Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_086511056.1 BZY95_RS16860 PLP-dependent aminotransferase family protein
Query= BRENDA::Q72LL6 (397 letters) >NCBI__GCF_002151265.1:WP_086511056.1 Length = 455 Score = 152 bits (383), Expect = 2e-41 Identities = 100/302 (33%), Positives = 151/302 (50%), Gaps = 13/302 (4%) Query: 62 EKGEVALQYSPTEGYAPLRAFVAEWIGVR-----PEEVLITTGSQQALDLVGKVFLDEGS 116 E+ E +Y +G+ PLR +A + R PE+VL+T G+ A DL+ + F+D G Sbjct: 128 EQDETHFEYGMPQGFEPLRDAIARVLAGRSIHAAPEQVLLTFGANHAFDLIIRHFVDAGD 187 Query: 117 PVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPT 176 VL+E P Y RL + + V +GPDL+ E +++ RPR +L P+ NPT Sbjct: 188 SVLVETPGYYPLFGKLRLARAKLVGVSRTAKGPDLEEFERKVRQYRPRLFFLQPNAHNPT 247 Query: 177 GGLTPLPARKRLLQMVMERGLVVVEDDAYRELY-FGEARLPSLFELAREAGYPGVIYLGS 235 G L +LL++ + G+V+VEDD + +L G A L +L G VIY+G+ Sbjct: 248 GTSMSLSNMHQLLKIAEQYGVVLVEDDVFADLLPQGSAHLAAL------DGLENVIYVGT 301 Query: 236 FSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRR 295 FSK LS GLR + ++ L K +++ + ++HEL+ +G R R Sbjct: 302 FSKTLSTGLRSGYIAGSRALIRSLTDIKMLTVVNSSTFIESVIHELIVKGRYRRHLVQLR 361 Query: 296 VYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGG 355 KA A REV + + P GG ++W LP GL+ L +RA EE + PG Sbjct: 362 ERVAKASASAQRALREVGID-DVSGPGGGYYLWARLPAGLNTLELAKRATEEGIFIAPGA 420 Query: 356 PF 357 F Sbjct: 421 IF 422 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: 458 Number of extensions: 26 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: 397 Length of database: 455 Length adjustment: 32 Effective length of query: 365 Effective length of database: 423 Effective search space: 154395 Effective search space used: 154395 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