Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_028487491.1 Q394_RS0100140 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >NCBI__GCF_000621325.1:WP_028487491.1 Length = 391 Score = 493 bits (1268), Expect = e-144 Identities = 248/395 (62%), Positives = 308/395 (77%), Gaps = 6/395 (1%) Query: 1 MKLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGF 60 ++LSQRV +KPSPTLA+TA AA+LKA G++IIGLGAGEPDFDTP +IK A I AI+ G Sbjct: 3 IQLSQRVGRVKPSPTLAITALAAQLKASGRDIIGLGAGEPDFDTPDYIKQAGIEAIQKGE 62 Query: 61 TKYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIP 120 T+YTAV GT +LKQAII KFKR+N L+F P +ILVS GGKQSF+NL A +D GDEVIIP Sbjct: 63 TRYTAVDGTPALKQAIIRKFKRDNGLDFTPKQILVSCGGKQSFYNLCQALLDAGDEVIIP 122 Query: 121 APYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVY 180 APYWVSYPD+VL+A+G PV + G E FK+SP +LE AIT +TR+FV+NSPSNP+G Y Sbjct: 123 APYWVSYPDMVLLADGVPVIVAAGQAEHFKLSPAKLEAAITSKTRLFVINSPSNPTGVAY 182 Query: 181 SLEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAY 240 +LEEL ALG VLR+YP +LIATDDMYEH+L G FVNIL+ACPDL RT+VLNGVSKAY Sbjct: 183 TLEELVALGEVLRRYPQVLIATDDMYEHVLFEGRKFVNILDACPDLYERTIVLNGVSKAY 242 Query: 241 AMTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRER 300 +MTGWRIGY GGP +I AM IQSQSTSNP SI+Q AA AL+GDQS + M+ AF +R Sbjct: 243 SMTGWRIGYAGGPEKLIQAMNIIQSQSTSNPTSISQYAAAIALDGDQSFIQTMVSAFEQR 302 Query: 301 NQFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEV 360 + F+ +A N++ G+ CL ++G FY+F +V I RL + +D A +Y+L+K V Sbjct: 303 HAFVLDAFNAMEGVECLPADGTFYSFPNVEGMIKRLGLE------NDAALASYLLDKTGV 356 Query: 361 AAVPGSAFGCEGYMRLSFATSMDNLQEAVKRIASL 395 A VPGSAFG EG++R+SFATSM NL+ A+ RIAS+ Sbjct: 357 AVVPGSAFGLEGHIRISFATSMANLENALGRIASV 391 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: 445 Number of extensions: 20 Number of successful extensions: 3 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: 391 Length adjustment: 31 Effective length of query: 366 Effective length of database: 360 Effective search space: 131760 Effective search space used: 131760 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