Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 262 bits (669), Expect = 1e-74 Identities = 143/381 (37%), Positives = 212/381 (55%), Gaps = 11/381 (2%) Query: 24 YNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLGHGNPEVVEAVKRQAETLMAMPQT 83 Y + + RGQGA +WD G EY+D + G V +LGH NPE+ A+ QA L+ Sbjct: 12 YARQPVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLLHTSNM 71 Query: 84 LPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANEAALKFARAHTGRK-----KFVAAMR 138 + + L A+ + R F NSG EANEAALK AR H + + + Sbjct: 72 FHIEWQEQLSERLCAL--SGMQRAFFCNSGAEANEAALKLARLHANARHVAQPQVLVMEN 129 Query: 139 GFSGRTMGSLSVTWEPKYREPFLPLVEPVEFIPYNDVEALKR--AVDEETAAVILEPVQG 196 F GRT+ +L+ T P + F PL+ +PY+++E +++ A + AV++EPVQG Sbjct: 130 SFHGRTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQSPDIVAVLVEPVQG 189 Query: 197 EGGVRPATPEFLRAAREITQEKGALLILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKAL 256 EGGV A+ +L+A R++ E L+++DE+QTGMGRTG F ++H GIVPD++TLAKAL Sbjct: 190 EGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIVPDVITLAKAL 249 Query: 257 GGGVPLGVAVMREEVARSMPKGGHGTTFGGNPLAMAAGVAAIRYLERTRLWERAAELGPW 316 G G P+G + R + A G H +TFGGNPLA G + +ER + +RAA G Sbjct: 250 GNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMERDHIPQRAATSGRR 309 Query: 317 FMEKLRAI--PSPKIREVRGMGLMVGLELKEKAAPYIARLEKEHRVLALQAGPTVIRFLP 374 + L+ ++ +RG+GLMVG+EL + A + R E R+L T +R LP Sbjct: 310 LLAALQEALGNHSEVVSIRGLGLMVGIELNRQCAELVGRALDEQRLLITVTRGTTLRLLP 369 Query: 375 PLVIEKEDLERVVEAVRAVLA 395 PL+ E ++ + V +L+ Sbjct: 370 PLICEDSQIDDIAARVSRLLS 390 Lambda K H 0.319 0.137 0.403 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: 367 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: 395 Length of database: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 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 (21.7 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