Align Putative aspartate aminotransferase YhdR; AspAT; EC 2.6.1.1; Transaminase A (uncharacterized)
to candidate WP_092052375.1 BQ4888_RS00670 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O07587 (393 letters) >NCBI__GCF_900111775.1:WP_092052375.1 Length = 396 Score = 333 bits (855), Expect = 4e-96 Identities = 176/392 (44%), Positives = 247/392 (63%), Gaps = 8/392 (2%) Query: 6 LSREVEENLNKGSWIRKLFDEGARLKKEFGEDQVFDFSLGNPIVEPPEAFKRALIEEAEK 65 ++ +V + + SWIRK+F+EGARL K G + VFDF++GNP VEPP+AF L E A Sbjct: 3 IAAKVLSAIERSSWIRKMFEEGARLSKLHGAENVFDFTIGNPSVEPPQAFCDQLRELANH 62 Query: 66 ---GSHGYIQNQGLLAAREKVAQFLGSRFEADFSAERIVMTVGAGGALNVALKSIVNPGE 122 G H Y+ N G R VA L + A ++VMT GAGGALNV LK+I+NPGE Sbjct: 63 PLPGMHRYMNNAGYEETRAAVAAVLSDKSPVPVKAAQVVMTCGAGGALNVVLKTILNPGE 122 Query: 123 EVIILAPYFAEYKLYIENYGGKAVSCPLTSR--FEIDIEAVRQSITPQTKGLILNTPHNP 180 EVIILAPYF EYK YI+N+GG + T+R F++D++A+ +I PQT+ LI+N P+NP Sbjct: 123 EVIILAPYFVEYKFYIDNHGGVSKEA-WTNRDTFQLDLQAIEAAIGPQTRALIVNNPNNP 181 Query: 181 TGTVLSQKNIDDLGALLKEIEEKSGQTIYVLFDEPYSQLIYD-EELANPFQSYHRVILAS 239 TG + ++ LG LL+ E++ G+TIYV+ DEPY+++ YD +++ F I+ + Sbjct: 182 TGVIYPAADLKSLGELLERKEKELGRTIYVISDEPYARIAYDGQQVPGIFGCVKNSIIVT 241 Query: 240 SFSKDLGIAGERLGYIGLDSRMPDADLLINAFVYCNRTLGFVNAPVMMQRAVARMDDLRV 299 S SKDL + GER+GY+ + M +L + V+CNR LGFVNAP +MQR V + V Sbjct: 242 SHSKDLALPGERIGYLAANPAMDQVELFMEGAVFCNRVLGFVNAPALMQRLVTNIQRESV 301 Query: 300 DASAYKERRDLMVDILKEAGFEFEMPKGGFFVFPKSPIEDEVAFCVHAAQKYKLLIVPSS 359 D Y+ +RDL+ D L GF P G F++FPKSP+ D+V F V AQK+ +L+VP Sbjct: 302 DIGEYQRKRDLLYDHLTALGFSMVKPGGAFYLFPKSPLADDVEF-VTQAQKHNILLVPGV 360 Query: 360 GFGMSGHFRLSFSVPIEQIKNSRDIFISLYKD 391 GFG G FR+++ + I+ S + L KD Sbjct: 361 GFGAPGFFRIAYCIDQGIIERSLPAWEKLAKD 392 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: 428 Number of extensions: 22 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: 396 Length adjustment: 31 Effective length of query: 362 Effective length of database: 365 Effective search space: 132130 Effective search space used: 132130 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