Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_055435119.1 ASC41_RS02745 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_001418085.1:WP_055435119.1 Length = 379 Score = 254 bits (650), Expect = 2e-72 Identities = 131/378 (34%), Positives = 215/378 (56%), Gaps = 2/378 (0%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 A+R+ + Y F++ + QG +I+LG+G+PD P V+ A ++ +D + H Sbjct: 4 ANRLHSVEEYYFSKKLKEVNSLILQGKPIINLGIGSPDLQPPGKVISAITESFKDGRAHK 63 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 Y ++G R AI +Y + V ++ +E LPL+GSKEG+ H+++A++N GD VL+P+ Sbjct: 64 YQSYQGIPELREAIAGFYKTHFQVDVNATTEVLPLMGSKEGIMHISMAFLNEGDAVLIPN 123 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 P YP + + L EN+W ++ + ++ K KI++ NYP PTGA A Sbjct: 124 PGYPTYTSVTKLLQAEPIFYNLDTENNWCPNIEELEKQDLSKVKIMWLNYPHMPTGAKAT 183 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 + FE ++ FA+K++ILLV+D Y+ + +P S+L I GAKD+ +E ++LSKT+NMA Sbjct: 184 KAVFESLITFAKKHDILLVNDNPYSFIL--NKEPLSILSIEGAKDVCLELNSLSKTFNMA 241 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 GWRVG ++GN ++ + +K+N+D G+F +Q A AL ++ + Y RR Sbjct: 242 GWRVGMLLGNNELLNAVLKVKSNMDSGMFYGIQQGAIEALNSSKMWFVSLNNIYEKRRKL 301 Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368 + + +L + +++W K P + S F LL++ + +TPG FG GEGYV Sbjct: 302 VWELATKLNCSFDENATGLFVWAKLPAALNSEAFIDKLLKEHNLFITPGTIFGSQGEGYV 361 Query: 369 RISLIADCDRLGEALDRI 386 R SL A L EA+ R+ Sbjct: 362 RFSLCATVKELEEAITRV 379 Lambda K H 0.321 0.140 0.427 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: 21 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: 403 Length of database: 379 Length adjustment: 31 Effective length of query: 372 Effective length of database: 348 Effective search space: 129456 Effective search space used: 129456 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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