Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_011190179.1 DP_RS14870 pyridoxal phosphate-dependent aminotransferase
Query= curated2:A5FRC5 (388 letters) >NCBI__GCF_000025945.1:WP_011190179.1 Length = 395 Score = 118 bits (296), Expect = 3e-31 Identities = 110/375 (29%), Positives = 161/375 (42%), Gaps = 30/375 (8%) Query: 14 LFVQISKKIAEKRAKGEDVISFAIGDPDLPTPKHILAELCKAAED--PSNHRYPETEGLP 71 +F Q K AE A E+V F++G+PD P P L K A D P H Y G Sbjct: 20 MFEQGGKMKAEFGA--ENVFDFSLGNPDAPPPAQFDQVLAKIAADNGPGTHSYMPNGGHL 77 Query: 72 VLRKAMAEWYQKRFGVKLNPDTEVLPLIGSKEGIGHAAWCFLDPGDIALVPNPAYPVYAI 131 +R+A+A K GVK+ +++L G+ GI L+PGD + P + Y Sbjct: 78 WVREAVAGQMAKEQGVKVVA-SDMLLSCGAAGGINVIMKSLLNPGDEVIFLAPYFVEYDF 136 Query: 132 SSQLAGAEVFNLPLNKGNNFLPNLEAIPQNILSKAKVLWINYPNNPTGAVAGLSFFQEVA 191 G + + + NF P++ AI + I K K + IN PNNPTG + E+ Sbjct: 137 YVDNHGGK--SRVVQTDENFNPDMAAIREAISEKTKAIIINSPNNPTGQIYSKEILAELG 194 Query: 192 NFAAK------HNLAVCHDGPYSEIAFDGYKPVSFLEADGAKDVGIEFHSLSKSYNMTGW 245 + + + D PY +I +DG + S A I S SK ++ G Sbjct: 195 LLLTEMGEKFGSTIYLISDEPYRKITYDGIEVPSIF---AAYSNSIIVSSYSKDLSLPGE 251 Query: 246 RIGMAV------GNAKMIDALRRFKSNLDSGIPQAIQLMAIAALNGSQEIINQNCAIYQR 299 RIG A+++ A+ L A+ IA L G I+ + Y R Sbjct: 252 RIGYVAVHPGISEKAELVSAMTLANRILGFVNAPALMQRVIAELQG----ISVDNERYAR 307 Query: 300 RRDRLVEALRNIGMEVTAPKASLYIWAPVPESYTSASFATELLDKTGVVVTPGTGYGTAG 359 RR+ + L G + PK + YI+ P A A +L + ++ PG G+G Sbjct: 308 RREAFCQILTEAGFDFVPPKGAFYIFPKSPIEDDVAFCA--ILQEEKILAVPGRGFG--A 363 Query: 360 EGYIRLSLTVPDEQI 374 GYIRL+ VPDE I Sbjct: 364 PGYIRLAFCVPDETI 378 Lambda K H 0.317 0.135 0.401 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: 346 Number of extensions: 22 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: 395 Length adjustment: 31 Effective length of query: 357 Effective length of database: 364 Effective search space: 129948 Effective search space used: 129948 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 Jul 25 2024. The underlying query database was built on Jul 25 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