Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.79 (characterized)
to candidate Synpcc7942_2545 Synpcc7942_2545 aspartate aminotransferase
Query= SwissProt::A3PMF8 (400 letters) >FitnessBrowser__SynE:Synpcc7942_2545 Length = 392 Score = 363 bits (933), Expect = e-105 Identities = 185/392 (47%), Positives = 251/392 (64%), Gaps = 11/392 (2%) Query: 4 LSDTLARVKPSQTIAVTNKARELAAAGRDVIGLGAGEPDFDTPDNIKAAAKRAIDAGRTK 63 LS+ + RV PS T+A+ +A+ + A G DV AGEPDF+TP +I+ AA +A+ G+T+ Sbjct: 3 LSERVGRVSPSLTLAIAAQAKAMKAEGLDVCSFSAGEPDFETPLHIRNAAAQALAEGKTR 62 Query: 64 YTAVDGIPELKRAICEKFERENGLKYTPAQVTVGTGGKQILYNALVATLNPGDEVIIPAP 123 Y G P+L+ AI +K +NGL Y A + V GGKQ LYN + L+PGDEVIIPAP Sbjct: 63 YGPAAGEPDLREAIAQKLRADNGLDYQAANILVTNGGKQSLYNLMQVLLDPGDEVIIPAP 122 Query: 124 YWVSYPDMVLLAGGTPVSVAAGMETGFKLTPEQLEAAITPRTKWFIFNSPSNPTGAAYTR 183 YW+SYP+MV LAGG PV V GFKL P+QL AITPRT+ + NSPSNPTG Y+R Sbjct: 123 YWLSYPEMVKLAGGVPVIVETFASDGFKLQPQQLAGAITPRTRLLVLNSPSNPTGMVYSR 182 Query: 184 AELAALCEVLMRHPQVWIMSDDMYEHLVFDDFDFTTPAQIEPGLYDRTLTCNGVSKAYCM 243 EL A+ ++ H W++SD++YE +++D D + + P ++RTL NG +KAY M Sbjct: 183 QELEAIAPIIEAH-DFWVVSDEIYEKILYDGADHHSIGSLSPACFERTLISNGFAKAYSM 241 Query: 244 TGWRIGYAAGPVELIRAMGTIQSQSTSNPCSIAQYAALEALSGPQEFLATNREAFQRRRD 303 TGWR+GY AGP ELI A ++QS STSN C+ AQY A+ AL GPQ+ +A AF RR Sbjct: 242 TGWRVGYLAGPSELIAAAASLQSHSTSNVCTFAQYGAIAALQGPQDCVAEMLAAFTERRQ 301 Query: 304 LVVSMLNEAKGVTCPNPEGAFYVYPDISGCIGKTSAGGAKITDDEAFASALLEETGVAVV 363 L+++ LN+ G++CP PEGAFYV+ DIS KT D + LL++ VA + Sbjct: 302 LILNGLNQIAGLSCPIPEGAFYVFVDIS----KTG------LDSMTYCRQLLDQHQVAAI 351 Query: 364 FGAAFGLSPNFRISYATADEVLREACARIQAF 395 G AFG + R+SYAT + + + R+Q F Sbjct: 352 PGIAFGDDRSIRLSYATDCQTIEKGLERLQLF 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: 428 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: 392 Length adjustment: 31 Effective length of query: 369 Effective length of database: 361 Effective search space: 133209 Effective search space used: 133209 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