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_068460957.1 APY04_RS06700 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_001541235.1:WP_068460957.1 Length = 396 Score = 357 bits (916), Expect = e-103 Identities = 174/380 (45%), Positives = 251/380 (66%), Gaps = 1/380 (0%) Query: 12 LFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTG 71 +F+PGP NIPE + +A++ D+RS + + ++ KK+FKTT G F+FP+TGTG Sbjct: 7 IFIPGPTNIPEVLRKAVDMPTIDHRSSLFGQILRPAIDGAKKVFKTTDGQLFIFPSTGTG 66 Query: 72 AWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLS 131 WE A+TN LSPGD++++ G FS WID +R +V +++ WG G + + + L+ Sbjct: 67 GWEIAITNVLSPGDKVLATCNGMFSQRWIDMCRRHQLDVTMIQQAWGDGISAERVEKILA 126 Query: 132 QDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWG 191 D++H I + HNETATGV +DI+A+R L+ KHPALL VDGVSSI ++DFRMDEWG Sbjct: 127 ADKHHRISVVLATHNETATGVKSDIAALRRSLNATKHPALLFVDGVSSIGSMDFRMDEWG 186 Query: 192 VDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTP 251 VDVA++GSQK LP GL IV S +ALEAT+ ++ + FFD D K L + PYTP Sbjct: 187 VDVAVSGSQKGFMLPPGLAIVGFSARALEATENARLPRTFFDIRDMAKSNALNGF-PYTP 245 Query: 252 SIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNTVTAV 311 + LL GL+ + +++ EEGL+N+ ARH R+ + R A+ AWG++ C + E S+TV+A+ Sbjct: 246 PVGLLNGLKLSTEMLLEEGLDNVFARHHRIAEGVRAAISAWGMQLCALRPELYSDTVSAI 305 Query: 312 MVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVEMILK 371 VP D ++IV RA Y ++ G G+ VAGKVFRIGHLG++ E L +A EM + Sbjct: 306 CVPDGFDANKIVARALNAYGVAFGTGIGAVAGKVFRIGHLGSLTEAMALSGIATAEMTMV 365 Query: 372 DVGYPVVMGSGVAAASTYLQ 391 D+G P+ +G+G AAA + + Sbjct: 366 DLGLPITLGAGTAAAQQHFR 385 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: 424 Number of extensions: 18 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: 401 Length of database: 396 Length adjustment: 31 Effective length of query: 370 Effective length of database: 365 Effective search space: 135050 Effective search space used: 135050 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