Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_013643724.1 METBO_RS00600 acetylornithine transaminase
Query= SwissProt::P40732 (405 letters) >NCBI__GCF_000191585.1:WP_013643724.1 Length = 390 Score = 286 bits (732), Expect = 7e-82 Identities = 151/373 (40%), Positives = 223/373 (59%), Gaps = 10/373 (2%) Query: 17 ILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWH 76 ++ Y VKGK + VWD G YID GIAV +GH +P + EA+ +Q + L H Sbjct: 14 VMQTYGRHKIALVKGKDTTVWDADGNSYIDCVAGIAVNNVGHSNPKVGEAICNQVKKLIH 73 Query: 77 TSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIA 136 TSN++ E + L + L+D + ++ F NSG EANE A KLAR +HS K +II Sbjct: 74 TSNLYYTEEQVTLAKLLVDVSPHQKAFFCNSGAEANEGAIKLAR-----KHSG-KGEIIT 127 Query: 137 FHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQ 196 N+FHGR++ T++ GQPKY GF P + P+ D+ AVK ++ T AV+VEP+Q Sbjct: 128 MINSFHGRTITTITATGQPKYQKGFEPLTPGFKYAPYGDIEAVKEMISPSTAAVLVEPVQ 187 Query: 197 GEGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKA 256 GE GV +LK L+++C++ LL+FDEVQ G GRTG++FA +GVTPDI + AKA Sbjct: 188 GESGVIVPPEGYLKQLKEVCEDSNVLLIFDEVQTGFGRTGEMFASQTFGVTPDITSLAKA 247 Query: 257 LGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQ 316 + GGFP+ A+L ++A +F G H +T+GGNPL CA A A+ + I ++L Sbjct: 248 IAGGFPMGAVLANNDVAESFVPGDHAATFGGNPLGCAAAKASINFILEEKLLDKSKENGS 307 Query: 317 QFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVM 376 FV+ L + Q ++ +++RG GL++G E+K G D L+ + G++V A +V+ Sbjct: 308 YFVEKLLKLQNQHELINEVRGKGLMVGVEMKTDC-GCMVDELF---KEGIIVNCAAGNVL 363 Query: 377 RFAPSLVVEEADI 389 RF P L + + I Sbjct: 364 RFVPPLTITKEQI 376 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: 394 Number of extensions: 12 Number of successful extensions: 3 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: 390 Length adjustment: 31 Effective length of query: 374 Effective length of database: 359 Effective search space: 134266 Effective search space used: 134266 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