Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate GFF1354 PS417_06885 dihydrodipicolinate synthase
Query= BRENDA::A9CFV4 (303 letters) >FitnessBrowser__WCS417:GFF1354 Length = 290 Score = 148 bits (374), Expect = 1e-40 Identities = 99/284 (34%), Positives = 145/284 (51%), Gaps = 4/284 (1%) Query: 5 GIYTPAITPLGHDGE-IDRDAFAAVLESLMEARVHGIIIGGSTGEYYAQTAQERFDLAAY 63 GI ITP DG+ ID + ++ L+E VH I GSTGE + E +++AY Sbjct: 8 GIIGYTITPFSTDGQRIDLNTLGRSIDRLIEGGVHAIAPLGSTGEGAYLSDAEWDEVSAY 67 Query: 64 ARQVIGTRLPLVVGTGATRTEDSIEYAKAAKEIGADAILVSSPPYALPTERENAVHALAV 123 + I R+P +V T ++ A+ A+ GAD ++V Y +E E H A+ Sbjct: 68 SLAKIARRVPTIVSVSDLTTAKAVRRARYAEANGADVVMVLPTSYWKLSEAEILAHYAAI 127 Query: 124 DRAANLPIMLYNYPARMGVVMGEEYFSRVGKS-KNVVAIKESSGDMGNLHLLARKFPQIA 182 + +PIMLYN PA G M + R+ K NV +KES+GD+ +H L R+ + Sbjct: 128 GDSIGVPIMLYNNPATSGTDMSVDLILRIIKQVPNVTMVKESTGDIQRMHHLHRQ-SDVP 186 Query: 183 LSCGWDDQALEFFAWGAKSWVCAGSNFLPREHVALYEACVVEKNFDKGRAIMTAMLPLMD 242 G + ALE FA GAK W A N +P ++ALYEA V+ + + R + LPL+D Sbjct: 187 FYNGCNPLALEAFAAGAKGWCTAAPNLIPELNLALYEA-VLANDLTQAREVFYRQLPLLD 245 Query: 243 FLECGKFVQSIKHGCEIIGLRAGSVRAPLRPLNSDEKRTLQTVV 286 F+ G +IK G + GL AG R P+ PL L+T++ Sbjct: 246 FILKGGLPATIKAGLRLTGLEAGDPRLPVFPLGEVGIEQLKTLL 289 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: 290 Length adjustment: 26 Effective length of query: 277 Effective length of database: 264 Effective search space: 73128 Effective search space used: 73128 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