Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_086509188.1 BZY95_RS06660 PLP-dependent aminotransferase family protein
Query= BRENDA::Q72LL6 (397 letters) >NCBI__GCF_002151265.1:WP_086509188.1 Length = 476 Score = 139 bits (349), Expect = 2e-37 Identities = 100/334 (29%), Positives = 160/334 (47%), Gaps = 11/334 (3%) Query: 68 LQYSPTEGYAPLRAFVAEWIG-----VRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEA 122 L Y +G LR V + P++VLITTG Q+AL L + + G V +++ Sbjct: 141 LNYDSLQGSLALRRQVVRLAAKSGCLLHPDDVLITTGCQEALSLALRTLTEPGDVVAVDS 200 Query: 123 PSYMGAIQAFRLQGPRFLTVPAGEE-GPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTP 181 PS+ G +Q + Q + L +P G L+ALE L++ + + + P+ NP G P Sbjct: 201 PSFYGTMQILKAQKLKALEIPTDPRTGISLEALELALEQWPIKAIQITPTCNNPLGYTMP 260 Query: 182 LPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLS 241 ++ L+ + + +VEDD Y +L F EA P + + G V+ +FSK L Sbjct: 261 EARKRALVALAQRFDVAIVEDDIYGDLSF-EAPRPRTLKSFDDDGR--VLLCSAFSKTLV 317 Query: 242 PGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREK 300 PGLRV + +A + + K + + L Q+ V E ++ G ER L + R YR Sbjct: 318 PGLRVGW-MAPGRYRDQALHMKYVSTGASATLPQLAVAEFVEHGHYERHLREMLRQYRRH 376 Query: 301 AQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFAN 360 M+ + R P + P+GG +W+ELP + L + E + PG F A+ Sbjct: 377 RDIMIDWVTRYFPAGTGVSFPQGGFLLWLELPGDIDCVRLKEQLANEGLHITPGSLFSAS 436 Query: 361 GGGENTLRLSYATLDREGIAEGVRRLGRALKGLL 394 G + LRL+YA + G++R+G A+ LL Sbjct: 437 GKFRHCLRLNYAAAMTPTVEAGIKRVGEAVAALL 470 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: 478 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 397 Length of database: 476 Length adjustment: 32 Effective length of query: 365 Effective length of database: 444 Effective search space: 162060 Effective search space used: 162060 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