Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate AZOBR_RS11880 AZOBR_RS11880 1-aminocyclopropane-1-carboxylate deaminase
Query= curated2:Q5L6M0 (398 letters) >FitnessBrowser__azobra:AZOBR_RS11880 Length = 384 Score = 120 bits (300), Expect = 9e-32 Identities = 105/328 (32%), Positives = 144/328 (43%), Gaps = 25/328 (7%) Query: 70 GYGPELGLPALREKLSEVFY--HGQVSPEEIFISEGAKMDIFRI--FSLFGPGKTIAVQD 125 GY LG+PALR ++ + +G PE + F++ + F PG +A+ Sbjct: 65 GYTGALGIPALRAAIAGWYRDRYGIDVPERRVVVTTGSSGAFQLGFLAAFDPGDRVAMAS 124 Query: 126 PSYPVYIDTALLTGSRKIIKLPCTKETHFFPEIPQDEAIDI----FCICSPNNPTGTVLN 181 PSYP Y T G + +LP E F P I E +D + SP NPTGT+L+ Sbjct: 125 PSYPAYRHTLTAIGVEPV-ELPTGPEHRFQPTIELLEQLDPPIQGLIVASPANPTGTMLS 183 Query: 182 REQLKELVDYANAQGSIILFDAAYSAFISDPTLPTSIFDIPGARSCAIEVNSFSKSLGFA 241 RE+L L + +A+G ++ D Y P T+ A+ VNSFSK Sbjct: 184 REELTALAAWCDAKGVRLVSDEIYHGLTYGPEAVTA----AEVSESALVVNSFSKYFSMT 239 Query: 242 GVRLGWNVVPKDLQYNDGLPVIRDWERLLFTTFNGVCLPVQESAIAGVSLFPNLEA-ISH 300 G RLGW +VP DL IR E L F Q +A+A L+ ++ Sbjct: 240 GWRLGWMIVPDDL--------IRSVECLAQNLFISAPSLSQAAAVAAFGCTEELDGHVAR 291 Query: 301 YRYNSSLLREALQKADF-SVYGGEQAPYLWVEVPGHIPDEDVF-DFFLHHYHIAITPGKG 358 Y N LL L KA F + + A Y++ +V D + F L IA TPG Sbjct: 292 YARNRELLLRELPKAGFDKLAPADGAFYIYADVTEMTDDSEAFCKRILAETGIACTPGVD 351 Query: 359 FGSC-GKGYVRFSSLGKTEDIVAACQRL 385 F G +VRFS G E I A +RL Sbjct: 352 FDPARGLRFVRFSFAGAEETIAEAARRL 379 Lambda K H 0.321 0.139 0.421 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: 368 Number of extensions: 19 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: 398 Length of database: 384 Length adjustment: 31 Effective length of query: 367 Effective length of database: 353 Effective search space: 129551 Effective search space used: 129551 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