Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_014448518.1 LFE_RS01525 LL-diaminopimelate aminotransferase
Query= BRENDA::Q8YTF2 (403 letters) >NCBI__GCF_000284315.1:WP_014448518.1 Length = 395 Score = 407 bits (1045), Expect = e-118 Identities = 191/383 (49%), Positives = 264/383 (68%) Query: 9 ADRIQQLPPYVFARLDELKAKAREQGIDLIDLGMGNPDGATPQPVVDAAIQALQDPKNHG 68 + RI+ LPPY+FAR+DE K +A +G+D+I+LG+G+PD T P+V+AA AL P++H Sbjct: 8 SQRIKSLPPYLFARIDEKKREAMAKGMDIINLGIGDPDTPTLPPIVEAARIALGRPEHHQ 67 Query: 69 YPPFEGTASFRRAITNWYNRRYGVVLDPDSEALPLLGSKEGLSHLAIAYVNPGDVVLVPS 128 YP +EG SFR +I +WY +R+ V LDP +E L L+GSKEG+ H+ +A+++PGD VLVP Sbjct: 68 YPSYEGMLSFRESIAHWYKKRFLVDLDPHTEVLGLIGSKEGIGHMPLAFIDPGDTVLVPE 127 Query: 129 PAYPAHFRGPVIAGGTVHSLILKPENDWLIDLTAIPEEVARKAKILYFNYPSNPTGATAP 188 P YP + G + AGG + + + N +L DL+AIP+ V R+ KI++ NYP+NPTGA AP Sbjct: 128 PGYPVYHAGTLFAGGETYYMPILESNGFLPDLSAIPDSVYRRTKIMFINYPNNPTGAVAP 187 Query: 189 REFFEEIVAFARKYEILLVHDLCYAELAFDGYQPTSLLEIPGAKDIGVEFHTLSKTYNMA 248 FF E++ A KY ++ HD Y+E+ FDG P S L PGAK++G+EFH+LSKT+NM Sbjct: 188 DSFFAEVIEKATKYGFIVAHDAAYSEIYFDGNAPKSFLSFPGAKEVGIEFHSLSKTFNMT 247 Query: 249 GWRVGFVVGNRHVIQGLRTLKTNLDYGIFAALQTAAETALQLPDIYLHEVQQRYRTRRDF 308 GWRVGF VGN V+ GL +K+N+D GIF ALQ A+ A+ LPD ++ ++ Y+ RRD Sbjct: 248 GWRVGFAVGNASVLAGLGKIKSNMDSGIFQALQEASIAAMALPDFWMENLRSMYQERRDV 307 Query: 309 LIQGLGELGWDVPKTKATMYLWVKCPVGMGSTDFALNLLQQTGVVVTPGNAFGVAGEGYV 368 L+ GL G V A+ YLW P GM S + +L LL +TG+V TPGN FG++GEGYV Sbjct: 308 LVSGLRTAGLRVIPPGASFYLWAGIPAGMKSEEASLALLSRTGIVATPGNGFGISGEGYV 367 Query: 369 RISLIADCDRLGEALDRIKQAGI 391 R +L D RL EA+DRI G+ Sbjct: 368 RFALTVDTPRLKEAIDRIVNEGL 390 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: 507 Number of extensions: 25 Number of successful extensions: 1 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: 395 Length adjustment: 31 Effective length of query: 372 Effective length of database: 364 Effective search space: 135408 Effective search space used: 135408 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 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