Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate AO353_16445 AO353_16445 succinyldiaminopimelate transaminase
Query= curated2:C6BUK3 (388 letters) >FitnessBrowser__pseudo3_N2E3:AO353_16445 Length = 399 Score = 184 bits (468), Expect = 3e-51 Identities = 132/395 (33%), Positives = 196/395 (49%), Gaps = 27/395 (6%) Query: 10 LATLPPYLFAEIDRLKAEVAAQ-GVDIISLGIGDPDLPTPDFIIEALHKAAKNPVNHQYP 68 L L PY F ++ L V I+L IG+P +P F+ EAL A+ YP Sbjct: 5 LNQLQPYPFEKLRALLGAVTPNPDKRPIALSIGEPKHRSPSFVAEAL--ASNLDQMAVYP 62 Query: 69 SYVGLLTFRQAVADWYKERFDVE---LDATKEVVSLIGSKEGIAHFPLAFVNPGDLVLVA 125 + +G+ R+A+A W + RF V +D + V+ + G++E + F VN GD L+ Sbjct: 63 TTLGIPALREAIAGWCERRFGVPSGWIDPARNVLPVNGTREALFAFTQTVVNRGDDALIV 122 Query: 126 SPN--YPVYPVASGFAGGEVEIVPLLEENDFLPNLDAISDEKWDKCKIFFVNYPNNPTSA 183 SPN Y +Y A+ AG + +P L+EN F P+ DA+SD+ W +C+I F+ P NPT A Sbjct: 123 SPNPFYQIYEGAAFLAGAKPHYLPCLDENGFNPDFDAVSDDIWKRCQILFLCSPGNPTGA 182 Query: 184 TATPEFYAELVAKAKKHNVIIAADAAYTEVYYDEDKKPISILET---PGAKDV--AIEFH 238 E +L+A A +H+ +IAAD Y+E+Y++E P +L G KD + FH Sbjct: 183 LIPVETLKKLIALADEHDFVIAADECYSELYFNEQTPPPGLLSACVELGRKDFKRCVVFH 242 Query: 239 SLSKTYNMTGWRCGMAVGNASLVAGLGKIKENVDSGIFQAVQ-EAGIVALKEGEPYVKEF 297 SLSK N+ G R G G+A ++ G + G VQ + VA E +V+ Sbjct: 243 SLSKRSNLPGLRSGFVAGDAEILKGF--LLYRTYHGCAMPVQTQLASVAAWNDEVHVRAN 300 Query: 298 RKIYKERRDCVIEALEKINISCKVPDASIFVWAKTPEGYTSSEFVSKLLKETGVVVTPG- 356 R +Y+E+ D V+E L + + + PD ++W EG + F L E V V PG Sbjct: 301 RALYREKYDAVLEILSPV-MDVQRPDGGFYLWPNV-EG-DDAAFCRDLFVEEHVTVVPGS 357 Query: 357 ------NGFGESGEGYFRISLTVDTDRLKEAVSRI 385 +GF G G R++L EA RI Sbjct: 358 YLSREVDGF-NPGAGRVRLALVAPLAECVEAAERI 391 Lambda K H 0.317 0.136 0.398 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: 440 Number of extensions: 30 Number of successful extensions: 5 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: 388 Length of database: 399 Length adjustment: 31 Effective length of query: 357 Effective length of database: 368 Effective search space: 131376 Effective search space used: 131376 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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