Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate WP_012407008.1 NPUN_RS00985 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >NCBI__GCF_000020025.1:WP_012407008.1 Length = 388 Score = 362 bits (928), Expect = e-104 Identities = 190/392 (48%), Positives = 256/392 (65%), Gaps = 11/392 (2%) Query: 4 LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTK 63 L+ +++V PS T+A+ KA+ L A G DV AGEPDFDTP +IKAAA +A+D G+TK Sbjct: 3 LAARVSQVTPSLTLAIAAKAKALKAEGIDVCSFSAGEPDFDTPAHIKAAAVKALDEGKTK 62 Query: 64 YTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAP 123 Y A G P+L+ AI K + +NGL Y V V GGK LYN +VA ++ GDEVIIPAP Sbjct: 63 YGAAAGEPKLREAIAHKLKNDNGLDYKSENVIVTNGGKHSLYNLIVALIDLGDEVIIPAP 122 Query: 124 YWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTR 183 YW+SYP+MV L GG V V TG+K+TPEQL AITP+TK FI NSPSNPTG YT Sbjct: 123 YWLSYPEMVTLVGGVAVIVPTDATTGYKITPEQLRKAITPKTKLFILNSPSNPTGMVYTP 182 Query: 184 AELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCM 243 E+ AL +V++ ++++SD++YE +++D + + + ++DRTL NG +KAY M Sbjct: 183 DEIKALAQVVV-DADIFVVSDEIYEKILYDGAEHISIGSLGKEIFDRTLISNGFAKAYSM 241 Query: 244 TGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRD 303 TGWRIGY AGPVE+I+A TIQ STSN C+ AQY A+ AL Q+ + R+AF +RR Sbjct: 242 TGWRIGYLAGPVEIIKAASTIQGHSTSNVCTFAQYGAIAALQSSQDCVEEMRQAFAKRRQ 301 Query: 304 LVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVV 363 +++ LN G++ P+GAFY++PDIS KT G K + F ALLE+ VAV+ Sbjct: 302 VMLDRLNAIPGLSTAKPDGAFYLFPDIS----KT---GLKSLE---FCDALLEKHQVAVI 351 Query: 364 FGAAFGLSPNFRISYATADEVLREACARIQAF 395 G AFG N R+SYAT + + R++ F Sbjct: 352 PGIAFGADDNIRLSYATDMATIEKGMDRLEKF 383 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: 444 Number of extensions: 20 Number of successful extensions: 4 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: 388 Length adjustment: 31 Effective length of query: 369 Effective length of database: 357 Effective search space: 131733 Effective search space used: 131733 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 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