Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_012044205.1 BBTA_RS19410 acetylornithine transaminase
Query= curated2:P59086 (404 letters) >NCBI__GCF_000015165.1:WP_012044205.1 Length = 398 Score = 268 bits (685), Expect = 2e-76 Identities = 153/365 (41%), Positives = 221/365 (60%), Gaps = 14/365 (3%) Query: 29 VKGKGSRLWDQKGKEYIDFSGGIAVTSLGHCHPVLNKVLRQQSKKLWHISNIFTNEPALR 88 V+GKGS LWD GK Y+DF G AV +LGH P L K L Q+ +L S + NE +L+ Sbjct: 23 VQGKGSWLWDDTGKRYLDFIQGWAVNALGHAPPELAKALADQAARLITPSPAYFNETSLK 82 Query: 89 LADKLISSSFASRVFFANSGAEANEAAFKLARYYSSKIYNLKKN---KIISFYNSFHGRT 145 LA L+ S +VFF NSGAEANE A KLAR Y + L+KN +II+F FHGRT Sbjct: 83 LAKALVDRSCFDQVFFTNSGAEANEGAIKLARKYGA----LRKNGAHEIITFEGGFHGRT 138 Query: 146 FFTVSVGGQAKYSDFFGPKPPAIMHAKFNEINSVKSIIDDNTCAVVMELIQGEGGIVPAD 205 T+S G+ + F PK P A+ N+I SV++++ D T A+++E IQGE G+ PA Sbjct: 139 LATMSASGKKAFEPLFEPKVPGFAKARLNDIASVEALMSDKTVAIMLEPIQGEAGVWPAT 198 Query: 206 VAFVREIRDLCYKYNALLIFDEIQTGIGRTSKLYAYEHYEVQPDILTIAKSLGSGFPISA 265 F++++R L ++ LLI DEIQTG+GRT KL YEH ++ PDI+T+ K +G G P++A Sbjct: 199 TGFLQQLRALTTQHGLLLIVDEIQTGMGRTGKLLGYEHADIVPDIMTLGKGIGGGVPLAA 258 Query: 266 TLTTNGIASVIKPGIHGTTYGGNPLACSIAESVVNIVNTKKFLLGVEKKSKKIISELNII 325 L TN AS G G T+ GNPL C+ +V++++ T FL V + SEL + Sbjct: 259 LLATNE-ASCFAHGDQGGTFNGNPLMCAAGLAVLDVIETPSFLKAVADSGIYLESELQRL 317 Query: 326 NKRFGLFTEIRGKGLLIGI-VLRPELSEEIHNILNALFLEGVIVLTAGKNVIRLAPSLII 384 + R GL E+RG+GLL+ + V+RP +I+ F G+++ + +R P+L + Sbjct: 318 SARHGL-GEVRGRGLLLALDVVRPIAP----SIVAEAFELGLLLNAPRADTLRFMPALNV 372 Query: 385 SKRDI 389 ++ +I Sbjct: 373 TRDEI 377 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: 402 Number of extensions: 21 Number of successful extensions: 3 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: 398 Length adjustment: 31 Effective length of query: 373 Effective length of database: 367 Effective search space: 136891 Effective search space used: 136891 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