Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate CCNA_01603 CCNA_01603 aspartate aminotransferase
Query= curated2:B1I544 (392 letters) >FitnessBrowser__Caulo:CCNA_01603 Length = 400 Score = 180 bits (457), Expect = 6e-50 Identities = 127/395 (32%), Positives = 192/395 (48%), Gaps = 18/395 (4%) Query: 4 VEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPAN 63 +E+ +R + P I KA G DVI+L G+PD TPD+I AA + +K Sbjct: 3 LESAALRRIAPSATIAISAKARALKAAGRDVIALSAGEPDFDTPDNIKNAAIEAIKA-GK 61 Query: 64 HQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLV 123 +Y GMP + A+ + R G+E P + V+ G K I + ++PGD V++ Sbjct: 62 TKYTDPDGMPELKAAICAKFKRENGLEYKPSQIHVAP-GGKPVIYNALVATLNPGDEVII 120 Query: 124 PDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAV 183 P P + Y T+LAGG P V TA +GF A+ A + K + IN P+NP+G Sbjct: 121 PAPYWVSYPDMTLLAGGTPVSVETTAESGFKITPEALEAAITPKTKWLIINSPSNPSGGA 180 Query: 184 ASKEFFARVVD-FAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAR-EVGIEFHSVSKT 241 S+ + D R + V D Y + FD + + +V + + + VSK Sbjct: 181 YSRAELQAIADVLLRHPQVWVLTDDMYEHLVFDDFEFTTIAQVEPKLYDRTLTMNGVSKG 240 Query: 242 YNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRE 301 Y+MTGWR G+AAG ++A+G++ S S + Q+AA+ ALNG QD ++ ++++E Sbjct: 241 YSMTGWRIGYAAGPEPLIKAMGKMISQTTSNPCSISQWAALEALNGTQDFIKPNAKLFQE 300 Query: 302 RRDLVVDTLND-LGWRLTRPRATFYIW--------APVPAGHDASS---FAEMVLEKAGV 349 RRDLVV LN G P FY++ P+G S FA +LE GV Sbjct: 301 RRDLVVSMLNQATGLHCPTPEGAFYVYPSCAGLIGKTAPSGKVIESDEDFATELLESEGV 360 Query: 350 VITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLR 384 + G +G +FRIS L +A R++ Sbjct: 361 AVVHGAAFGL--SPFFRISYATSNEVLEDACSRIQ 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: 304 Number of extensions: 14 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