Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (characterized)
to candidate WP_106717222.1 CU100_RS10730 ornithine--oxo-acid transaminase
Query= SwissProt::P40732 (405 letters) >NCBI__GCF_003010935.1:WP_106717222.1 Length = 396 Score = 244 bits (622), Expect = 4e-69 Identities = 136/379 (35%), Positives = 201/379 (53%), Gaps = 6/379 (1%) Query: 21 YAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNV 80 Y P D + +G+G VWD G Y+D + GHCHP ++EA+ Q L TS Sbjct: 13 YKPLDVVLERGEGVHVWDIDGNRYLDCLSAYSAVNQGHCHPKILEAMVEQAGKLTLTSRA 72 Query: 81 FTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYAC-VRHSPFKT-KIIAFH 138 F N+ +L T + ++L MNSG EA ETA K R + V+ P +II Sbjct: 73 FRNDQLALFYEELAALTGSHKILPMNSGAEAVETAIKAVRKWGYEVKGVPENAAEIIVCS 132 Query: 139 NAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGE 198 + FHGR++ V P D FGP VPF D+ A A + +T +VEPIQGE Sbjct: 133 DNFHGRTMGIVGFSTDPSARDNFGPFAPGFKVVPFGDIDAFSAALTPNTVGFLVEPIQGE 192 Query: 199 GGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALG 258 GV + +R+LC E+ L+ DE+Q G+GRTG L A H G+ D+ KAL Sbjct: 193 AGVIIPPKGYFTKVRELCTENNITLILDEIQTGLGRTGALLAEAHEGIEADVTLIGKALS 252 Query: 259 GGF-PVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGAAFDIINTPEVLQGIHTKRQQ 317 GGF PVSA+L+ ++ G HGST+GGNPLACA+A AA ++ +++ + + Sbjct: 253 GGFYPVSAVLSNSDVLGVLKPGQHGSTFGGNPLACAIARAALRVLTEENMIENSRIEGEY 312 Query: 318 FVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMR 377 F++ L+ I + +I ++RG GL++ EL P+ G A F Y G++ + D +R Sbjct: 313 FLEELKGI--RSNIVREVRGRGLMLAVELHPE-AGGANRFCYELKARGILAKDTHGDTIR 369 Query: 378 FAPSLVVEEADIHEGMQRF 396 AP LV++ + +++F Sbjct: 370 IAPPLVIKRDQVDWALEQF 388 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: 401 Number of extensions: 16 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: 405 Length of database: 396 Length adjustment: 31 Effective length of query: 374 Effective length of database: 365 Effective search space: 136510 Effective search space used: 136510 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 Jul 26 2024. The underlying query database was built on Jul 25 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