Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 233 bits (594), Expect = 8e-66 Identities = 141/394 (35%), Positives = 213/394 (54%), Gaps = 36/394 (9%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 PV R + +++WD G EY+D G+AV + GH +P++ AA+ EQ G+L HT Sbjct: 16 PVSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQAGQLLHTSNMF--- 72 Query: 85 EPYIELAEEIAKRVPG-DFPKKTLLVTSGSEAVENAVKIARAATG-----RAGVIAFTGA 138 +IE E++++R+ ++ SG+EA E A+K+AR + V+ + Sbjct: 73 --HIEWQEQLSERLCALSGMQRAFFCNSGAEANEAALKLARLHANARHVAQPQVLVMENS 130 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198 +HGRT+ TL TG LMPG + V D+ IE I K AQ Sbjct: 131 FHGRTLATLAATGNPAVQRGFEPLMPGFL----------RVPYDN----IEEIRKVAAQS 176 Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258 DI A+++EPVQGEGG + S ++Q LR LCD+H L++ DEVQTG GRTG +F + Sbjct: 177 PDIVAVLVEPVQGEGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHA 236 Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318 GIVPD+ T AK++G GFPI + + + +PG T+ G+P+AC VL + E Sbjct: 237 GIVPDVITLAKALGNGFPIGACLARGKAAELFSPGHHASTFGGNPLACRVGCTVLDIMER 296 Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378 + + +R+ G RL A L+E H + +RGLG MV IEL ++ AELV + + Sbjct: 297 DHIPQRAATSGRRLLAALQEALGNHSEVVSIRGLGLMVGIEL------NRQCAELVGRAL 350 Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 ++ LI ++ GT +R L P+ D+Q++ Sbjct: 351 --DEQRLLITVTRGT---TLRLLPPLICEDSQID 379 Lambda K H 0.319 0.137 0.393 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: 359 Number of extensions: 17 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: 426 Length of database: 390 Length adjustment: 31 Effective length of query: 395 Effective length of database: 359 Effective search space: 141805 Effective search space used: 141805 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 Sep 17 2021. The underlying query database was built on Sep 17 2021.
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