Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 159 bits (402), Expect = 1e-43 Identities = 118/395 (29%), Positives = 187/395 (47%), Gaps = 17/395 (4%) Query: 8 RIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYP 67 R+ +L P + Q + KAQG+DVI+L +G+PD TPDHI EAA+K + + +Y Sbjct: 7 RLNSLSPSATLAMSQKSNELKAQGIDVINLSVGEPDFNTPDHIKEAAKKAIDDNFS-RYS 65 Query: 68 SSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPG 127 G PA R A+ + + G+E ++ G+K+ + + V+PGD V+VP P Sbjct: 66 PVPGYPALRNAIVEKLKKENGLEYTAA-QISCANGAKQSVCNAILVLVNPGDEVIVPAPY 124 Query: 128 YPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKE 187 + Y +A G P V F + A + K + + P+NPTG+V SKE Sbjct: 125 WVSYPEMVKMAEGTPVIVSAGIEQDFKITPKQLEAAITPKTKALILCSPSNPTGSVYSKE 184 Query: 188 FFARVVDFAREYG-ILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTG 246 A + +Y ++V D Y I + G S + +E + + VSK Y MTG Sbjct: 185 ELAGLAAVLAKYPQVVVIADEIYEHINYIGAHQ-SIAQFPEMKERTVIVNGVSKAYAMTG 243 Query: 247 WRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLV 306 WR G+ AG V+A +L+ SG V Q AA AA G Q+ V+ + + + RRDL+ Sbjct: 244 WRIGFIAGPEWIVKACNKLQGQYTSGPCSVSQKAAEAAYVGTQEPVKEMQKAFERRRDLI 303 Query: 307 VDTLNDL-GWRLTRPRATFYIWAPVP----------AGHDASSFAEMVLEKAGVVITPGT 355 V ++ G+ + P+ FY++ ++ A +LE A V GT Sbjct: 304 VKLAKEVPGFEVNVPQGAFYLFPKCSYFFGKSNGERKIENSDDLAMYLLEDAHVACVGGT 363 Query: 356 GYGTYGEGYFRISLTLPTPRLVEAMERLRGCLGRV 390 +G R+S +VEA+ R++ L ++ Sbjct: 364 SFG--APECIRMSYATSDENIVEAIRRIKEALAKL 396 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: 287 Number of extensions: 13 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: 397 Length adjustment: 31 Effective length of query: 361 Effective length of database: 366 Effective search space: 132126 Effective search space used: 132126 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 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