Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_013554564.1 NITSA_RS08235 aspartate aminotransferase family protein
Query= curated2:P59086 (404 letters) >NCBI__GCF_000186245.1:WP_013554564.1 Length = 395 Score = 272 bits (695), Expect = 1e-77 Identities = 155/375 (41%), Positives = 229/375 (61%), Gaps = 9/375 (2%) Query: 29 VKGKGSRLWDQKGKEYIDFSGGIAVTSLGHCHPVLNKVLRQQSKKLWHISNIFTNEPALR 88 V+G+G++L+D G+E+IDF GI V S+GH HP L++ L Q+ KL H+SN+ EP R Sbjct: 24 VRGEGAKLYDDTGREFIDFGSGIGVCSIGHAHPKLSEALCDQASKLIHVSNLQVIEPQAR 83 Query: 89 LADKLIS-SSFASRVFFANSGAEANEAAFKLARYYSSKIYNLKKNKIISFYNSFHGRTFF 147 LA++++ S + R FF NSGAEANEAA K+AR Y ++ K+ K+I+ +SFHGRT Sbjct: 84 LAERIVKLSGYDMRCFFGNSGAEANEAALKIARKYGETAFDTKRYKVITLKHSFHGRTIT 143 Query: 148 TVSVGGQAK-YSDFFGPKPPAIMHAKFNEINSVKSIIDDNTCAVVMELIQGEGGIVPADV 206 TV GQ + + F P P + + I+++ IDD T AV++EL+QGEGG+ P D Sbjct: 144 TVKATGQKEMHKPDFSPYPAGFAYVE--SIDAIYDAIDDETVAVMIELVQGEGGVQPFDK 201 Query: 207 AFVREIRDLCYKYNALLIFDEIQTGIGRTSKLYAYEHYEVQPDILTIAKSLGSGFPISAT 266 V+++ + LLI DE+QTG+ RT + A + YE++PDI+T+AK LG G PI Sbjct: 202 GEVQDLAKFLRSRDLLLIVDEVQTGVYRTGEFLASQLYEIEPDIITLAKGLGGGVPIGVA 261 Query: 267 LTTNGIASVIKPGIHGTTYGGNPLACSIAESVVNIVNTKKFLLGVEKKSKKIISELNIIN 326 +T + + KPG HG+T+GGN L+ +V+ ++ ++ + ++ + S L + Sbjct: 262 MTR--LKEIFKPGDHGSTFGGNYLSTRAGLTVLEVLKAEQDRGALAERIEIFSSYLKGLA 319 Query: 327 KRF-GLFTEIRGKGLLIGIVLRPELSEEIHNILNALFLEGVIVLTAGKNVIRLAPSLIIS 385 +R FTE G GL+ G LR +E IL A F EG+IVL AG+N +R P L I+ Sbjct: 320 ERLPEYFTEAVGLGLMRG--LRCVDAEIQGAILKAAFDEGLIVLKAGRNTVRFLPPLTIT 377 Query: 386 KRDIVEGMKRFYCAL 400 + +I EG KRF AL Sbjct: 378 RDEIDEGFKRFEKAL 392 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: 371 Number of extensions: 19 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: 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 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