Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_006747533.1 THITH_RS08315 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >NCBI__GCF_000227685.2:WP_006747533.1 Length = 395 Score = 470 bits (1210), Expect = e-137 Identities = 238/392 (60%), Positives = 297/392 (75%), Gaps = 6/392 (1%) Query: 1 MKLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGF 60 ++LS+RVQ IKPSPTLAV+A AA+L++EG++I+GLGAGEPDFDTP HIK AI A+ G Sbjct: 3 IQLSERVQRIKPSPTLAVSALAAQLRSEGRDIVGLGAGEPDFDTPEHIKQGAIDALARGE 62 Query: 61 TKYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIP 120 TKYTAV GTA+LKQAII+KF+R+N +F P EILVSSGGKQS FNL A ++PGDEV+IP Sbjct: 63 TKYTAVDGTAALKQAIIAKFERDNGFQFKPNEILVSSGGKQSIFNLAQALLNPGDEVLIP 122 Query: 121 APYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVY 180 APYWVSYPDI L+A+ PVFI E F+I+ +QL AITPR+R+ +NSPSNP+G+ Y Sbjct: 123 APYWVSYPDIALLADATPVFITATQESGFRINAEQLRAAITPRSRLIFLNSPSNPTGAAY 182 Query: 181 SLEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAY 240 S +EL AL VLR++P+++IATDDMYEHIL G FVNILN PDL RTVVLNGVSKAY Sbjct: 183 SADELSALAEVLREHPNLVIATDDMYEHILFGGAKFVNILNVAPDLAPRTVVLNGVSKAY 242 Query: 241 AMTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRER 300 AMTGWRIGY GGPA +I AM+N+QSQSTSNP SIAQ AA ALNGDQ C+ M F +R Sbjct: 243 AMTGWRIGYAGGPAKLIGAMKNVQSQSTSNPTSIAQAAAVVALNGDQQCVRDMCVEFEKR 302 Query: 301 NQFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEV 360 + + + LN+I G+ CL+ +G FY F V A+ Q + DI F +L+ V Sbjct: 303 ARHVVDGLNAIPGVECLMPDGTFYCFPRVTGAM------QARGIADDIEFSRRLLDDVGV 356 Query: 361 AAVPGSAFGCEGYMRLSFATSMDNLQEAVKRI 392 A VPGSAFG +G++R+SFATS+ L +A++RI Sbjct: 357 ALVPGSAFGLDGHVRISFATSLAVLDQALERI 388 Lambda K H 0.318 0.133 0.380 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: 431 Number of extensions: 16 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 366 Effective length of database: 364 Effective search space: 133224 Effective search space used: 133224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 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