Align Acetylornithine/succinyldiaminopimelate aminotransferase; ACOAT; DapATase; Succinyldiaminopimelate transferase; EC 2.6.1.11; EC 2.6.1.17 (uncharacterized)
to candidate WP_092053439.1 BQ4888_RS01605 adenosylmethionine--8-amino-7-oxononanoate transaminase
Query= curated2:P59317 (406 letters) >NCBI__GCF_900111775.1:WP_092053439.1 Length = 449 Score = 173 bits (439), Expect = 8e-48 Identities = 133/418 (31%), Positives = 203/418 (48%), Gaps = 42/418 (10%) Query: 27 IPV-KGQGSRIWDQQGKEYVDFAGGIAVTALGHCHPALVNALKTQ-GETLWHISNVFTNE 84 IP+ +G G+ ++D GK Y+D V GH HP L AL Q G+ HI FT+E Sbjct: 30 IPIARGDGAYLYDFDGKGYIDGVSSWWVNLFGHNHPRLNRALSKQAGKVAHHIFAGFTHE 89 Query: 85 PALRLGRKLIEAT--FAERVVFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFH 142 PA L +L E E+V F ++G+ A E A K++ Y KT+ ++ A+H Sbjct: 90 PAATLAARLCELAPPGLEKVFFTDNGSAAVEAALKMSFQYWRQTGQGEKTRFVSITEAYH 149 Query: 143 GRSLFTVSVGG--------QPKYSDGFGPKPADIIHVPFND---------LHAVKAVMDD 185 G +L +SVGG QP DGF + D P+ A++ V+ + Sbjct: 150 GETLGALSVGGCGLYKDIYQPLLLDGFQVQGPDCFRCPYGCERESCNAECFAAMEEVVAE 209 Query: 186 H---TCAVVVEP-IQGEGGVTAATPEFLQGLRELCDQHQALLVFDEVQCGMGRTGDLFAY 241 H AV++EP IQ G+ P +L+ LRELCD+ + + DE+ G GRTG LFA Sbjct: 210 HHRQIAAVIIEPLIQCAAGMRIYPPIYLKKLRELCDRWRIHYIADEIAVGFGRTGRLFAN 269 Query: 242 MHYGVTPDILTSAKALGGGF-PVSAMLTTAEIASAFHPG-------SHGSTYGGNPLACA 293 H GV+PD+L +K + GG+ P+S +LT E+ AF+ H +Y GNPLACA Sbjct: 270 EHAGVSPDLLCLSKGITGGYMPLSVVLTRQEMYDAFYDDYATLKAFLHSHSYSGNPLACA 329 Query: 294 VAGAAFDIINTPEVLE------GIQAKRQHFVDHLQKIDQ--QYDVFSDIRGMGLLIGAE 345 +A +I ++LE I A ++H + L ++ + Q + I + +G Sbjct: 330 LACEVLNIFTEEKILEKMVPKMAILASQKHRFEALPQVGEFRQLGLVGAIELVRDKVGKT 389 Query: 346 LKPQYKGRARDFLYAGAEEGVMVLNAGPDVMRFAPSLVVEDADIDEGMHRFAHAVAKV 403 P + R E+G ++ G +V+ F P L +E AD+ + A+ +V Sbjct: 390 PYPWQERRGYAVYRKALEKGALLRPLG-NVVYFMPPLTIEKADLSRLVDIAYEAIVEV 446 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: 434 Number of extensions: 24 Number of successful extensions: 7 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: 449 Length adjustment: 32 Effective length of query: 374 Effective length of database: 417 Effective search space: 155958 Effective search space used: 155958 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 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