Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate WP_061533103.1 CAter10_RS08670 PLP-dependent aminotransferase family protein
Query= metacyc::MONOMER-6727 (397 letters) >NCBI__GCF_001584165.1:WP_061533103.1 Length = 397 Score = 344 bits (882), Expect = 3e-99 Identities = 182/396 (45%), Positives = 261/396 (65%), Gaps = 18/396 (4%) Query: 3 PLSWSEAFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILRE 62 PL W F + A ++Q+S IRE+LK+T RP I+SFAGGLP+P FP E+ A ++L E Sbjct: 8 PLEWR--FSERAQKLQSSAIREILKITMRPEIISFAGGLPSPATFPVEQLKVAFDKVLSE 65 Query: 63 KGEVALQYSPTEGYAPLRAFVAEWIG-----VRPEEVLITTGSQQALDLVGKVFLDEGSP 117 +G+VALQY PT+GY PLR +VA+ + + P +VL+T+GSQQ LDL+GKV +DEGS Sbjct: 66 QGKVALQYGPTDGYGPLREWVADSLSTNGAKILPNQVLMTSGSQQGLDLLGKVLIDEGSK 125 Query: 118 VLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKR--ERPRFLYLIPSFQNP 175 VL+E PSY+GA+QAF L GP F++VP+ E G L E + + R LY +P+FQNP Sbjct: 126 VLVETPSYLGALQAFSLYGPEFVSVPSDEGG----LLPETVATLGQGARMLYALPNFQNP 181 Query: 176 TGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGS 235 TG + R L+ + GL ++EDD Y L + LP + L+ G GVIY+GS Sbjct: 182 TGRTLSVERRHALVDICARLGLPLIEDDPYGALSYRTEPLPKM--LSMNPG--GVIYMGS 237 Query: 236 FSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGF-SERLERVR 294 FSK+L+PG+R+ + VA ++KL QAKQ DLHT L QM+V+ +K+GF +E + +R Sbjct: 238 FSKILTPGIRLGYVVAPRPLIEKLEQAKQATDLHTAQLTQMVVYNTIKDGFLNEHIPTIR 297 Query: 295 RVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPG 354 ++Y ++ AML AL P E +T+P+GGMF+W+ LPK + + L A++++VAFVPG Sbjct: 298 KLYSDQCDAMLDALKTYFPSECSWTKPEGGMFIWVTLPKHIDSMKLLDEAVQQHVAFVPG 357 Query: 355 GPFFANGGGENTLRLSYATLDREGIAEGVRRLGRAL 390 PF+ N ++TLRLS+ T+ I EG+ RLG+ + Sbjct: 358 APFYGNTPEKHTLRLSFVTVPPAKIREGIERLGKLI 393 Lambda K H 0.320 0.139 0.401 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: 516 Number of extensions: 26 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: 397 Length adjustment: 31 Effective length of query: 366 Effective length of database: 366 Effective search space: 133956 Effective search space used: 133956 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