Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_006747791.1 THITH_RS07035 succinyldiaminopimelate transaminase
Query= curated2:C6BUK3 (388 letters) >NCBI__GCF_000227685.2:WP_006747791.1 Length = 397 Score = 166 bits (419), Expect = 1e-45 Identities = 118/391 (30%), Positives = 191/391 (48%), Gaps = 20/391 (5%) Query: 13 LPPYLFAEIDRLKAEVAAQGVDI-ISLGIGDPDLPTPDFIIEALHKAAKNPVNHQYPSYV 71 L PY F + L A++ A I+L IG+P P F+ E L A ++YP+ Sbjct: 8 LQPYPFQRLRALFADLPAHTAPPPIALSIGEPRHAMPPFVAEVL--GASMSGFNRYPTTR 65 Query: 72 GLLTFRQAVADWYKERFDV-ELDATKEVVSLIGSKEGIAHFPLAFVNP--GDLVLVASPN 128 G L R+A++ W + RF + +D +VV + G++E + F A V+P G VL+ +P Sbjct: 66 GELALREAISGWLQRRFGLARVDPDTQVVPVNGTREALFAFAQAVVDPRPGAAVLMPNPF 125 Query: 129 YPVYPVASGFAGGEVEIVPLLEENDFLPNLDAISDEKWDKCKIFFVNYPNNPTSATATPE 188 Y +Y A+ AG E PL ++ + P+ AI D WD+ ++ ++ P NP A Sbjct: 126 YQIYEGAALLAGAEPLFYPLTADHGYRPDFAAIPDAVWDRVQLVYLCNPGNPAGAVIPEA 185 Query: 189 FYAELVAKAKKHNVIIAADAAYTEVYYDEDKKPISIL---ETPG--AKDVAIEFHSLSKT 243 AEL+ +A++H+ +IAAD Y+E+Y D P +L E G A + FHSLSK Sbjct: 186 DLAELIRRAERHDFVIAADECYSEIYRPGDMPPPGLLGAAERLGNTAFSRCVVFHSLSKR 245 Query: 244 YNMTGWRCGMAVGNASLVAGLGKIKENVDSGIFQAVQEAGIVALKEGEPYVKEFRKIYKE 303 N+ G R G G+A+++ + A +A A E +V R++Y + Sbjct: 246 SNLPGIRSGFVAGDAAVLQRFA-LYRTYHGCTMPAPLQAVSRAAWSDETHVATNRELYAQ 304 Query: 304 RRDCVIEALEKINISCKVPDASIFVWAKTPEGYTSSEFVSKLLKETGVVVTPG------N 357 + V+ L + + +PDA ++W + P G F +L ++ V V PG Sbjct: 305 KFAAVVPLLAPV-LEVSMPDAGFYLWPRVPGG-DDEAFARQLQRDANVTVLPGRYLSRPG 362 Query: 358 GFGESGEGYFRISLTVDTDRLKEAVSRISKL 388 G+ G G+ R++L + + EA RI +L Sbjct: 363 ADGDPGAGHVRMALVAEPEACIEAAGRIREL 393 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: 438 Number of extensions: 24 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: 388 Length of database: 397 Length adjustment: 31 Effective length of query: 357 Effective length of database: 366 Effective search space: 130662 Effective search space used: 130662 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 10 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