Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate GFF2092 PGA1_c21250 aspartate aminotransferase AatA
Query= curated2:B1I544 (392 letters) >FitnessBrowser__Phaeo:GFF2092 Length = 400 Score = 158 bits (400), Expect = 2e-43 Identities = 119/380 (31%), Positives = 181/380 (47%), Gaps = 20/380 (5%) Query: 20 IEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQYPSSAGMPAYRRAV 79 I L + +A G DVI L G+PD TPD+I EAA + ++ +Y + G+ ++AV Sbjct: 19 ITTLAGELRAAGRDVIGLSAGEPDFDTPDNIKEAAIRAIQA-GKTKYTAPDGIAELKQAV 77 Query: 80 ADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAG 139 D +AR G+E P + V G K+ + + ++PGD V++P P + Y LAG Sbjct: 78 CDKFARDNGLEYTPAQVSVGT-GGKQILYNALMATLNPGDEVVIPAPYWVSYPDMVRLAG 136 Query: 140 GIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVD-FARE 198 G P V + GF + A + K N P+NPTGA + D R Sbjct: 137 GTPICVESSLETGFKITPDQLEAAITPKTKWFVFNSPSNPTGAGYHPNELKALTDVLLRH 196 Query: 199 YGILVCHDAAYSEIAFDGYR--PPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNA 256 + V D Y + FD + P+ +E + + + VSK Y MTGWR G+AAG Sbjct: 197 PHVWVMTDDMYEHLVFDDFTFCTPAQIEPK-LYDRTLTCNGVSKAYAMTGWRIGYAAGPK 255 Query: 257 GAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDL-GW 315 ++A+ +++S S + Q+AA+ ALNG QD + ++R RRDLV+ L+ + G Sbjct: 256 PLIDAMRKIQSQSTSNPCTISQWAAVEALNGTQDYILPNTAVFRRRRDLVISMLSQIEGV 315 Query: 316 RLTRPRATFYIWAPVP-----------AGHDASSFAEMVLEKAGVVITPGTGYGTYGEGY 364 P FY++ + A D +FA+ +LE+A V + G YG Sbjct: 316 ACPVPDGAFYVYPSIAGLIGRTSAGGVAITDDEAFAKALLEEADVAVVHGAAYGL--SPN 373 Query: 365 FRISLTLPTPRLVEAMERLR 384 FRIS L EA R++ Sbjct: 374 FRISYAAADETLTEACRRIQ 393 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: 335 Number of extensions: 19 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: 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 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