Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_014147931.1 MEALZ_RS07070 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:P59086 (404 letters) >NCBI__GCF_000968535.2:WP_014147931.1 Length = 425 Score = 148 bits (373), Expect = 3e-40 Identities = 106/309 (34%), Positives = 164/309 (53%), Gaps = 30/309 (9%) Query: 19 PVYNPAFFIPVKGKGSRLWDQKGKEYIDFSGGIAVTSLGHCHPVLNKVLRQQSKKLWHIS 78 PVY+ A G L G+E ID G+ HP LN+ +Q + + H+ Sbjct: 27 PVYHVA-----SASGVMLKLGDGRELIDGMSSWWSAIHGYNHPKLNQAATEQLQSMAHVM 81 Query: 79 -NIFTNEPALRLADKL--ISSSFASRVFFANSGAEANEAAFKLARYYSSKIYNLKKNKII 135 T+ PA+ L ++L I+ S VF ++SG+ + E A K+A Y + +KN+ + Sbjct: 82 FGGITHTPAIELVERLLKITPEGLSSVFLSDSGSVSVEVALKMAIQYWQALGKPEKNRFV 141 Query: 136 SFYNSFHGRTFFTVSVGGQAK-YSDFFGPKPPAIMHA-----KFNE------INSVKSII 183 + +HG TF +SV F P P + A +F E I+S++SI+ Sbjct: 142 ALRGGYHGDTFGAMSVCDPVTGMHHLFNPVLPQHLFAQRPACRFGESWNPSDIDSLESIL 201 Query: 184 D---DNTCAVVME-LIQGEGGIVPADVAFVREIRDLCYKYNALLIFDEIQTGIGRTSKLY 239 D+ AV++E ++QG GG+ +++ + LC KY+ LLI DEI TG GRT KL+ Sbjct: 202 SKHGDSCAAVILEPIVQGAGGMWFYHPEYLKSVSALCKKYDVLLIADEIATGFGRTGKLF 261 Query: 240 AYEHYEVQPDILTIAKSLGSGF-PISATLTTNGIASVIKPG-----IHGTTYGGNPLACS 293 A EH + PDIL + K+L G+ ++ATLTT+ +A I G +HG T+ GNPLACS Sbjct: 262 ACEHAGISPDILCLGKALTGGYLTLAATLTTDKVAESISEGPAGCFMHGPTFMGNPLACS 321 Query: 294 IAESVVNIV 302 IA + ++++ Sbjct: 322 IASASIDLL 330 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: 351 Number of extensions: 20 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: 425 Length adjustment: 31 Effective length of query: 373 Effective length of database: 394 Effective search space: 146962 Effective search space used: 146962 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