188 PFYNGCNPLALEAFAAGAKGWCTAAPNLIPQLNLDLY-AAVLANDLSQARALFYRQLPLL 246 Query: 242 DFLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVVTTL 289 DF+ G +IK G +GL G R P+ PL+ + LQT++ L Sbjct: 247 DFILKGGLPATIKAGLRTLGLEVGDPRLPVFPLDEARNQQLQTMLKQL 294 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: 195 Number of extensions: 11 Number of successful extensions: 4 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: 295 Length adjustment: 27 Effective length of query: 276 Effective length of database: 268 Effective search space: 73968 Effective search space used: 73968 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 Aug 03 2021. The underlying query database was built on Aug 03 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