Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= curated2:P59086 (404 letters) >FitnessBrowser__Btheta:350970 Length = 804 Score = 149 bits (375), Expect = 4e-40 Identities = 123/397 (30%), Positives = 201/397 (50%), Gaps = 34/397 (8%) Query: 18 LPVYNPAFFIPVKGKGSRLWDQKGKEYIDFSGGIAVTSLGHCHPVLNKVLRQQSKKLWHI 77 LPVY + G+ + + G+ I+ G+ HPVLN+ + Q K+ H+ Sbjct: 403 LPVYKVK-----RADGATITLEDGRTLIEGMSSWWCAVHGYNHPVLNQAAKDQLDKMSHV 457 Query: 78 S-NIFTNEPALRLADKLISSSFAS--RVFFANSGAEANEAAFKLARYYSSKIYNLKKNKI 134 T++PA+ L L+ S ++F+A+SG+ A E A K+A Y KN Sbjct: 458 MFGGLTHDPAIELGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQYWYAAGKPDKNNF 517 Query: 135 ISFYNSFHGRTFFTVSVG----------GQAKYSDFFGPKPPAIMHAKFN--EINSVKSI 182 ++ + +HG T+ +SV G + +F P P + ++N EI ++ Sbjct: 518 VTIRSGYHGDTWNAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFDGEWNPDEIIPLRET 577 Query: 183 IDDNT---CAVVME-LIQGEGGIVPADVAFVREIRDLCYKYNALLIFDEIQTGIGRTSKL 238 I+ ++ A+++E ++QG GG+ ++RE LC +++ LLIFDEI TG GRT KL Sbjct: 578 IEKHSKELAALILEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLIFDEIATGFGRTGKL 637 Query: 239 YAYEHYEVQPDILTIAKSLGSGF-PISATLTTNGIASVI-----KPGIHGTTYGGNPLAC 292 +A+EH V+PDI+ I K+L G+ +SA L +N IA I K +HG T+ GNPLAC Sbjct: 638 FAWEHAGVEPDIMCIGKALTGGYMTLSAVLASNQIADTISNHAPKAFMHGPTFMGNPLAC 697 Query: 293 SIAESVVNIVNTKKFLLGVEKKSKKIISELNIINKRFGLFTEIRGKGLLIGIVLRPELSE 352 ++A + V ++ + V++ ++ EL K F ++R G IG V++ E S Sbjct: 698 AVACASVRLLLDSGWAENVKRIEAQLKEELAPARK-FPQVADVRILG-AIG-VIQTERSV 754 Query: 353 EIHNILNALFLEGVIVLTAGKNVIRLAPSLIISKRDI 389 + + EG+ V GK ++ L P IIS + Sbjct: 755 SMAYMQRRFVEEGIWVRPFGK-LVYLMPPFIISPEQL 790 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: 656 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 404 Length of database: 804 Length adjustment: 36 Effective length of query: 368 Effective length of database: 768 Effective search space: 282624 Effective search space used: 282624 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: 53 (25.0 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