Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate 209328 DVU0392 aromatic aminotransferase
Query= curated2:B1I544 (392 letters) >MicrobesOnline__882:209328 Length = 399 Score = 176 bits (445), Expect = 1e-48 Identities = 121/360 (33%), Positives = 175/360 (48%), Gaps = 5/360 (1%) Query: 35 ISLGIGDPDVPTPDHIIEAAEKELKIPANH-QYPSSAGMPAYRRAVADWYARRFGVELDP 93 +SLG G P TP+HI+EA + L+ A+ +Y GMPA R A+A A R G ++P Sbjct: 33 VSLGQGVPSFRTPEHIVEAVCRALRDKADAGRYTLQPGMPALREAIAADLAARKGYMVNP 92 Query: 94 QREVVSLIGSKEGIAHLPWCFVDPGDVVLVPDPGYPVYAGGTILAGGIPHPVPLTAGNGF 153 EV +G+ E + VD GD V++P PGY +A ++A G+P VPL A + Sbjct: 93 DSEVGVTVGAMEALLMALLTVVDRGDEVIIPSPGYASHAEQVLMAEGVPVHVPLRADDWG 152 Query: 154 LPDLAAIPAETARRAKVMFINYPNNPTGAVASKEFFARVVDFAREYGILVCHDAAYSEIA 213 L D+ AI A R + + + P NPTG V + + A E I++ D Y + Sbjct: 153 L-DVDAIRAAVTPRTRAVIVCNPGNPTGTVYDDADVRALCELALERNIMLISDETYDYMV 211 Query: 214 FDGYRPPSFLEVAGAREVGIEFHSVSKTYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGV 273 + G P S + R I +S SK Y +TGWR G+ A +A + L ++ Sbjct: 212 YGGGEPLSPASLPEMRRHVIVVNSFSKKYALTGWRVGYCAADAAWMGELLKVHDAAAICA 271 Query: 274 FQVVQYAAIAALNGPQDGVQSLCEMYRERRDLVVDTLNDLG--WRLTRPRATFYIWAPVP 331 V QYAA+AAL GPQD V + RR+L L+ + + +PR FYI A Sbjct: 272 PAVSQYAALAALTGPQDCVDDMRAALSARRNLACARLDAMAPHFDYVQPRGAFYIMARYT 331 Query: 332 AGHDASSF-AEMVLEKAGVVITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRGCLGRV 390 S A +LE+ V+ PG +G GE + R+S + L EA +R+ RV Sbjct: 332 FTDAPSDMVARRLLEEGRVITVPGASFGPTGERHLRLSFGMEEAELDEAFDRMAAWTQRV 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: 280 Number of extensions: 11 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: 399 Length adjustment: 31 Effective length of query: 361 Effective length of database: 368 Effective search space: 132848 Effective search space used: 132848 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