Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_012759228.1 RLEG_RS19395 ornithine--oxo-acid transaminase
Query= curated2:P59317 (406 letters) >NCBI__GCF_000023185.1:WP_012759228.1 Length = 399 Score = 252 bits (643), Expect = 2e-71 Identities = 138/384 (35%), Positives = 209/384 (54%), Gaps = 6/384 (1%) Query: 21 YAPAEFIPVKGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQGETLWHISNV 80 Y P + + +G+G +WD G Y+D + GHCHP ++ A+ Q L S Sbjct: 19 YKPLDVVLTRGEGVYVWDTDGNRYLDCLSAYSAVNQGHCHPKILAAMVEQAGRLTLTSRA 78 Query: 81 FTNEPALRLGRKLIEATFAERVVFMNSGTEANETAFKLARHYAC-VRHSPF-KTKIIAFH 138 F N+ L +L T + +++ MNSG EA ETA K R + V+ P K +II Sbjct: 79 FRNDQLAYLYEELAALTGSHKILPMNSGAEAVETAIKAVRKWGYEVKGVPEGKAEIIVCA 138 Query: 139 NAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGE 198 + FHGR+L +S P+ GFGP + +PF D A AV++ +T A ++EPIQGE Sbjct: 139 DNFHGRTLSIISFSTDPEARSGFGPYTSGFRIIPFGDAEAFAAVINRNTVAALIEPIQGE 198 Query: 199 GGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALG 258 GV + +RELC + L+ DE+Q G+GRTG L A H G+ D+ KAL Sbjct: 199 AGVIIPPAGYFTRIRELCTANNVTLILDEIQTGLGRTGKLLAEEHEGIEADVTLIGKALS 258 Query: 259 GGF-PVSAMLTTAEIASAFHPGSHGSTYGGNPLACAVAGAAFDIINTPEVLEGIQAKRQH 317 GGF PVSA+L+ +E+ PG HGST+GGNPLACAVA AA ++ ++E + Sbjct: 259 GGFYPVSAVLSNSEVLGVLKPGQHGSTFGGNPLACAVARAALKVLTEEGMIENAAVMGDY 318 Query: 318 FVDHLQKIDQQYDVFSDIRGMGLLIGAELKPQYKGRARDFLYAGAEEGVMVLNAGPDVMR 377 F++ L+ I + ++ D+RG GL++ EL+P+ G AR + +A E G++ + +R Sbjct: 319 FLEGLRSI--RSNIVRDVRGRGLMMAIELEPE-AGGARQYCHALKERGLLAKDTHDHTIR 375 Query: 378 FAPSLVVEDADIDEGMHRFAHAVA 401 AP LV+ +D + + ++ Sbjct: 376 LAPPLVISREQVDWAVSQIEETIS 399 Lambda K H 0.322 0.138 0.416 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: 399 Number of extensions: 18 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: 406 Length of database: 399 Length adjustment: 31 Effective length of query: 375 Effective length of database: 368 Effective search space: 138000 Effective search space used: 138000 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