Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_011189789.1 DP_RS12955 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:P59086 (404 letters) >NCBI__GCF_000025945.1:WP_011189789.1 Length = 435 Score = 159 bits (403), Expect = 1e-43 Identities = 121/397 (30%), Positives = 200/397 (50%), Gaps = 31/397 (7%) Query: 18 LPVYNPAFFIPVKGKGSRLWDQKGKEYIDFSGGIAVTSLGHCHPVLNKVLRQQSKKLWHI 77 LPVY+ A S L G++ +D G+ +PVLN+ L +Q ++ H+ Sbjct: 29 LPVYSVA-----SASSSTLTLTDGRQLVDGMSSWWAAIHGYNNPVLNRALVEQVSRVSHV 83 Query: 78 S-NIFTNEPALRLADKLIS--SSFASRVFFANSGAEANEAAFKLARYYSSKIYNLKKNKI 134 T+EPA+ L L+ +R+F+ +SG+ A E A K+A Y + +K + Sbjct: 84 MFGGLTHEPAVELGKILLQLVPKSLNRIFYCDSGSVAIEVAMKMAMQYMHALGQPQKKRF 143 Query: 135 ISFYNSFHGRTFFTVSV-----GGQAKYSD-----FFGPKPPAIMHAKFNEINSV--KSI 182 ++ +HG TF +SV G Y+ FF +P A ++ + V + + Sbjct: 144 VTIRGGYHGDTFHGMSVCDPVNGMHGLYAGVLPEYFFADRPTTSFFASWDAADFVGMRRL 203 Query: 183 IDDNT---CAVVME-LIQGEGGIVPADVAFVREIRDLCYKYNALLIFDEIQTGIGRTSKL 238 +++N CA+++E ++QG GG+ ++RE+R LC +Y LLI DEI TG GRT KL Sbjct: 204 VEENQQNICAIILEPIVQGAGGMYFYHPQYLREVRALCDEYGLLLIADEIATGFGRTGKL 263 Query: 239 YAYEHYEVQPDILTIAKSLGSGF-PISATLTTNGIASVIK---PGI--HGTTYGGNPLAC 292 +A EH ++PDIL + K++ G+ +ATL T + VI PG+ HG T+ GNPLAC Sbjct: 264 FACEHAGIEPDILCLGKAITGGYMSFAATLATEEVGRVISSAAPGVFMHGPTFMGNPLAC 323 Query: 293 SIAESVVNIVNTKKFLLGVEKKSKKIISELNIINKRFGLFTEIRGKGLLIGIVLRPELSE 352 S+A++ + ++ + VE +K + L E+R G + + L LS Sbjct: 324 SVAKASLQLLIENDWQTQVEGLAKGLEEGLAPC-LDLDCVAEVRVLGGIGVVELHAPLSS 382 Query: 353 EIHNILNALFLEGVIVLTAGKNVIRLAPSLIISKRDI 389 + + A F+E I + ++ L P I+SK ++ Sbjct: 383 QGMVQIQAAFVEAGIWVRPFGRLVYLMPPYIMSKEEL 419 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: 406 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: 404 Length of database: 435 Length adjustment: 32 Effective length of query: 372 Effective length of database: 403 Effective search space: 149916 Effective search space used: 149916 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