Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate 5209240 Shew_1718 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= SwissProt::P40732 (405 letters) >FitnessBrowser__PV4:5209240 Length = 446 Score = 159 bits (401), Expect = 2e-43 Identities = 115/334 (34%), Positives = 168/334 (50%), Gaps = 38/334 (11%) Query: 18 LPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHT 77 LPVY V +G + G+ ID G+ HP ++EA++ Q TL H Sbjct: 27 LPVYGV-----VSAEGCELILDDGRRLIDGTSSWWACVHGYGHPYILEAMQKQLSTLSHV 81 Query: 78 S-NVFTNEPALRLGRKLIDATFAE--RVLFMNSGTEANETAFKLARHYACVRHSPFKTKI 134 T+ A+ + +KL+ T +V +SG+ A E A K+A Y R +P K +I Sbjct: 82 MFGGITHPSAIAVSKKLLAMTSDNLTKVFLADSGSIAVEVAMKMALQYWQGRGAPSKQRI 141 Query: 135 IAFHNAFHGRSLFTVSVG----------GQPKYSDGFGPKPADIIHVPF------NDLHA 178 + + +HG + +SV G+ F P P PF +DL A Sbjct: 142 LTVKHGYHGDTFAAMSVCDPEGGMHTMFGEAVTQQLFAPAPK----TPFGETLIADDLEA 197 Query: 179 VKAVMDDH---TCAVVVEPI-QGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGR 234 ++A+++ H AV++EPI QG G + + ++LKGLR LCD ++ LL+ DE+ G GR Sbjct: 198 MEALLNAHHQTIAAVIIEPIMQGAGAMHFYSADYLKGLRALCDRYKVLLILDEIATGFGR 257 Query: 235 TGDLFAYMHYGVTPDILTSAKALGGGF-PVSAMLTTQEIA-----SAFHVGSHGSTYGGN 288 TG LFAY H G+ DIL KAL GG+ ++A L + E+A S V HG T+ GN Sbjct: 258 TGKLFAYQHAGIEADILCLGKALTGGYISLAATLCSDEVALGISDSPSGVFMHGPTFMGN 317 Query: 289 PLACAVAGAAFDIINTPEVLQGIHTKRQQFVQHL 322 PLACA A A+ D+IN + + + QQ Q L Sbjct: 318 PLACAAASASLDLINQHQWPEQVAAIEQQMKQEL 351 Lambda K H 0.322 0.137 0.412 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: 437 Number of extensions: 28 Number of successful extensions: 4 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: 405 Length of database: 446 Length adjustment: 32 Effective length of query: 373 Effective length of database: 414 Effective search space: 154422 Effective search space used: 154422 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: 51 (24.3 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