Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_041101949.1 SUTH_RS07520 pyridoxal phosphate-dependent aminotransferase
Query= curated2:P63499 (429 letters) >NCBI__GCF_000828635.1:WP_041101949.1 Length = 408 Score = 493 bits (1268), Expect = e-144 Identities = 228/400 (57%), Positives = 306/400 (76%), Gaps = 1/400 (0%) Query: 30 QSAKLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYA 89 +SAKL +V Y+IRGPV A ++E EGH+I+KLNIGN A FGF++P+ I +D+I+ LP A Sbjct: 6 KSAKLNNVCYDIRGPVLARAKQMEEEGHKIIKLNIGNLAAFGFDSPEEIQQDMIRNLPSA 65 Query: 90 QGYSDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLI 149 GY DS+GI SAR+AV+ Y ++D+Y+GNGVSELI M + ALLD+GD+VL+ Sbjct: 66 AGYVDSKGIFSARKAVM-HYTQQKHIKGVTIEDIYIGNGVSELIVMAMNALLDSGDEVLL 124 Query: 150 PSPDYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAV 209 P+PDYPLWTA+ SL+GGTP HYLCDE GW PD+ D+ +KIT +T+A+V+INPNNPTGAV Sbjct: 125 PAPDYPLWTAAVSLSGGTPRHYLCDEGAGWLPDLDDIRAKITPQTRAIVIINPNNPTGAV 184 Query: 210 YSCEILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRV 269 Y E+L +++++AR++ L++ ADE+YDK+LYD H S+A+++ D+L +TFNGLSK YR Sbjct: 185 YPDEVLKEIIEIARQNDLIIYADEVYDKVLYDGVTHTSIAALSEDVLTITFNGLSKNYRS 244 Query: 270 AGYRAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGG 329 GYR+GW+ ++G K+HA +I+G+ +LA+MRLC NVP Q IQ ALGG+QSI+DLV PGG Sbjct: 245 CGYRSGWMIVSGEKKHARDYIDGLDMLASMRLCANVPGQWGIQTALGGYQSIDDLVAPGG 304 Query: 330 RLLEQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVT 389 R+ QRD+A + IPGVSCVKP LY FPRLDP++Y I DD+ + +LL++EK+L+ Sbjct: 305 RMCRQRDVAHELITAIPGVSCVKPRATLYMFPRLDPKMYPISDDQDFIAELLVAEKVLLV 364 Query: 390 QGTGFNWPAPDHLRLVTLPWSRDLAAAIERLGNFLVSYRQ 429 QGTGFNWP PDH RLV LP DL AI R+ FL YR+ Sbjct: 365 QGTGFNWPHPDHFRLVFLPHEDDLREAIGRIARFLEGYRK 404 Lambda K H 0.320 0.138 0.419 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: 562 Number of extensions: 20 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: 429 Length of database: 408 Length adjustment: 32 Effective length of query: 397 Effective length of database: 376 Effective search space: 149272 Effective search space used: 149272 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 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