Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::Q8TQ40 (389 letters) >FitnessBrowser__PS:Dsui_0132 Length = 385 Score = 170 bits (430), Expect = 7e-47 Identities = 121/388 (31%), Positives = 193/388 (49%), Gaps = 10/388 (2%) Query: 4 PMYSDRINALPPYLFAAIDEAKDEMIAKGVDVIDLGVGDPDLPTHPHIVEAMREAVCDPK 63 P+ + R+ + P+ + E+ A+G D+I + VG+PD PT I+ A RE + D + Sbjct: 2 PVSAPRLADIAPFHVMELLGRARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGR 61 Query: 64 THQYPSYAGMPEFREAAAEWCKKYKGIELDPATEVLSLIGSKEAVAHIPLAFVNPGDVVL 123 P+ G+PE REA + + ++ GI + PA+ + G+ A+ PG L Sbjct: 62 VFYTPAL-GLPELREAISGFYRQRYGIAV-PASRIAITAGASGALTLALACLAAPGSEWL 119 Query: 124 YTDPGYPVYKIGTLFAGGEPYSLPLKAENSFLPDLDSIPADILKRAKLFFFNYPNNPTSA 183 TDPGYP + G P S+P+ A ++F P + +R F P NPT Sbjct: 120 LTDPGYPCNRHFVRAFEGVPVSIPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGT 179 Query: 184 TADMKFFEKVVEFCKKNDIIAVHDNAYSQMVYDGYDAPSFLAAEGAMDIGIELYSHSKTY 243 D + +F ++ + D Y + Y+G DAP+ LAA + + + S SK + Sbjct: 180 MLDAAELADIADFVRQRQGQLIIDEIYHGLTYNG-DAPTALAAGDNIFV---VQSFSKYF 235 Query: 244 NMTGWRLGFAVGSKALIKGLGKVKSNVDSGVFDAIQIAGIAALS-SSQACVDDTNKIYEE 302 MTGWRLG+ V + ++ + K+ N+ Q A +AA + A ++ ++ Sbjct: 236 QMTGWRLGWLVIPEPFVRDVEKLAQNLFISASTPAQHAALAAFQPETIALLEQRRAEFKA 295 Query: 303 RRNVLIEGLTAMGLEV-KPPKATFYVWAPVPT-GFTSIEFAKLLLEEAGIVATPGVGFGD 360 RR+ L L A+G + P+ FY++A T S FA+ LLEEAG+ TPG+ FG+ Sbjct: 296 RRDYLAPALEAIGFRITAQPEGAFYLYADCSTLTDDSFGFARRLLEEAGVAITPGIDFGN 355 Query: 361 AG-EGYVRFALTKPVERIKEAVERMKKL 387 G +VRFA T R+ E VER+++L Sbjct: 356 HGASSHVRFAYTNAQARLAEGVERIRQL 383 Lambda K H 0.319 0.137 0.409 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: 364 Number of extensions: 22 Number of successful extensions: 6 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: 389 Length of database: 385 Length adjustment: 30 Effective length of query: 359 Effective length of database: 355 Effective search space: 127445 Effective search space used: 127445 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 (21.7 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