Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_011736058.1 PPRO_RS10870 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::A0A6F8T0V6 (393 letters) >NCBI__GCF_000015045.1:WP_011736058.1 Length = 397 Score = 413 bits (1061), Expect = e-120 Identities = 211/394 (53%), Positives = 273/394 (69%), Gaps = 4/394 (1%) Query: 1 MKLAKRVASLTPSATLAITAKAKELKAAGYDVIGLGAGEPDFNTPQHIIAAAIKTMNEGH 60 MKLA RV + PS TLAI AKAK LKA G DVI GAGEPDF+TP I AA ++ G Sbjct: 1 MKLADRVHRIQPSPTLAIDAKAKALKAQGVDVISFGAGEPDFDTPDAIRDAARNAIDSGF 60 Query: 61 TKYTPSGGLPALKEEIIKKFARDQGLSYEPAEIIVCVGAKHALYTLFQVLLDEGDEVIIP 120 T+Y P GG LK+ II K RD G+ Y AEI V GAKH+LY + Q L+ EGDEVIIP Sbjct: 61 TRYMPVGGADDLKDAIILKMKRDHGIEYSRAEICVSCGAKHSLYNISQALIQEGDEVIIP 120 Query: 121 TPYWVSYPEQVKLAGGVPVYVEGLEENDFKMTPDQLKQAITPKTKAVIINSPSNPTGMIY 180 PYWVSYP+QV LAGG P++++ E++DFK+TP QL+ AITP+TKA+I+NSP NPTG Y Sbjct: 121 APYWVSYPDQVVLAGGTPIFIQTDEKSDFKITPRQLEAAITPRTKAMILNSPCNPTGTSY 180 Query: 181 TAEELKALGEVCLAHGVLIVSDEIYEKLIYGGAKHVSIAELSPELKEQTIIINGVSKSHS 240 T EEL+A+ +VCLAH +I+SD+IYE+LIY G +I +++PELK++ +++NGVSK+++ Sbjct: 181 TGEELRAIAQVCLAHDFIIISDDIYERLIYDGQVFSNIVQVAPELKQRVVLVNGVSKTYA 240 Query: 241 MTGWRIGYAAGPKDIIQAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEERL 300 MTGWRIGYA GP+++I AMT + S STSN SIAQ A++ A +G QE V M Q FE+R Sbjct: 241 MTGWRIGYACGPQELIAAMTKMQSQSTSNACSIAQKASVEAIAGSQEKVTAMVQEFEKRR 300 Query: 301 NIIYDKLVQIPGFTCIKPQGAFYLFPNAR----KAADMAGCRTVDEFVAALLEEAKVALV 356 I +L +PG TC GAFY FPN K+ + + + LLEEAKVALV Sbjct: 301 TYIVQRLNAMPGVTCFNSTGAFYAFPNFSALYGKSFNGKIIASSTDLADYLLEEAKVALV 360 Query: 357 PGSGFGAPDYVRLSYATSLEALETAIERIRRFME 390 PG FG Y RLSYA LE++ ++R+ R ++ Sbjct: 361 PGVAFGDDRYARLSYAIGLESIAEGMDRLERAIQ 394 Lambda K H 0.316 0.133 0.380 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: 405 Number of extensions: 17 Number of successful extensions: 2 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: 393 Length of database: 397 Length adjustment: 31 Effective length of query: 362 Effective length of database: 366 Effective search space: 132492 Effective search space used: 132492 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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