Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_011383786.1 AMB_RS06965 PLP-dependent aminotransferase family protein
Query= BRENDA::Q72LL6 (397 letters) >NCBI__GCF_000009985.1:WP_011383786.1 Length = 547 Score = 136 bits (343), Expect = 1e-36 Identities = 117/367 (31%), Positives = 167/367 (45%), Gaps = 17/367 (4%) Query: 37 FAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEWIG----VR-- 90 FA G+P FP E R+ R + G+APLR +AE +G VR Sbjct: 189 FAPGVPDLAAFPHAEWRRVLGRLWRRPPLELMGGIDPLGHAPLRHAIAEHLGRSRAVRCD 248 Query: 91 PEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPD 150 P +V+I GSQQALDLV +V L+ G VL+E P Y G R G + V +G D Sbjct: 249 PAQVMIMGGSQQALDLVARVLLEPGEAVLVEDPCYGGLTGVLRAAGAQVQAVAVDGQGFD 308 Query: 151 LDALEEVLKRERP--RFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYREL 208 E+ +R+ P R ++ PS Q PTG PL R L+ G V+EDD + Sbjct: 309 ----PELAERQCPSARLTFVTPSHQFPTGATMPLSRRLALIHWAERVGGWVIEDDYDSDF 364 Query: 209 YFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADL 268 + + SL L R +YLG+FSK + PGLR+ + V P L V A++ AD+ Sbjct: 365 HHAGSPTASLQGLDRGG---RTLYLGTFSKSMFPGLRLGWLVVPPPLLPAFVAARRIADM 421 Query: 269 HTPMLNQMLVHELLKEG-FSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFV 327 L Q + + EG F L R+R +Y ++ +A+L A R + + T + G+ Sbjct: 422 APAGLTQAAMAAFMTEGHFGAHLRRMRTLYGQRRRALLDAAPRILGPNLPVTAGEAGLHA 481 Query: 328 WMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYATLDREGIAEGVRRLG 387 + LP G A +A P F G L L Y L + E ++RL Sbjct: 482 ILWLPAGCDDFQAAEAARARGLAPSPLS-FHRVTKGCPGLVLGYGNLAGSSLEEALQRLR 540 Query: 388 RALKGLL 394 A+ L+ Sbjct: 541 EAIITLI 547 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: 524 Number of extensions: 32 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: 397 Length of database: 547 Length adjustment: 33 Effective length of query: 364 Effective length of database: 514 Effective search space: 187096 Effective search space used: 187096 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 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