Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_004222844.1 KVAR_RS20445 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000025465.1:WP_004222844.1 Length = 400 Score = 186 bits (472), Expect = 1e-51 Identities = 127/398 (31%), Positives = 198/398 (49%), Gaps = 19/398 (4%) Query: 6 AKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQ 65 A R++N+ + Q D AQG+DV+ L G+PD PTP H+I+AA + + Sbjct: 5 ADRLKNVTVSASVAMTQKARDLAAQGIDVVGLSTGEPDFPTPPHVIDAAYAAA-CAGDTR 63 Query: 66 YPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPD 125 YP + G PA R A+ + R + D ++++ G+++ I + ++PGD VL+P Sbjct: 64 YPPTDGTPALRAAIQRKFLRDNELRYDIS-QILTAGGARQIIFNAMMATINPGDEVLIPM 122 Query: 126 PGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVAS 185 P + YA AGG P PVP GF P + A + K + +NYP+NPTG+VA+ Sbjct: 123 PSWISYADIVKFAGGTPVPVPCHEEYGFKPLPQDVEAAITPKTKWLLLNYPSNPTGSVAT 182 Query: 186 K-EFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAR-EVGIEFHSVSKTYN 243 E A R I + D Y + +DG + + +V + + + VSK Y+ Sbjct: 183 HAELLALGETLLRHPHIWIMTDDIYEHLLYDGVKFWTLAQVEPRLYDRVLTVNGVSKAYS 242 Query: 244 MTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERR 303 MTGWR G+ G ++A+ + + GV + Q ++AAL+GPQ + E+YR+RR Sbjct: 243 MTGWRLGFCGGPLTLIKAMSNVNTQNSGGVTTLAQAGSVAALDGPQGLLAERAEIYRQRR 302 Query: 304 DLVVDTLNDL-GWRLTRPRATFYIWAPVPA--------GHDASSFAEMV---LEKAGVVI 351 D V++ L + G R +P+ FY++ + A GH +S A+ V +E+ VV Sbjct: 303 DYVLERLAGIPGLRCHKPQGAFYLFVNIEAFIGKTSASGHFIASDADFVMALIEEQHVVT 362 Query: 352 TPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRG-CLG 388 G YG YFR+S RL +RL C G Sbjct: 363 VQGAAYGM--SPYFRLSYATSMERLQTGCDRLAAFCAG 398 Lambda K H 0.321 0.139 0.430 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: 351 Number of extensions: 21 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: 392 Length of database: 400 Length adjustment: 31 Effective length of query: 361 Effective length of database: 369 Effective search space: 133209 Effective search space used: 133209 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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