Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_012969598.1 ALVIN_RS01795 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >NCBI__GCF_000025485.1:WP_012969598.1 Length = 396 Score = 491 bits (1263), Expect = e-143 Identities = 247/391 (63%), Positives = 300/391 (76%), Gaps = 5/391 (1%) Query: 2 KLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGFT 61 KL+ RVQA+KPS TLA+TA+AA L+AEGK++IGLG GEPDFDTP HIK AAI AI +GFT Sbjct: 4 KLAARVQAVKPSATLAITARAAALRAEGKDVIGLGVGEPDFDTPEHIKAAAIRAIESGFT 63 Query: 62 KYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIPA 121 KYTAV GT LK+AII+KF+REN L++ P +ILVS GGKQSFFNL A +DPGDEV+IPA Sbjct: 64 KYTAVDGTPDLKRAIIAKFQRENGLDYAPNQILVSCGGKQSFFNLAQALLDPGDEVVIPA 123 Query: 122 PYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVYS 181 PYWVSYPD+VL+A G PVF+ G + FKI+P QL+ A+ +TR+ V+NSPSNP+G YS Sbjct: 124 PYWVSYPDMVLLAGGLPVFVQAGAAQSFKITPAQLKGAMNEKTRLVVINSPSNPTGMAYS 183 Query: 182 LEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAYA 241 EEL+ALG VLR +P ++IATDDMYEHI S FVNILNACPDL RT+VLNGVSKAY+ Sbjct: 184 REELEALGEVLRDFPKVIIATDDMYEHIRWSSAPFVNILNACPDLAPRTLVLNGVSKAYS 243 Query: 242 MTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRERN 301 MTGWRIGY GPA II AM IQSQSTSNP SI+QVAA+ AL+G Q C+ M++AF ER+ Sbjct: 244 MTGWRIGYAAGPAHIIKAMNTIQSQSTSNPTSISQVAAQVALDGPQECIGVMLKAFMERH 303 Query: 302 QFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEVA 361 F+ LN I GI CL ++G FY F V++ I RL ++D+ Y++EKA VA Sbjct: 304 DFVVERLNQIPGIECLPTDGTFYVFPKVQKLIERLEGV-----NNDLELGEYLIEKAGVA 358 Query: 362 AVPGSAFGCEGYMRLSFATSMDNLQEAVKRI 392 VPGSAFG GYMRLS ATS + L+ A+ RI Sbjct: 359 VVPGSAFGLGGYMRLSIATSRETLERALDRI 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: 407 Number of extensions: 11 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: 396 Length adjustment: 31 Effective length of query: 366 Effective length of database: 365 Effective search space: 133590 Effective search space used: 133590 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