Align acetylornithine transaminase (EC 2.6.1.11); 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= BRENDA::P73133 (429 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 318 bits (816), Expect = 1e-91 Identities = 163/384 (42%), Positives = 244/384 (63%), Gaps = 13/384 (3%) Query: 33 TYVMNTYGRFPIAIARGQGSTLWDTEGKSYLDFVAGIATCTLGHAHPALVRAVSDQIQKL 92 +Y+M+ Y R P++ +RGQG++LWD G YLD +AG+A +LGHA+P + A+++Q +L Sbjct: 6 SYLMHNYARQPVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQL 65 Query: 93 HHVSNLYYIPEQGELAKWIVEHSCADRVFFCNSGAEANEAAIKLVRKYAHTVLDFLEQPV 152 H SN+++I Q +L++ + S R FFCNSGAEANEAA+KL R +A+ + QP Sbjct: 66 LHTSNMFHIEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANA--RHVAQPQ 123 Query: 153 ILTAKASFHGRTLATITATGQPKYQQYFDPLVPGFDYVPYNDIRSLENKVADLDEGNSRV 212 +L + SFHGRTLAT+ ATG P Q+ F+PL+PGF VPY++I + A + + Sbjct: 124 VLVMENSFHGRTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQSPD----I 179 Query: 213 AAIFLEPLQGEGGVRPGDLAYFKRVREICDQNDILLVFDEVQVGVGRTGKLWGYEHLGVE 272 A+ +EP+QGEGGV Y + +R++CD++D L++ DEVQ G+GRTG +GY+H G+ Sbjct: 180 VAVLVEPVQGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIV 239 Query: 273 PDIFTSAKGLAGGVPIGAMMCK-KFCDVFEPGNHASTFGGNPLACAAGLAVLKTIEGDRL 331 PD+ T AK L G PIGA + + K ++F PG+HASTFGGNPLAC G VL +E D + Sbjct: 240 PDVITLAKALGNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMERDHI 299 Query: 332 LDNVQARGEQLRSGLAEIKNQYPTLFTEVRGWGLINGLEISAESSLTSVEIVKAAM-EQG 390 G +L + L E + + +RG GL+ G+E++ + + E+V A+ EQ Sbjct: 300 PQRAATSGRRLLAALQEALGNHSEV-VSIRGLGLMVGIELNRQCA----ELVGRALDEQR 354 Query: 391 LLLAPAGPKVLRFVPPLVVTEAEI 414 LL+ LR +PPL+ +++I Sbjct: 355 LLITVTRGTTLRLLPPLICEDSQI 378 Lambda K H 0.320 0.137 0.405 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: 416 Number of extensions: 17 Number of successful extensions: 4 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: 429 Length of database: 390 Length adjustment: 31 Effective length of query: 398 Effective length of database: 359 Effective search space: 142882 Effective search space used: 142882 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