Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate AZOBR_RS12970 AZOBR_RS12970 aspartate aminotransferase
Query= curated2:B1I544 (392 letters) >FitnessBrowser__azobra:AZOBR_RS12970 Length = 401 Score = 173 bits (438), Expect = 9e-48 Identities = 122/401 (30%), Positives = 194/401 (48%), Gaps = 22/401 (5%) Query: 6 AKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQ 65 A R+ + P + Q + A G DVI LG G+PD TPD+I +AA K ++ + + Sbjct: 5 ASRLSRIKPSPTIAVTQKARELAAAGRDVIGLGAGEPDFDTPDNIKDAAIKAIQA-GDTK 63 Query: 66 YPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPD 125 Y + G PA ++A+ + R G++ P + V +G K+ + + + PGD V++P Sbjct: 64 YTAVDGTPALKKAICAKFERENGLKYAPDQITVG-VGGKQVLYNALMATLTPGDEVIIPA 122 Query: 126 PGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVAS 185 P + Y LA G P V A GF A + + K + +N P+NP+GA + Sbjct: 123 PYWVSYPDMVELAEGTPVFVSCPAEQGFKLQPADLEKAITPKTKWLILNSPSNPSGAAYT 182 Query: 186 KEFFARVVD-FAREYGILVCHDAAYSEIAFDG--YRPPSFLEVAGAREVGIEFHSVSKTY 242 ++ + D + + V D Y + +DG + P+ +E A + + + VSK+Y Sbjct: 183 RDEMKALTDVLVKHPQVWVMTDDMYEHLLYDGIEFVTPAQVEPA-LYDRTLTVNGVSKSY 241 Query: 243 NMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRER 302 MTGWR G+A G ++A+G ++S S + Q AA+ ALNGPQD + ++ +R Sbjct: 242 AMTGWRIGYAGGPKALIKAMGVIQSQSTSNPTSIAQAAAVEALNGPQDFIAERAAVFAQR 301 Query: 303 RDLVVDTLNDL-GWRLTRPRATFYIWAPVPAG------------HDASSFAEMVLEKAGV 349 RDLVV LN G +P FY++ P AG F +LE GV Sbjct: 302 RDLVVSMLNQAKGISCPKPEGAFYVY-PSCAGTIGKTTPDGKVIETDEDFVTYLLESEGV 360 Query: 350 VITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRGCLGRV 390 + G+ +G +FRIS T L EA +R++ G + Sbjct: 361 AVVQGSAFGL--APHFRISYATSTEALEEACKRIQRACGNL 399 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: 322 Number of extensions: 18 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: 401 Length adjustment: 31 Effective length of query: 361 Effective length of database: 370 Effective search space: 133570 Effective search space used: 133570 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