Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_010962186.1 MCA_RS14695 PLP-dependent aminotransferase family protein
Query= BRENDA::Q72LL6 (397 letters) >NCBI__GCF_000008325.1:WP_010962186.1 Length = 452 Score = 256 bits (653), Expect = 1e-72 Identities = 154/383 (40%), Positives = 217/383 (56%), Gaps = 20/383 (5%) Query: 16 RIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEG 75 R+ +S IR++L++TQRPG++SFAGGLPA E+ P+ + AA + QY P+EG Sbjct: 73 RLTSSLIRDILQITQRPGVISFAGGLPAEEMMPELDFGACAAD--------SRQYGPSEG 124 Query: 76 YAPLRAFVAEWI---GVR--PEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQ 130 LR +A + G+R E+VL+TTGSQQ +DLVGK+F+DEG+PVLLE+P+Y+ A+Q Sbjct: 125 EPVLRDLIARGLSGLGLRCQTEQVLVTTGSQQGIDLVGKLFIDEGTPVLLESPTYLAALQ 184 Query: 131 AFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQ 190 FR+ G F +P G D DAL+ + R RP F+YLIPSFQNP+G AR+ + Sbjct: 185 CFRVYGAEFHGLPLQVGGIDPDALKAAIVRHRPAFVYLIPSFQNPSGCCYADAARRAVAA 244 Query: 191 MVMERGLVVVEDDAYRELYFGEA-RLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFA 249 ++ E G +VEDD YR+L + R P L R +YLGSFSK+ +PGLRV + Sbjct: 245 VLDETGTPLVEDDPYRDLVYTSCDRTPVCAYLERAPW----VYLGSFSKITAPGLRVGYL 300 Query: 250 VAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEG-FSERLERVRRVYREKAQAMLHAL 308 + P LV+ KQ +DLHT Q + L G F + L + VY + M AL Sbjct: 301 ASSPGLFPWLVRLKQSSDLHTGRTGQAWLARFLSSGDFGKHLAHMNGVYAGRRDTMQAAL 360 Query: 309 DREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGE-NTL 367 +R ++ P GG+F W+ L + + AL +VAF+PG PFF L Sbjct: 361 ERHFSGLAEWSAPAGGLFFWLRLVGNIDTLAALKVALGRDVAFMPGEPFFPVADQRYPAL 420 Query: 368 RLSYATLDREGIAEGVRRLGRAL 390 RL+++ E I G+ L L Sbjct: 421 RLNFSHATPEKIERGIGLLSEVL 443 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: 485 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: 452 Length adjustment: 32 Effective length of query: 365 Effective length of database: 420 Effective search space: 153300 Effective search space used: 153300 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 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