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_092487417.1 BM299_RS17360 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_900115975.1:WP_092487417.1 Length = 383 Score = 246 bits (627), Expect = 1e-69 Identities = 140/380 (36%), Positives = 221/380 (58%), Gaps = 11/380 (2%) Query: 9 RHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTT 68 + +L +PGP +P V+ AM +RS A+ K ++ ++K+F+T + ++ ++ Sbjct: 4 KSYLMIPGPTPVPPSVVAAMTAPMFGHRSEDFQAMHKEIIGKLQKLFQTQNEI-YVLTSS 62 Query: 69 GTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLAS 128 GTG ESA+ NT+SPGD++++ + G+F W + + V + +WG + Q + Sbjct: 63 GTGGMESAVANTVSPGDKVLTLVGGKFGERWSELANQYGAEVIELNYEWGTCVDPQAVQE 122 Query: 129 KLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMD 188 +L+ N IK + NET+TGVTNDI A+ ++ + PAL +VDGVS + ++ ++D Sbjct: 123 QLAA--NPDIKVVFATQNETSTGVTNDIEALGKIVA--QTPALFVVDGVSGVGGIEIKVD 178 Query: 189 EWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYW- 247 EW VD+ TGSQK+L LP GL I S KA + + +KS + +F LK K W Sbjct: 179 EWNVDILTTGSQKSLMLPPGLAIQSISDKAWKKIEENKSPRYYFS---LLKARKQYPKWN 235 Query: 248 -PYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISN 306 YTP++ L GL AALD+I EGL+N+ ARH + ATR A+ A GL N + + S Sbjct: 236 TAYTPAVSLFVGLNAALDMILNEGLDNVYARHKLMRDATRAAIRALGL-NLMTDDAYASP 294 Query: 307 TVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGV 366 VT+V P I +I + Q YN++ G K+ K+ RI H+G +++ ++ ++G+ Sbjct: 295 VVTSVYAPEGIGADDIRKVLKQEYNITFAGGQAKLKNKILRIAHMGFADKMDIIIAVSGL 354 Query: 367 EMILKDVGYPVVMGSGVAAA 386 EM L+ VGYPV +G+GV AA Sbjct: 355 EMALQKVGYPVELGAGVKAA 374 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: 374 Number of extensions: 13 Number of successful extensions: 6 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: 383 Length adjustment: 31 Effective length of query: 370 Effective length of database: 352 Effective search space: 130240 Effective search space used: 130240 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