Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_026185985.1 THITHI_RS0102270 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000378965.1:WP_026185985.1 Length = 389 Score = 173 bits (438), Expect = 9e-48 Identities = 126/391 (32%), Positives = 194/391 (49%), Gaps = 20/391 (5%) Query: 6 AKRIRNLPPY----LFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIP 61 A+R+ ++ P+ L AR +L +A G ++ L IG+P PTP+ I+EA K L Sbjct: 9 ARRMADIEPFHVMDLLARARRL----EAAGRRIVHLEIGEPGFPTPEPIMEAGRKALADG 64 Query: 62 ANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVV 121 H Y + G+PA R A+A +Y R GV++ P+R +++ G+ + + +DPGD V Sbjct: 65 HTH-YTPAVGLPALREAIAGFYRDRHGVDVSPERIIIT-PGASGALLLVMAVLLDPGDQV 122 Query: 122 LVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTG 181 L+ DPGYP G VP+ + + + R+ + P NPTG Sbjct: 123 LMADPGYPCNRHFVRTFEGQAVAVPVGPDTAYQLTAEHLESRWGNRSVAAMVASPANPTG 182 Query: 182 AVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSKT 241 + E R++DF + D Y + +D + +A +R+V + +S SK Sbjct: 183 TLVPVETMKRMLDFTAARSGRLIVDEIYHGLVYD---DEAVTALAYSRDVFV-INSFSKY 238 Query: 242 YNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQ--DGVQSLCEMY 299 + MTGWR GW V A+ +L NL Q+AA+AA P+ + + + E + Sbjct: 239 FGMTGWRLGWIVAPEDYVRAIDKLAQNLFLAAPTPAQHAALAAFR-PETLEILDARREAF 297 Query: 300 RERRDLVVDTLNDLGWRL-TRPRATFYIWAPVPA-GHDASSFAEMVLEKAGVVITPGTGY 357 RERRD ++ L +LG+ + P FYI+A A D+ AE +LE+AGV ITPG + Sbjct: 298 RERRDFLLPALRELGFGIPVTPEGAFYIYADSSAFDADSQRLAERLLEEAGVAITPGLDF 357 Query: 358 GTY-GEGYFRISLTLPTPRLVEAMERLRGCL 387 G Y E + R + T L E +ERLR L Sbjct: 358 GHYRPEAHVRFAYTREIGELQEGVERLRRSL 388 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: 340 Number of extensions: 19 Number of successful extensions: 5 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: 389 Length adjustment: 31 Effective length of query: 361 Effective length of database: 358 Effective search space: 129238 Effective search space used: 129238 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 10 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