Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_020562716.1 A3OW_RS0107000 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >NCBI__GCF_000372865.1:WP_020562716.1 Length = 393 Score = 479 bits (1232), Expect = e-140 Identities = 239/392 (60%), Positives = 307/392 (78%), Gaps = 5/392 (1%) Query: 1 MKLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGF 60 +KLS RVQ++KPSPTLA+TA+AA+++A GK+I+GLGAGEPDFDTP HIK AA+ A+ GF Sbjct: 3 IKLSNRVQSVKPSPTLAITARAAQMRAAGKDIVGLGAGEPDFDTPEHIKAAAVQALAKGF 62 Query: 61 TKYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIP 120 TKYTAV G SLK+AII KFK++N L++ +ILVS GGKQS FNL A ++PGDEVIIP Sbjct: 63 TKYTAVDGIPSLKKAIIDKFKKDNGLDYQAKQILVSCGGKQSSFNLTQALLNPGDEVIIP 122 Query: 121 APYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVY 180 AP+WVSYPD+VL+A+G PV IDT ++FKISP+QL AITP+TR+ +NSPSNPSG Y Sbjct: 123 APFWVSYPDMVLLADGVPVIIDTTQAQRFKISPEQLRAAITPKTRLIFINSPSNPSGIAY 182 Query: 181 SLEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAY 240 +L+EL+ LG VL+++P+I+IATDDMYEHIL FVNILNA PDL RTVV+NGVSKAY Sbjct: 183 TLDELKVLGNVLKEHPNIIIATDDMYEHILWKEGTFVNILNAHPDLYDRTVVMNGVSKAY 242 Query: 241 AMTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRER 300 +MTGWRIGY GPA +I AM +QSQSTSNP SI+QVAAEAAL GDQS + M F++R Sbjct: 243 SMTGWRIGYAAGPADLIEAMTTVQSQSTSNPTSISQVAAEAALTGDQSFIHDMCVEFKQR 302 Query: 301 NQFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEV 360 + ++ LN I GI C+ ++G FY F +V + ++RL+ D+AF Y++E+A V Sbjct: 303 HDYVVAELNKIDGIDCMETDGTFYVFPNVEKLLARLD-----GIDDDLAFSEYLIEQAGV 357 Query: 361 AAVPGSAFGCEGYMRLSFATSMDNLQEAVKRI 392 A VPGSAFG G++R+S ATSM NL++A++RI Sbjct: 358 ALVPGSAFGTPGHIRISIATSMANLEKALERI 389 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: 430 Number of extensions: 19 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: 393 Length adjustment: 31 Effective length of query: 366 Effective length of database: 362 Effective search space: 132492 Effective search space used: 132492 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 09 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