Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_089323505.1 CHB58_RS07585 aspartate aminotransferase family protein
Query= curated2:P59086 (404 letters) >NCBI__GCF_900188395.1:WP_089323505.1 Length = 395 Score = 342 bits (877), Expect = 1e-98 Identities = 177/387 (45%), Positives = 259/387 (66%), Gaps = 6/387 (1%) Query: 9 TRDSFNKLILPVYNPAFFIPVKGKGSRLWDQKGKEYIDFSGGIAVTSLGHCHPVLNKVLR 68 T + ++ YN VKG+G L+D+ GK+Y+DF GIAV +LGH H + + + Sbjct: 3 THEMTENYVMKTYNRYPISFVKGEGCYLYDENGKKYLDFLAGIAVCNLGHSHKEIAETIC 62 Query: 69 QQSKKLWHISNIFTNEPALRLADKLISSSFASRVFFANSGAEANEAAFKLARYYSSKIYN 128 +Q+K L H SN+F +P LA + +SF S+VFF NSGAEANE A KLAR Y+ + Sbjct: 63 KQAKTLIHTSNLFHIKPQAELAKLICENSFGSKVFFCNSGAEANEGAIKLARRYAFE-RG 121 Query: 129 LKKNKIISFYNSFHGRTFFTVSVGGQAKYSDFFGPKPPAIMHAKFNEINSVKSIIDDNTC 188 K +II+F NSFHGRTF +VSV GQ KY++ FGP + A+FN I+SVK II TC Sbjct: 122 KKGYEIIAFKNSFHGRTFASVSVTGQGKYNEGFGPMLSDVKFAEFNNIDSVKKIISKKTC 181 Query: 189 AVVMELIQGEGGIVPADVAFVREIRDLCYKYNALLIFDEIQTGIGRTSKLYAYEHYEVQP 248 +++E IQGEGGI+PA+ F++E+R+L Y+A+LIFDE+QTGIGRT KL+AY+HY V+P Sbjct: 182 GIIVEPIQGEGGIIPAEKEFLKELRNLANNYDAVLIFDEVQTGIGRTGKLFAYQHYGVEP 241 Query: 249 DILTIAKSLGSGFPISATLTTNGIASVIKPGIHGTTYGGNPLACSIAESVVNIVNTKKFL 308 D++T+AK+LG+G PI A +T + ++KPG+H +T+GGN L+ + V+ I++ +KFL Sbjct: 242 DVMTLAKALGNGVPIGAIVTNERTSQILKPGLHASTFGGNFLSTAAGVKVMEIISDEKFL 301 Query: 309 LGVEKKSKKIISEL-NIINKRFGLFTEIRGKGLLIGIVLRPELSEEIHNILNALFLEGVI 367 VE K K + +L I N+ G +EIRG GL+IG +L+ + + + L G+I Sbjct: 302 KNVEAKGKYLTEKLKEIKNELQGTISEIRGIGLMIGAILKIDGKKLVEKALK----NGLI 357 Query: 368 VLTAGKNVIRLAPSLIISKRDIVEGMK 394 + G+NV+RL P L I++++I EG++ Sbjct: 358 INVTGENVLRLVPPLTITQQEIDEGIE 384 Lambda K H 0.322 0.139 0.404 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: 456 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: 404 Length of database: 395 Length adjustment: 31 Effective length of query: 373 Effective length of database: 364 Effective search space: 135772 Effective search space used: 135772 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 (21.9 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