Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= curated2:B1I544 (392 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 172 bits (435), Expect = 2e-47 Identities = 116/382 (30%), Positives = 185/382 (48%), Gaps = 7/382 (1%) Query: 6 AKRIRNLPPYLFARIEQLIADKKAQGVDVISLGIGDPDVPTPDHIIEAAEKELKIPANHQ 65 ++R+ + P L I KA+G+DV S G+PD TP HI AA + L + Sbjct: 4 SERVGRVSPSLTLAIAAQAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALA-EGKTR 62 Query: 66 YPSSAGMPAYRRAVADWYARRFGVELDPQREVVSLIGSKEGIAHLPWCFVDPGDVVLVPD 125 Y +AG P R A+A G++ +V+ G K+ + +L +DPGD V++P Sbjct: 63 YGPAAGEPDLREAIAQKLRADNGLDYQAANILVTN-GGKQSLYNLMQVLLDPGDEVIIPA 121 Query: 126 PGYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVAS 185 P + Y LAGG+P V A +GF + R +++ +N P+NPTG V S Sbjct: 122 PYWLSYPEMVKLAGGVPVIVETFASDGFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVYS 181 Query: 186 KEFFARVVDFAREYGILVCHDAAYSEIAFDGYRPPSFLEVAGAR-EVGIEFHSVSKTYNM 244 ++ + + V D Y +I +DG S ++ A E + + +K Y+M Sbjct: 182 RQELEAIAPIIEAHDFWVVSDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAYSM 241 Query: 245 TGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYRERRD 304 TGWR G+ AG + + A L+S+ S V QY AIAAL GPQD V + + ERR Sbjct: 242 TGWRVGYLAGPSELIAAAASLQSHSTSNVCTFAQYGAIAALQGPQDCVAEMLAAFTERRQ 301 Query: 305 LVVDTLNDL-GWRLTRPRATFYIWAPV-PAGHDASSFAEMVLEKAGVVITPGTGYGTYGE 362 L+++ LN + G P FY++ + G D+ ++ +L++ V PG +G + Sbjct: 302 LILNGLNQIAGLSCPIPEGAFYVFVDISKTGLDSMTYCRQLLDQHQVAAIPGIAFG--DD 359 Query: 363 GYFRISLTLPTPRLVEAMERLR 384 R+S + + +ERL+ Sbjct: 360 RSIRLSYATDCQTIEKGLERLQ 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: 305 Number of extensions: 14 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: 392 Length adjustment: 31 Effective length of query: 361 Effective length of database: 361 Effective search space: 130321 Effective search space used: 130321 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