Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate 3606628 Dshi_0060 aminotransferase class I and II (RefSeq)
Query= curated2:B1I544 (392 letters) >FitnessBrowser__Dino:3606628 Length = 393 Score = 169 bits (429), Expect = 1e-46 Identities = 124/396 (31%), Positives = 193/396 (48%), Gaps = 24/396 (6%) Query: 7 KRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQY 66 +R LP Y F R+ L+ D G +++ IG+P P P +A + L P ++Y Sbjct: 5 ERFSALPEYAFPRLRALL-DGHPPGGSTLAMSIGEPQHPFPQIATDALAEAL--PLFNKY 61 Query: 67 PSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGI-----AHLPWCFVDPGDVV 121 P + G P A+ADW R+GV+LDP R+V++L G++EG+ A P +V Sbjct: 62 PPNDGAPELCAAIADWVQGRYGVKLDPARQVLALNGTREGLFAACLALCPDTKAGGQPLV 121 Query: 122 LVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTG 181 +P+P Y VYA G AG P V TA GFLP+L +P ET R + ++ P+NP G Sbjct: 122 AMPNPFYQVYAVGAQAAGARPLFVNATAETGFLPNLTTLPPETLDRIAIAYVCSPSNPQG 181 Query: 182 AVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAR----EVGIEFHS 237 AVA ++ ++ A ++ V D Y+EI + P LE+A A E + FHS Sbjct: 182 AVADAGYWRALIGLAEKHDFYVFADECYAEI-YRETPPCGALEIATAMGADPERVVIFHS 240 Query: 238 VSKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCE 297 +SK N+ G R+G+AAG A+ + +L++ + + + A A V++ Sbjct: 241 LSKRSNLPGLRSGFAAGGPRAMAEMKKLRAYAGAPLPGPLHPVATAVWRDEAHVVENRA- 299 Query: 298 MYRERRDLVVDTLNDLGWRLTRPRATFYIWAPVPAGHDASSFAEMVLEKAGVVITPG--- 354 +Y + D DT+ T P A F++W PV D + A + + GV + PG Sbjct: 300 LYAAKFD-TADTILGAVPGYTSPAAGFFLWLPV---EDGEAAALKLWTETGVRVLPGAYL 355 Query: 355 ---TGYGTYGEGYFRISLTLPTPRLVEAMERLRGCL 387 T G G G+ R++L P + + +R L Sbjct: 356 SRDTETGNPGAGFIRVALVADAPDVARGLTLIRDSL 391 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: 396 Number of extensions: 21 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: 393 Length adjustment: 31 Effective length of query: 361 Effective length of database: 362 Effective search space: 130682 Effective search space used: 130682 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