Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_018231675.1 THITHI_RS0103415 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= SwissProt::P40732 (405 letters) >NCBI__GCF_000378965.1:WP_018231675.1 Length = 460 Score = 164 bits (414), Expect = 6e-45 Identities = 112/349 (32%), Positives = 168/349 (48%), Gaps = 35/349 (10%) Query: 32 KGSRVW--DQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNV-FTNEPALR 88 +G VW D G YID V GH +P + +A++ Q + L H FT+EP +R Sbjct: 34 RGEGVWLEDFDGNRYIDAVSSWWVNLFGHANPRINQAIRDQLDRLEHVILAGFTHEPVIR 93 Query: 89 LGRKLIDAT--FAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSL 146 L KL+ T R F +SG+ A E A K++ HY R KT+ I N++HG +L Sbjct: 94 LSEKLVAITPPGLSRCFFADSGSAAVEVALKMSYHYWRNRGQGGKTRFICLTNSYHGETL 153 Query: 147 FTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMD--------------------DH 186 +SVG P Y + + I V D + +A D Sbjct: 154 GALSVGDVPLYKETYKSLLMQSITVQAPDCYLREAGEDCAQLAERMFVHMEQALARHAHE 213 Query: 187 TCAVVVEP-IQGEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYG 245 TCAV+VEP +Q GG++ P +L LR+ CD H L+ DE+ G GRTG +FA G Sbjct: 214 TCAVIVEPLVQCAGGMRMYDPRYLSLLREACDRHGMHLIADEIAVGFGRTGTMFACEQAG 273 Query: 246 VTPDILTSAKALGGGF-PVSAMLTTQEIASAFH-------VGSHGSTYGGNPLACAVAGA 297 +TPD L +K L GG+ P+SA++TT+ + AF+ H +Y GNPLACA A Sbjct: 274 ITPDFLCLSKGLTGGYLPLSAVVTTEGVYQAFYDEYEKLNAFLHSHSYTGNPLACAAALG 333 Query: 298 AFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAEL 346 I +V+ + + L + + ++ +++R G++ E+ Sbjct: 334 TLGIFEGEDVIGNNRHLAKVMAEALAPLQDHPNV-AEVRQTGMIAAVEM 381 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: 428 Number of extensions: 26 Number of successful extensions: 7 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: 405 Length of database: 460 Length adjustment: 32 Effective length of query: 373 Effective length of database: 428 Effective search space: 159644 Effective search space used: 159644 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