Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_109967711.1 DK846_RS04615 PLP-dependent aminotransferase family protein
Query= BRENDA::Q72LL6 (397 letters) >NCBI__GCF_003173355.1:WP_109967711.1 Length = 401 Score = 324 bits (830), Expect = 3e-93 Identities = 167/382 (43%), Positives = 245/382 (64%), Gaps = 11/382 (2%) Query: 20 STIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPL 79 S IRE+LK+TQ+P I+SFAGGLP PELFP +E A A +++ E+G ALQY+ TEG+ PL Sbjct: 15 SFIREILKVTQKPEIISFAGGLPNPELFPVQELAATAEKVIAEEGTAALQYATTEGHPPL 74 Query: 80 RAFVAE------WIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFR 133 R ++A+ I + P E+LIT GSQQ LDL+GK+F+++GS V +E P Y+GAIQAF Sbjct: 75 RQWIADRYKKRLGIEISPNEILITNGSQQCLDLIGKIFINKGSNVAIERPGYLGAIQAFS 134 Query: 134 LQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVM 193 + P F T+ EGPD++ LE VL R++P F Y +P+ QNP+G RK + + + Sbjct: 135 MYEPNFSTISLTSEGPDINELERVLTRDKPCFFYGVPNSQNPSGITWSRENRKAVAETLE 194 Query: 194 ERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHP 253 + VEDDAY EL F ++PS+ EL + + GSFSK+++PG+R+ + A Sbjct: 195 RFSTIFVEDDAYGELKFRGKQMPSIKELIPDL----TVMTGSFSKIIAPGMRMGWICAPK 250 Query: 254 EALQKLVQAKQGADLHTPMLNQMLVHELLKE-GFSERLERVRRVYREKAQAMLHALDREV 312 + L++ V KQG DLH+ +L+Q ++ L + + R+ Y + ML A+ E Sbjct: 251 QILEQAVTVKQGTDLHSNILSQRIISRFLADFPVDAHISRISEAYSNQCDCMLSAIKAEF 310 Query: 313 PKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYA 372 P+ V TRP GGMF+W LP+G S+ LF RA++++VA +PG PF+ +GGG +T+RL+++ Sbjct: 311 PEGVTCTRPDGGMFIWATLPEGYSSMELFERAIKQDVAILPGIPFYTDGGGLDTVRLNFS 370 Query: 373 TLDREGIAEGVRRLGRALKGLL 394 E I EG+ RLG+ LK L Sbjct: 371 NSTPERIEEGIYRLGQVLKEYL 392 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: 471 Number of extensions: 21 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: 401 Length adjustment: 31 Effective length of query: 366 Effective length of database: 370 Effective search space: 135420 Effective search space used: 135420 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 24 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