Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate GFF1185 HP15_1162 aminotransferase, class I and II
Query= curated2:C6BUK3 (388 letters) >FitnessBrowser__Marino:GFF1185 Length = 400 Score = 173 bits (438), Expect = 9e-48 Identities = 122/393 (31%), Positives = 193/393 (49%), Gaps = 23/393 (5%) Query: 10 LATLPPYLFAEIDRLKAEVAAQG-VDIISLGIGDPDLPTPDFIIEALHKAAKNPVNHQYP 68 L L PY F ++ +LKA ++ + ISLGIG+P P+PDF+ + + N YP Sbjct: 5 LDRLHPYPFEKLAKLKAGISVPDHLRPISLGIGEPKHPSPDFVKQVIANNLDKLAN--YP 62 Query: 69 SYVGLLTFRQAVADWYKERFDVE---LDATKEVVSLIGSKEGIAHFPLAFVNPGDLVLVA 125 + G R+A++ W RF+++ L A +V + G++E I A V+ V Sbjct: 63 TTRGTDELREAISGWATRRFNLKAGSLSAANNIVPVNGTREAIFSLVQAVVDATKPATVV 122 Query: 126 SPN--YPVYPVASGFAGGEVEIVPLLEENDFLPNLDAISDEKWDKCKIFFVNYPNNPTSA 183 SPN Y VY A+ AG +P N F+P+ D++ + W +C+I F+ P NP+ A Sbjct: 123 SPNPFYQVYEGAAFLAGATPVYIPCDGSNGFIPDFDSVPESIWQECQILFLCSPGNPSGA 182 Query: 184 TATPEFYAELVAKAKKHNVIIAADAAYTEVYYDEDKKPISILET---PGAKDVA--IEFH 238 + E ++A A KH+ I+A+D Y+E+Y +E P +L+T G D A + FH Sbjct: 183 VISREALTRVIALADKHDFIVASDECYSELYPEEGNAPEGLLQTCAAIGRDDYARCVVFH 242 Query: 239 SLSKTYNMTGWRCGMAVGNASLVAGLGKIKENVDSGIFQAVQEAGIVALKEGEPYVKEFR 298 SLSK N+ G R G G+A+++ G K + + Q A I A + E +V+E R Sbjct: 243 SLSKRSNLPGLRSGFVAGDANILDGYLKYRTYHGCAMPIHNQLASIAAWSD-EDHVRENR 301 Query: 299 KIYKERRDCVIEALEKINISCKVPDASIFVWAKTPEGYTSSEFVSKLLKETGVVVTPGNG 358 Y+ + + V+ L ++ + PDA ++W TP F +L + V V PG Sbjct: 302 AAYRAKFEAVVPILREV-MDVDFPDAGFYLWPITP--MDDETFARELSAQQNVHVLPGRY 358 Query: 359 FGES------GEGYFRISLTVDTDRLKEAVSRI 385 + GE R++L + EA RI Sbjct: 359 LSRTVDGHNPGENRVRMALVAPLEECVEAAERI 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: 473 Number of extensions: 28 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: 388 Length of database: 400 Length adjustment: 31 Effective length of query: 357 Effective length of database: 369 Effective search space: 131733 Effective search space used: 131733 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