Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_057508908.1 ABB28_RS12185 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_001431535.1:WP_057508908.1 Length = 397 Score = 154 bits (390), Expect = 3e-42 Identities = 120/387 (31%), Positives = 182/387 (47%), Gaps = 20/387 (5%) Query: 6 AKRIRNLPPY----LFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIP 61 ++R + P+ L AR + L + G DVI L IG+PD T ++ A + L Sbjct: 13 SRRSHEIAPFHVMSLLARAQAL----EQAGHDVIHLEIGEPDFTTAAPVVRAGQAALA-- 66 Query: 62 ANH-QYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDV 120 A H +Y ++ G+PA R A+A +Y + +++DPQR +V+ G + VDPG Sbjct: 67 AGHTRYTAARGLPALREAIAGFYRSHYLLDIDPQRILVT-PGGSGALLLASSLLVDPGRH 125 Query: 121 VLVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPT 180 L+ DPGYP L G VP+ AG + + + + P NPT Sbjct: 126 WLLADPGYPCNRHFLRLVEGGAQLVPVDAGTAYQLTPELVARHWNEHSVGALLASPANPT 185 Query: 181 GAVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAREVGIEFHSVSK 240 G V S +R+ G + D Y + + G S L+V + V +S SK Sbjct: 186 GTVLSAAELSRLSQSLHARGGHMVVDEIYHGLTY-GMDAASVLQVDDSAFV---LNSFSK 241 Query: 241 TYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGV-QSLCEMY 299 + MTGWR GW AV L +L NL + Q+AA+A + + E + Sbjct: 242 YFGMTGWRLGWLVAPPAAVPELEKLAQNLYISASSIAQHAALACFQDEAMAIFEQRREAF 301 Query: 300 RERRDLVVDTLNDLGWRL-TRPRATFYIWAPVPA-GHDASSFAEMVLEKAGVVITPGTGY 357 R+RRD ++ L +LG+R+ P+ FY++A V A DA +F LE V TPG + Sbjct: 302 RQRRDFLLPALRELGFRINVEPQGAFYLYADVSAFTDDAQAFCAHFLETEHVAFTPGLDF 361 Query: 358 GTY-GEGYFRISLTLPTPRLVEAMERL 383 G + + R++ T PRL EA+ER+ Sbjct: 362 GFHRANQHVRLAYTQEIPRLQEAVERI 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: 305 Number of extensions: 22 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: 397 Length adjustment: 31 Effective length of query: 361 Effective length of database: 366 Effective search space: 132126 Effective search space used: 132126 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