Align Probable aspartate aminotransferase; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_057508832.1 ABB28_RS11865 pyridoxal phosphate-dependent aminotransferase
Query= curated2:P63499 (429 letters) >NCBI__GCF_001431535.1:WP_057508832.1 Length = 425 Score = 338 bits (868), Expect = 1e-97 Identities = 177/392 (45%), Positives = 242/392 (61%), Gaps = 1/392 (0%) Query: 33 KLQDVLYEIRGPVHQHAARLEAEGHRILKLNIGNPAPFGFEAPDVIMRDIIQALPYAQGY 92 +L +V YEIRG + + A LEA+G ++KLNIGNP FGF AP+ + R I + Y Sbjct: 14 RLSEVRYEIRGELARRARELEAQGRTLIKLNIGNPGNFGFRAPEHLQRAIADDMGRTDPY 73 Query: 93 SDSQGILSARRAVVTRYELVPGFPRFDVDDVYLGNGVSELITMTLQALLDNGDQVLIPSP 152 + QG+ AR A+ Y G P D V++GNGVSELI ++L+ALL+ GD+VL+PSP Sbjct: 74 THQQGLPEAREAIAAAYAR-RGAPDAHPDRVFIGNGVSELIDLSLRALLNPGDEVLVPSP 132 Query: 153 DYPLWTASTSLAGGTPVHYLCDETQGWQPDIADLESKITERTKALVVINPNNPTGAVYSC 212 DYPLW+A+T L G PV+Y C G+QPD +++E+ ++ RT+A+V+INPNNP+GA YS Sbjct: 133 DYPLWSAATILNDGRPVYYRCAPENGFQPDPSEIEALVSSRTRAIVLINPNNPSGASYSR 192 Query: 213 EILTQMVDLARKHQLLLLADEIYDKILYDDAKHISLASIAPDMLCLTFNGLSKAYRVAGY 272 E+L ++V +ARKH LLL+ DEIYD+ILYDDA +A +A D C+TF+GLSK +R G+ Sbjct: 193 ELLERIVAIARKHNLLLMVDEIYDQILYDDAVFQPVAPLAGDQPCITFSGLSKVHRACGW 252 Query: 273 RAGWLAITGPKEHASSFIEGIGLLANMRLCPNVPAQHAIQVALGGHQSIEDLVLPGGRLL 332 R GW ++G F + LL+ +RLC NVP Q+AI A+ G +I L PGGRL Sbjct: 253 RVGWAMLSGDAGRLGEFRAAMDLLSALRLCANVPGQYAIDAAVNGPDTITPLCTPGGRLY 312 Query: 333 EQRDIAWTKLNEIPGVSCVKPAGALYAFPRLDPEVYDIDDDEQLVLDLLLSEKILVTQGT 392 E R +S V PAGALYAFP + + DD LDL+ E +LV G+ Sbjct: 313 ETRRAVIDACAASEHLSLVAPAGALYAFPAVVGDAAKGLDDHDFALDLMTDEGVLVVPGS 372 Query: 393 GFNWPAPDHLRLVTLPWSRDLAAAIERLGNFL 424 FN P H R+ LP + + R+ L Sbjct: 373 SFNVPYRHHFRVTLLPEATVMREVFSRIDRAL 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: 549 Number of extensions: 23 Number of successful extensions: 3 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: 425 Length adjustment: 32 Effective length of query: 397 Effective length of database: 393 Effective search space: 156021 Effective search space used: 156021 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: 51 (24.3 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