Align asparagine-oxo-acid transaminase (EC 2.6.1.14); alanine-glyoxylate transaminase (EC 2.6.1.44); serine-glyoxylate transaminase (EC 2.6.1.45) (characterized)
to candidate WP_026223456.1 A3OW_RS0109275 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000372865.1:WP_026223456.1 Length = 390 Score = 423 bits (1088), Expect = e-123 Identities = 206/382 (53%), Positives = 276/382 (72%), Gaps = 2/382 (0%) Query: 8 GRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPT 67 GR+HL++PGP N+P V+ AM+ ED+RSP P L K LLED+KK+F+T G F+FP Sbjct: 3 GRNHLYIPGPTNVPHEVLSAMHAPMEDHRSPKFPTLFKPLLEDLKKVFRTEDGQCFIFPA 62 Query: 68 TGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLA 127 TGT WE ALTNTL+PGD+++ + GQFS LW + KRL F+V++ + WG+G L L Sbjct: 63 TGTAGWEVALTNTLNPGDKVLIYRFGQFSHLWAEMAKRLGFDVEIHQETWGRGIPLDKLE 122 Query: 128 SKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRM 187 ++L +D+NH IKA+ HNETATGVT+DI+ VR L+ HPALL VDGVSSI +LDFRM Sbjct: 123 ARLKEDKNHEIKAVLATHNETATGVTSDIAGVRKALNSADHPALLFVDGVSSIASLDFRM 182 Query: 188 DEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYW 247 DEWGVD A++GSQK LP G +C S KAL+AT+TSK + F D D + K G Y Sbjct: 183 DEWGVDGAISGSQKGFMLPAGGAFLCFSQKALKATETSKYPRCFLDLRDQMNQNKDG-YT 241 Query: 248 PYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNT 307 PYTP++ +LYGLR ALDL+ EEG++N+ ARH RL + TR A++AWGL C + S+T Sbjct: 242 PYTPALPILYGLRKALDLLLEEGMDNVYARHHRLAEGTRRAIKAWGLGLCAH-PGFESDT 300 Query: 308 VTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVE 367 V+AV+VP H D E++ A+++YNLSLG GL++++GKVFRIGH+G++N++ +LG AGVE Sbjct: 301 VSAVVVPEHKDAREVISTAFKKYNLSLGAGLSELSGKVFRIGHVGDMNDVSMLGAFAGVE 360 Query: 368 MILKDVGYPVVMGSGVAAASTY 389 M + D G+ + GSGVAAA Y Sbjct: 361 MAMLDCGFDIKPGSGVAAAVEY 382 Lambda K H 0.320 0.137 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: 456 Number of extensions: 19 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: 401 Length of database: 390 Length adjustment: 31 Effective length of query: 370 Effective length of database: 359 Effective search space: 132830 Effective search space used: 132830 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