Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_015739359.1 ADEG_RS06970 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000024605.1:WP_015739359.1 Length = 398 Score = 389 bits (1000), Expect = e-113 Identities = 203/393 (51%), Positives = 254/393 (64%), Gaps = 2/393 (0%) Query: 1 MAFLSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAG 60 M L++ ++ PS T++V KA+EL G VI GAGEPDFDTP++IK AAKRA+D G Sbjct: 1 MRKLAERAQKLSPSPTLSVDTKAKELLRQGERVINFGAGEPDFDTPEHIKEAAKRALDQG 60 Query: 61 RTKYTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVII 120 TKYT V GI L+ AICEK R+N L+Y+P ++ V G K ++NAL L+PGDEVII Sbjct: 61 FTKYTPVAGILPLREAICEKLYRDNQLEYSPNEIVVSCGAKHSIFNALQVLLDPGDEVII 120 Query: 121 PAPYWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAA 180 P PYW SYP+ V LAGG PV V E FKL PE L AA+TPRT+ I NSP+NPTG Sbjct: 121 PVPYWTSYPEQVKLAGGVPVFVPTSPENDFKLRPEDLRAAVTPRTRLLILNSPANPTGTV 180 Query: 181 YTRAELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKA 240 Y R EL L EV + +WI+SD++YE L++D + + A ++P + RT+ NGVSKA Sbjct: 181 YRREELIGLAEVAL-EADLWILSDEIYEKLIYDGMEHVSIAALDPEVKKRTIVVNGVSKA 239 Query: 241 YCMTGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQR 300 Y MTGWRIGYAA P + +AM +QS STSNP S+AQ AAL AL GPQE + R AFQ+ Sbjct: 240 YAMTGWRIGYAAAPRPIAQAMTNLQSHSTSNPTSVAQAAALAALKGPQEPVENMRRAFQK 299 Query: 301 RRDLVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGV 360 RRD + LN GV CP P GAFYV+P++SG +G+ G +I A LLEE V Sbjct: 300 RRDFIWQYLNSLPGVRCPKPLGAFYVFPEVSGLLGR-RLKGREIATASDLALFLLEEIKV 358 Query: 361 AVVFGAAFGLSPNFRISYATADEVLREACARIQ 393 A V GAAFG R SYA E + E R + Sbjct: 359 ATVAGAAFGDDRYLRFSYALRLEDIEEGMQRFK 391 Lambda K H 0.318 0.134 0.399 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: 465 Number of extensions: 19 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: 400 Length of database: 398 Length adjustment: 31 Effective length of query: 369 Effective length of database: 367 Effective search space: 135423 Effective search space used: 135423 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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