Align LL-diaminopimelate aminotransferase; DAP-AT; DAP-aminotransferase; LL-DAP-aminotransferase; EC 2.6.1.83 (uncharacterized)
to candidate WP_086509348.1 BZY95_RS07615 succinyldiaminopimelate transaminase
Query= curated2:B1I544 (392 letters) >NCBI__GCF_002151265.1:WP_086509348.1 Length = 408 Score = 169 bits (429), Expect = 1e-46 Identities = 126/405 (31%), Positives = 195/405 (48%), Gaps = 33/405 (8%) Query: 12 LPPYLFARIEQLIADKKAQG-VDVISLGIGDPD-VPTPDHIIEAAEKELKIPANHQYPSS 69 L PY F ++ L A + I L IG+P P + +L +YP++ Sbjct: 8 LKPYPFEKLATLKAGVTPPAQLAHIPLTIGEPQHAPFAGALATLHAHQLDFA---RYPAT 64 Query: 70 AGMPAYRRAVADWYARRFGVE-LDPQREVVSLIGSKEGIAHLPWCFVDPGDV--VLVPDP 126 +G+P R A+A W RRF ++ LDP+R+V+ + G++E I +D V VP+P Sbjct: 65 SGIPELRGAIAAWARRRFRLDGLDPERQVLPVNGTREAIFAFVQAALDRSRPARVAVPNP 124 Query: 127 GYPVYAGGTILAGGIPHPVPLTAGNGFLPDLAAIPAETARRAKVMFINYPNNPTGAVASK 186 Y +Y G T+LAGG PH + A +GF PD A+PAE R +++F+ P NPTGAV + Sbjct: 125 FYQIYEGATLLAGGQPHYLDCRAESGFRPDFDAVPAEVWREVQILFLCSPGNPTGAVTPR 184 Query: 187 EFFARVVDFAREYGILVCHDAAYSEIAFD-GYRPPSFLEVAGAR-----EVGIEFHSVSK 240 F +++ A E+ ++ D YSE+ D PP LE A + FHS+SK Sbjct: 185 AEFQKLIALADEFDFIIASDECYSELYLDEDAPPPGLLEACAAMGRHDYRRCLVFHSLSK 244 Query: 241 TYNMTGWRAGWAAGNAGAVEALGRLKSNLDSGVFQVVQYAAIAALNGPQDGVQSLCEMYR 300 N+ G R+G+ AG+A + R ++ + +Q+A+I A N + V++ + YR Sbjct: 245 RSNLPGLRSGFVAGDAELIAPFKRYRTYHGCAMSLPLQHASITAWN-DEAHVRANRDAYR 303 Query: 301 ERRDLVVDTLNDLGWRLTRPRATFYIWAPVPAGHDASSFAEMVLEKAGVVITPGTGYG-- 358 E+ V + L + P A+FY+W VP G D +F + V + PG+ G Sbjct: 304 EKFAAVTEILAPV-LEFPAPEASFYLWPAVPGGDD-EAFTRELFAAEHVSVLPGSYMGRP 361 Query: 359 --------------TYGEGYFRISLTLPTPRLVEAMERLRGCLGR 389 G G R++L VEA R+R + R Sbjct: 362 TTGDGRGRADGRGDNPGAGRIRLALVAELEPTVEAAGRIRRFIER 406 Lambda K H 0.321 0.139 0.430 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: 391 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: 392 Length of database: 408 Length adjustment: 31 Effective length of query: 361 Effective length of database: 377 Effective search space: 136097 Effective search space used: 136097 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 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