Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate GFF973 Psest_1004 Aspartate/tyrosine/aromatic aminotransferase
Query= curated2:B1I544 (392 letters) >FitnessBrowser__psRCH2:GFF973 Length = 390 Score = 152 bits (384), Expect = 2e-41 Identities = 116/381 (30%), Positives = 182/381 (47%), Gaps = 12/381 (3%) Query: 8 RIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANH-QY 66 R R + P+ + + + QG DVI L IG+PD T I+ A + L A H +Y Sbjct: 8 RSRAIEPFHVMALLERANQLQVQGHDVIHLEIGEPDFTTAAPIVAAGQAALA--AGHTRY 65 Query: 67 PSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDP 126 + G+P R A+A +YA+R+G+ +DP R +++ G + VDPG L+ DP Sbjct: 66 TPARGLPQLREAIAAFYAQRYGLSIDPGRILIT-PGGSGALLLAASLLVDPGKHWLLADP 124 Query: 127 GYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASK 186 GYP L G VP+ + + R + + P NPTG + + Sbjct: 125 GYPCNRHFLRLVEGAAQLVPVGPDVRYQLTPELVERYWDRDSVGALVASPANPTGTLLER 184 Query: 187 EFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTG 246 + AR+ +E G + D Y + + G S LEV + +S SK + MTG Sbjct: 185 DELARLSAALKERGGHLVVDEIYHGLTY-GVDAASVLEV---DDDAFVLNSFSKYFGMTG 240 Query: 247 WRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALN-GPQDGVQSLCEMYRERRDL 305 WR GW AV L +L NL + Q+AA+A + +++ + RRD Sbjct: 241 WRLGWLVAPPTAVPELEKLAQNLYISAPSMAQHAALACFEPATLEILEARRAEFARRRDF 300 Query: 306 VVDTLNDLGWRL-TRPRATFYIWAPVPA-GHDASSFAEMVLEKAGVVITPGTGYGTYGEG 363 ++ L +LG+ + P+ FY++A + A G DA +F + +LE V ITPG +G + G Sbjct: 301 LLPALRELGFGIAVEPQGAFYLYADISAFGGDAYAFCQHMLETEFVAITPGLDFGRFQAG 360 Query: 364 -YFRISLTLPTPRLVEAMERL 383 + R + T PRL +A+ER+ Sbjct: 361 HHVRFAYTQDLPRLQQAVERI 381 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: 313 Number of extensions: 26 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: 390 Length adjustment: 31 Effective length of query: 361 Effective length of database: 359 Effective search space: 129599 Effective search space used: 129599 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