Align Putative [LysW]-aminoadipate semialdehyde/glutamate semialdehyde transaminase; EC 2.6.1.118; EC 2.6.1.124 (uncharacterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= curated2:Q5JFW3 (362 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 249 bits (637), Expect = 7e-71 Identities = 142/378 (37%), Positives = 217/378 (57%), Gaps = 24/378 (6%) Query: 5 RKRLRLVRGEGVYVWDEKGRRYLDLIAGIGVNVLGHAHPEWVLDMSRQLEKIVVAGPMFE 64 R+ + RG+G +WD+ G YLD IAG+ V LGHA+PE ++ Q +++ MF Sbjct: 14 RQPVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLLHTSNMFH 73 Query: 65 HDEREEMLEELSHWVDYEYVYMGNSGTEAVEAAIKFARL-----ATGRSEIVAMTNAFHG 119 + +E++ E L + + NSG EA EAA+K ARL + +++ M N+FHG Sbjct: 74 IEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANARHVAQPQVLVMENSFHG 133 Query: 120 RTLGSLSATWKKKYREGFGPLVPGFKHIPFNNVEAAKE--AITKETAAVIFEPIQGEGGI 177 RTL +L+AT + GF PL+PGF +P++N+E ++ A + + AV+ EP+QGEGG+ Sbjct: 134 RTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQSPDIVAVLVEPVQGEGGV 193 Query: 178 VPADEEFVKTLRDLTEDVGALLIADEVQSGL-RTGKFLAIEHYGVRPDIVTMGKGIGNGF 236 A +++ LR L ++ L++ DEVQ+G+ RTG + +H G+ PD++T+ K +GNGF Sbjct: 194 HAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIVPDVITLAKALGNGF 253 Query: 237 PVSLTL-----TDLEIPRGKHGSTFGGNPLACRAVATTLRILRRDRLVEKA---GEKFME 288 P+ L +L P G H STFGGNPLACR T L I+ RD + ++A G + + Sbjct: 254 PIGACLARGKAAELFSP-GHHASTFGGNPLACRVGCTVLDIMERDHIPQRAATSGRRLLA 312 Query: 289 FSGE------RVVKTRGRGLMIGIVLRRPAGNYV-KALQERGILVNTAGNRVIRLLPPLI 341 E VV RG GLM+GI L R V +AL E+ +L+ +RLLPPLI Sbjct: 313 ALQEALGNHSEVVSIRGLGLMVGIELNRQCAELVGRALDEQRLLITVTRGTTLRLLPPLI 372 Query: 342 IEGDTLEEARKEIEGVLN 359 E +++ + +L+ Sbjct: 373 CEDSQIDDIAARVSRLLS 390 Lambda K H 0.320 0.140 0.410 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: 345 Number of extensions: 16 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: 362 Length of database: 390 Length adjustment: 30 Effective length of query: 332 Effective length of database: 360 Effective search space: 119520 Effective search space used: 119520 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 (21.8 bits) S2: 50 (23.9 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