Align Probable N-acetyl-LL-diaminopimelate aminotransferase; Putative aminotransferase A; EC 2.6.1.- (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= SwissProt::P16524 (393 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 231 bits (588), Expect = 4e-65 Identities = 129/360 (35%), Positives = 209/360 (58%), Gaps = 9/360 (2%) Query: 25 AQHEDVISLTIGQPDFFTPHHVKAAAKKAIDENVTSYTPNAGYLELRQAVQLYMKKKADF 84 A+ DV S + G+PDF TP H++ AA +A+ E T Y P AG +LR+A+ ++ Sbjct: 27 AEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGKTRYGPAAGEPDLREAIAQKLRADNGL 86 Query: 85 NYDAESEIIITTGASQAIDAAFRTILSPGDEVIMPGPIYPGYEPIINLCGAKPVIVDT-T 143 +Y A + I++T G Q++ + +L PGDEVI+P P + Y ++ L G PVIV+T Sbjct: 87 DYQA-ANILVTNGGKQSLYNLMQVLLDPGDEVIIPAPYWLSYPEMVKLAGGVPVIVETFA 145 Query: 144 SHGFKLTARLIEDALTPNTKCVVLPYPSNPTGVTLSEEELKSIAALLKGRNVFVLSDEIY 203 S GFKL + + A+TP T+ +VL PSNPTG+ S +EL++IA +++ + +V+SDEIY Sbjct: 146 SDGFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVYSRQELEAIAPIIEAHDFWVVSDEIY 205 Query: 204 SELTYD-RPHYSIATY---LRDQTIVINGLSKSHSMTGWRIGFLFAPKDIAKHILKVHQY 259 ++ YD H+SI + ++T++ NG +K++SMTGWR+G+L P ++ + + Sbjct: 206 EKILYDGADHHSIGSLSPACFERTLISNGFAKAYSMTGWRVGYLAGPSELIAAAASLQSH 265 Query: 260 NVSCASSISQKAALEAVTNGFDDALIMREQYKKRLDYVYDRLVSM-GLDVVKPSGAFYIF 318 + S + +Q A+ A+ D M + +R + + L + GL P GAFY+F Sbjct: 266 STSNVCTFAQYGAIAALQGPQDCVAEMLAAFTERRQLILNGLNQIAGLSCPIPEGAFYVF 325 Query: 319 PSIKSFGMTSFDFSMALLEDAGVALVPGSSFSTYGEGYVRLSFACSMDTLREGLDRLELF 378 I G+ S + LL+ VA +PG +F + +RLS+A T+ +GL+RL+LF Sbjct: 326 VDISKTGLDSMTYCRQLLDQHQVAAIPGIAFG--DDRSIRLSYATDCQTIEKGLERLQLF 383 Lambda K H 0.319 0.135 0.388 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: 337 Number of extensions: 18 Number of successful extensions: 6 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: 393 Length of database: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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