Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_004514449.1 GMET_RS03670 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_000012925.1:WP_004514449.1 Length = 397 Score = 309 bits (792), Expect = 8e-89 Identities = 157/382 (41%), Positives = 239/382 (62%), Gaps = 8/382 (2%) Query: 6 LSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAEK 65 ++ ++ +++K SWIRK+F+EG RL++ G + V+DF+LGNP EPP F+ A Sbjct: 3 IATKIAGHISKSSWIRKMFEEGERLRQVHGAENVYDFTLGNPDTEPPREFQEEFARLATN 62 Query: 66 ---GSHGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPGE 122 G H Y+ N G R VA+ L A +VMT GAGGALNV LK+I+NPGE Sbjct: 63 PIPGMHRYMNNAGYQETRAAVAEVLAEASGLPVEAGHVVMTCGAGGALNVVLKTILNPGE 122 Query: 123 EVIILAPYFAEYKLYIENYGGKAVSCPLTSR--FEIDIEAVRQSITPQTKGLILNTPHNP 180 EVIIL PYF EYK YI+N+GG T+R F+++I A+ +IT +T+ +I+ +P+NP Sbjct: 123 EVIILTPYFVEYKFYIDNHGGVPKEV-WTNRETFQLNIPAIEAAITNKTRAVIICSPNNP 181 Query: 181 TGTVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYD-EELANPFQSYHRVILAS 239 TG + ++++ +LG +L E + + IYV+ DEPY+++ +D + + N F+ ++ + Sbjct: 182 TGVIYPEESLKELGEMLARAERRYDRQIYVISDEPYARIAFDGKHVPNIFRYVESSVIVT 241 Query: 240 SFSKDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRV 299 S SKDL + GER+GY+ ++ + + V+ NR LG+VNAP +MQR V ++ V Sbjct: 242 SHSKDLALPGERIGYLAVNPSARGVEQFVEGAVFSNRVLGYVNAPALMQRLVTKLQRASV 301 Query: 300 DASAYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSS 359 D Y+ +RDL+ D L GFE P G F++FPKSP+ D+V F V AQK+++L+VP + Sbjct: 302 DIGEYQSKRDLLYDRLTAMGFEMVRPDGAFYLFPKSPLTDDVEF-VKMAQKHRILLVPGA 360 Query: 360 GFGMSGHFRLSFSVPIEQIKNS 381 GFG G FR+++ V I+ S Sbjct: 361 GFGAPGFFRIAYCVDRGMIERS 382 Lambda K H 0.320 0.139 0.396 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: 418 Number of extensions: 23 Number of successful extensions: 5 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 ( 7.4 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 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