Align aspartate transaminase; EC 2.6.1.1 (characterized)
to candidate WP_092483105.1 BM299_RS08755 pyridoxal phosphate-dependent aminotransferase
Query= CharProtDB::CH_017144 (393 letters) >NCBI__GCF_900115975.1:WP_092483105.1 Length = 397 Score = 416 bits (1069), Expect = e-121 Identities = 206/394 (52%), Positives = 275/394 (69%), Gaps = 4/394 (1%) Query: 1 MKLAKRVASLTPSATLAITEKAKELKAAGHDVIGLGAGEPDFNTPQHILDAAIKAMNEGH 60 MKLA+R +++PS TL+I +AK++ A G VI GAGEPDF TP++I A +KA+ Sbjct: 1 MKLAERAKNISPSPTLSIDAQAKKMIAEGIKVINFGAGEPDFGTPENIKQAGVKAIENDM 60 Query: 61 TKYTPSGGLPALKEEIIKKFARDQGLDYEPAEVIVCVGAKHALYTLFQVLLDEGDEVIIP 120 T+YTP G+ L+ I+KK A D GLDYEP +++V GAKH+LY FQVL EGDEVI+P Sbjct: 61 TRYTPVAGIEPLRRAIVKKLAEDNGLDYEPGQIVVSAGAKHSLYNAFQVLCQEGDEVILP 120 Query: 121 TPYWVSYPEQVKLAGGVPVYVEGLEQNHFKITPEQLKQAITPRTKAVIINSPSNPTGMIY 180 PYWVSY EQ+KL G PV V +N+FK+TP++L++AITP T+ +++NSPSNPTG +Y Sbjct: 121 APYWVSYLEQIKLTGARPVIVSTRVENNFKLTPDELRRAITPNTRLIVLNSPSNPTGAVY 180 Query: 181 TAEELKALGEVCLAHGVLIVSDEIYEKLTYGGAKHVSIAELSPELKAQTVIINGVSKSHS 240 T +EL ALGE+ + + ++SDEIYEKL Y G +HVSIA LSP LK TV+INGVSKS++ Sbjct: 181 TGDELVALGEILEQNKIAVISDEIYEKLIYDGLEHVSIAALSPGLKELTVVINGVSKSYA 240 Query: 241 MTGWRIGYAAGPKDIIKAMTDLASHSTSNPTSIAQYAAIAAYSGPQEPVEQMRQAFEQRL 300 MTGWRIGYAA P + KAM DL SHSTSNPTSIAQ A++ A G QEPV QM F +R Sbjct: 241 MTGWRIGYAAAPAPVAKAMADLQSHSTSNPTSIAQAASVEALEGTQEPVRQMVAEFVKRR 300 Query: 301 NIIYDKLVQIPGFTCVKPQGAFYLFPNARE--AAAMAGCR--TVDEFVAALLEEAKVALV 356 + + ++L +PG C +P GAFY+FP + + G + + + LLE+A VA+V Sbjct: 301 DYMVERLNAMPGVNCNRPGGAFYVFPEIKPLLGKSYEGVKIDSASDLAKVLLEKAHVAIV 360 Query: 357 PGSGFGAPDNVRLSYATSLDALETAVERIHRFME 390 PG FG RLSYATS+D + ++RI + ++ Sbjct: 361 PGIAFGDDTCFRLSYATSMDNIREGLDRIEKVLQ 394 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: 458 Number of extensions: 21 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 09 2024. 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