Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_093392445.1 BM091_RS00080 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q82WA8 (397 letters) >NCBI__GCF_900114975.1:WP_093392445.1 Length = 398 Score = 372 bits (954), Expect = e-107 Identities = 186/396 (46%), Positives = 261/396 (65%), Gaps = 2/396 (0%) Query: 1 MKLSQRVQAIKPSPTLAVTAKAARLKAEGKNIIGLGAGEPDFDTPLHIKDAAITAIRNGF 60 M+LS+R+ ++PS TL++ AKA +L+ EG ++ GEPDFDTP H+K AA+ A+ Sbjct: 1 MELSKRLARVQPSATLSINAKAQQLRREGVRVVNFAVGEPDFDTPAHVKQAAVQALHFDR 60 Query: 61 TKYTAVGGTASLKQAIISKFKRENSLEFMPGEILVSSGGKQSFFNLVLATIDPGDEVIIP 120 T+YT V G LKQA+ + L + P +LVS GGK + +N++ A ++PGDEVIIP Sbjct: 61 TRYTPVSGIPELKQAVCDWIRDFYGLNYSPSSVLVSCGGKHAIYNVLQAILNPGDEVIIP 120 Query: 121 APYWVSYPDIVLIAEGKPVFIDTGIEEKFKISPDQLEKAITPRTRMFVVNSPSNPSGSVY 180 APYWVSYP++V + +G PV +D E+ +K++P LE AIT +TR+ ++NSPSNP+G Y Sbjct: 121 APYWVSYPEMVALCDGVPVIVDCDFEKDYKLTPALLENAITDKTRLVILNSPSNPTGCYY 180 Query: 181 SLEELQALGAVLRKYPDILIATDDMYEHILLSGDGFVNILNACPDLKARTVVLNGVSKAY 240 +EL L AVL K+P + + +DD+Y HIL + +VN+ + RTV++ VSK Y Sbjct: 181 DRDELVELVAVLNKHPHVTVLSDDIYSHILFNNRKWVNVAMVDETMLPRTVIIQAVSKTY 240 Query: 241 AMTGWRIGYCGGPAAIITAMENIQSQSTSNPNSIAQVAAEAALNGDQSCMVPMIEAFRER 300 AMTGWRIG+ GP II+A +QSQSTSNP SIAQ AA AAL GDQ+C+ M E F R Sbjct: 241 AMTGWRIGFAVGPEEIISAASTVQSQSTSNPCSIAQWAAIAALRGDQTCVARMAEEFENR 300 Query: 301 NQFLTNALNSIAGIHCLLSEGAFYAFVDVRQAISRLNTQQILQNSSDIAFCNYVLEKAEV 360 Q+L L I G+ C+ +GAFYAF DV + +++NS ++A Y+++KA V Sbjct: 301 CQYLVERLRQIPGVKCVEPQGAFYAFPDVSAFYGKKYDGIVVRNSVEMA--EYLIDKANV 358 Query: 361 AAVPGSAFGCEGYMRLSFATSMDNLQEAVKRIASLL 396 A VPGSAFG + +RLSFA S + L+E + RI + L Sbjct: 359 AVVPGSAFGNDRCIRLSFALSWNELEEGLNRIDTAL 394 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: 369 Number of extensions: 9 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: 398 Length adjustment: 31 Effective length of query: 366 Effective length of database: 367 Effective search space: 134322 Effective search space used: 134322 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 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