Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate AO356_27160 AO356_27160 dihydrodipicolinate synthase
Query= BRENDA::Q7D0E8 (302 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_27160 Length = 297 Score = 233 bits (594), Expect = 4e-66 Identities = 139/299 (46%), Positives = 185/299 (61%), Gaps = 14/299 (4%) Query: 5 FKGLSAFPITPADEAGRVDIEAFSALIARLDAAEVDSVGILGSTGIYMYLTREERRR--- 61 F GLSAFP+TP DE G VD AF+ L+ +L AA+VDS+G LGSTG Y YL+R ER R Sbjct: 2 FTGLSAFPLTPMDEQG-VDEIAFARLVQQLVAAKVDSIGALGSTGSYAYLSRAERFRVAQ 60 Query: 62 -AIEAAATILRGRRTLMAGIGALRTDEAVALAKDAEAAGADALLLAPVSYTPLTQEEAYH 120 A+EAA + +M IGALRT + + LA+DA+A G ALLL PVSY LTQ++ + Sbjct: 61 LAVEAAEDV-----PVMVSIGALRTRDVLLLAEDAQAVGVQALLLPPVSYQKLTQDDVFS 115 Query: 121 HFAAVAGATALPLAIYNNPTTTRFTFSDELLVRLAYIPNIRAIKMPLPADADYAGE--LA 178 + V+ ++PL +Y+NP TT F FSDEL R+A +PN+R+IK+P +A Y + + Sbjct: 116 MYEMVSANISVPLCVYDNPGTTHFEFSDELHRRIAELPNVRSIKIPGVPEAPYLAKERVE 175 Query: 179 RLRPKLSDDFAIGYSGDWGCTDATLAGGDTWYSVVAGLLPVPALQLMRAAQAGNAEEAKR 238 RLR + IG SGD AG D WYSV+ GL P AL + RAA +G+A EA R Sbjct: 176 RLRKLIPSHVTIGISGDASAAVGMNAGCDAWYSVMGGLFPNTALAITRAALSGDALEATR 235 Query: 239 LDATFQPLWALFKEF-GSIRVIYAAANILSLTVS-EPPRPILPLTSAERQRVEEALEAL 295 L + +PLWALF +F GS RVI AA + T S P P+ + R+++ +EAL Sbjct: 236 LSESLKPLWALFSQFGGSFRVIATAAELRGFTHSASVPLPLRTIDGEGREQIAAVIEAL 294 Lambda K H 0.319 0.133 0.381 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: 173 Number of extensions: 6 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: 302 Length of database: 297 Length adjustment: 27 Effective length of query: 275 Effective length of database: 270 Effective search space: 74250 Effective search space used: 74250 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