Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_011939366.1 GURA_RS12735 pyridoxal phosphate-dependent aminotransferase
Query= CharProtDB::CH_017144 (393 letters) >NCBI__GCF_000016745.1:WP_011939366.1 Length = 397 Score = 425 bits (1093), Expect = e-123 Identities = 217/389 (55%), Positives = 276/389 (70%), Gaps = 4/389 (1%) Query: 1 MKLAKRVASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGH 60 MKLA RV + PS TLAI KAK LKA G DVIG GAGEPDF+TP +I +A KA++ G Sbjct: 1 MKLADRVNKIQPSPTLAIDAKAKALKAQGVDVIGFGAGEPDFDTPANIREAGKKAIDAGF 60 Query: 61 TKYTPSGGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIP 120 T+Y P GG LK+ II K +D GL+Y E+ V GAKH LY + Q L+ EGDEVIIP Sbjct: 61 TRYMPVGGADDLKDAIIAKMKKDHGLEYSRDEISVACGAKHTLYNISQALIQEGDEVIIP 120 Query: 121 TPYWVSYPEQVKLAGGVPVYVEGLEQNHFKITPEQLKQAITPRTKAVIINSPSNPTGMIY 180 PYWVSYP+QV LAGG V++E E+ FKITP QL++A+TP+TKA+I+NSP NPTG Y Sbjct: 121 APYWVSYPDQVVLAGGTSVFIETGEETAFKITPAQLEKAVTPKTKALILNSPCNPTGTSY 180 Query: 181 TAEELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHS 240 T EELKA+G+VCL H LI+SD+IYE+L Y G K +I ++ PELK++TV++NGVSK+++ Sbjct: 181 TEEELKAIGQVCLKHDFLIISDDIYERLIYDGLKFANIVQVVPELKSRTVVVNGVSKTYA 240 Query: 241 MTGWRIGYAAGPKDIIKAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEQRL 300 MTGWRIGYA GPK++I AMT + S STSN TSIAQ A++ A +GPQE V M+ FE+R Sbjct: 241 MTGWRIGYACGPKELIGAMTKMQSQSTSNATSIAQKASVEALNGPQEAVAAMKVEFEKRR 300 Query: 301 NIIYDKLVQIPGFTCVKPQGAFYLFPNAREAAAMAGCRTV----DEFVAALLEEAKVALV 356 I ++L +PG TC + GAFY+FPN + V +F A LLEEAKVALV Sbjct: 301 TYIVERLNAMPGVTCFRSTGAFYVFPNFSAVYGKSFNGKVISNSTDFAAYLLEEAKVALV 360 Query: 357 PGSGFGAPDNVRLSYATSLDALETAVERI 385 PG FGA RLSYA S++ ++ ++RI Sbjct: 361 PGVAFGADKYARLSYAISMENIKKGMDRI 389 Lambda K H 0.316 0.133 0.381 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: 434 Number of extensions: 22 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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