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_013644166.1 METBO_RS02880 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000191585.1:WP_013644166.1 Length = 389 Score = 215 bits (547), Expect = 2e-60 Identities = 132/376 (35%), Positives = 213/376 (56%), Gaps = 9/376 (2%) Query: 12 LFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTG 71 L +PGP + V++AM+ + ++RS + E + ++F+T + + +L +GT Sbjct: 6 LMIPGPTRVSSRVLKAMSESIVNHRSAVFGEILTETNEMMSEVFQTQNQS-YLITGSGTA 64 Query: 72 AWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDV-VESDWGQGANLQVLASKL 130 A E+AL N +S GD++++ + G+F ++ Q + V V +E +WG AN + + L Sbjct: 65 AMEAALGNVISEGDKVLNIVGGKFGERFM-QITETHGGVPVELEVEWGNAANPEDIRYIL 123 Query: 131 SQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEW 190 ++E IKA+ +VHNET+TGV N I V +L + AL +VD VSS+ D ++D + Sbjct: 124 EEEEE--IKAVTMVHNETSTGVENPIEEVGKILKDFD--ALYVVDTVSSLGGADVQVDNF 179 Query: 191 GVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKF-YKLGTYWPY 249 G+D+ +TGSQK L+ P G+ + + A + ++S + + Y K K PY Sbjct: 180 GIDICVTGSQKCLAAPPGMAAITLNDDAWKVVDKTESKTYYLNLKKYRKSGSKAVPETPY 239 Query: 250 TPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNTVT 309 TPS+ L+Y + AL +I EEGLE I RH + KAT V+A GL+ E+ S+TVT Sbjct: 240 TPSVSLMYAMNEALKIIMEEGLEARIKRHEQAAKATVNGVKAIGLE-LFASEDASSSTVT 298 Query: 310 AVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVEMI 369 AV +P + +Y + L G + + G VFRIGH+GN+ +++ +A +EM Sbjct: 299 AVNMPEGMTDKNFRGTMRNKYRIELAGGQDHLKGNVFRIGHMGNITHREIISTIAAIEMS 358 Query: 370 LKDVGYPVVMGSGVAA 385 LK+ GY V +G+GVAA Sbjct: 359 LKEFGYEVELGTGVAA 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: 342 Number of extensions: 17 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: 389 Length adjustment: 31 Effective length of query: 370 Effective length of database: 358 Effective search space: 132460 Effective search space used: 132460 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