Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_011766198.1 AZO_RS12450 PLP-dependent aminotransferase family protein
Query= BRENDA::Q72LL6 (397 letters) >NCBI__GCF_000061505.1:WP_011766198.1 Length = 467 Score = 167 bits (424), Expect = 4e-46 Identities = 115/373 (30%), Positives = 186/373 (49%), Gaps = 11/373 (2%) Query: 22 IRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRA 81 I E+L + P ++ +P LFP ++ A A R A G LR Sbjct: 95 IFEILDAVKDPAVVPLGSSFASPALFPLDKLARCLAAAARHMDPRATVTDLPPGNDELRR 154 Query: 82 -----FVAEWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQG 136 ++A V P E+++T+G+ +AL+L + G V +E+P++ +Q +G Sbjct: 155 QIALRYLAAGATVSPGEIVVTSGAMEALNLSLEATTQPGDLVAIESPTFHAILQMIERRG 214 Query: 137 PRFLTVPAG-EEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMER 195 + + +P +G DL ALE L + + L+ +FQ+PTG P +R LL ++ Sbjct: 215 LKVIELPTHPRDGVDLPALEAALATQPVKACMLMLNFQHPTGACVPDASRPALLDLLRRH 274 Query: 196 GLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEA 255 + ++EDD Y EL+F + + P + + G V+++ FSK L+PG R+ + A A Sbjct: 275 QVPLIEDDTYAELHF-DRQPPLPTKALDDDGL--VLHVSGFSKSLAPGYRLGWVAAGRYA 331 Query: 256 LQKLVQAKQGADLHTPMLNQMLVHELLKEG-FSERLERVRRVYREKAQAMLHALDREVPK 314 QK+ + K A L T + Q+ + + L++G F L R+R + A+ A++R P Sbjct: 332 -QKVQRLKLSASLATTIPVQIAIADFLRQGAFDAHLRRLRSALEIQEAALAAAVERHFPA 390 Query: 315 EVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATL 374 R TRP+GG F W+ELP G A L RRAL+E ++ PG F A N +RL++ Sbjct: 391 GTRLTRPRGGYFSWVELPAGTDALALHRRALDEGISIAPGPIFSAGREYANFIRLNFGHP 450 Query: 375 DREGIAEGVRRLG 387 I +RRLG Sbjct: 451 WSGEIERAMRRLG 463 Lambda K H 0.320 0.139 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: 468 Number of extensions: 24 Number of successful extensions: 6 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: 397 Length of database: 467 Length adjustment: 32 Effective length of query: 365 Effective length of database: 435 Effective search space: 158775 Effective search space used: 158775 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: 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