Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_014449573.1 LFE_RS07250 pyridoxal phosphate-dependent aminotransferase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_000284315.1:WP_014449573.1 Length = 401 Score = 181 bits (458), Expect = 4e-50 Identities = 120/402 (29%), Positives = 197/402 (49%), Gaps = 16/402 (3%) Query: 2 SFVEAKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIP 61 S+ A R+ NL P ++ + KA G+DV G+PD TP+ I +AA LK Sbjct: 4 SYHLADRLSNLKPSPTLKLASRAREMKANGIDVRDFTGGEPDFDTPEPIKDAAIAALKSG 63 Query: 62 ANHQYPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVV 121 +Y + G+P + A+ + + R G+ P VVS G+K + + V+PGD V Sbjct: 64 FT-KYTAVGGIPELKSAIIEKFERDQGIVYKPSEIVVSS-GAKHSLFQIFQALVNPGDHV 121 Query: 122 LVPDPGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTG 181 L+P P + Y +L GG+ VP +GF A+ R++V+ +N PNNP+G Sbjct: 122 LLPTPAWVSYPDQILLNGGVVIGVPCLPSDGFRLRPQALLEAITPRSRVLVLNSPNNPSG 181 Query: 182 AVASKEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLE-VAGAREVGIEFHSVSK 240 A+ KE R+ + +++ ++V D Y +I FDG S V R+ + + VSK Sbjct: 182 AIIPKEDLLRIAEIVKKHNLIVISDEIYEKIVFDGQETSSIASLVPEIRDRTVIVNGVSK 241 Query: 241 TYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYR 300 TY MTGWR G+AAG A +EA+ ++S S + Q AA+ A+ + + + Y Sbjct: 242 TYAMTGWRIGYAAGPAPIIEAVETIQSQTASNPTSIAQKAAVVAIRSGEIYFKPMLAEYT 301 Query: 301 ERRDLVVDTLNDL-GWRLTRPRATFYIWAPVPA----------GHDASSFAEMVLEKAGV 349 RR +++++LN + G R++ P FY + V + +E L +A V Sbjct: 302 RRRAMLLESLNAIDGIRMSPPDGAFYAFPDVSGLLGKRFGDMEIRTVTDLSEFFLAEARV 361 Query: 350 VITPGTGYGTYGEGYFRISLTLPTPRLVEAMERLRGCLGRVT 391 + PG+ +G+ + + R+S L E + RL+ +T Sbjct: 362 ALVPGSAFGS--DHHMRMSFATSPENLEEGVRRLKEACALLT 401 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: 332 Number of extensions: 14 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: 401 Length adjustment: 31 Effective length of query: 361 Effective length of database: 370 Effective search space: 133570 Effective search space used: 133570 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