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_010936375.1 DET_RS03175 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000011905.1:WP_010936375.1 Length = 362 Score = 203 bits (517), Expect = 6e-57 Identities = 120/365 (32%), Positives = 202/365 (55%), Gaps = 7/365 (1%) Query: 11 HLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGT 70 +L +PGP PE V+ AM + ++R P + A+ K + E +K F+T + + +GT Sbjct: 3 NLRIPGPTPCPEEVLTAMGQQMINHRGPEMAAIMKEVAEKLKYFFQTKNDV-LVLTGSGT 61 Query: 71 GAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKL 130 G E+A N LSPG+ ++S IG F + + + + G+ A+ ++ L Sbjct: 62 GGLEAAAVNFLSPGETVLSVSIGVFGERFAKIASIFGAKIIALNFEHGKAADPALVKKAL 121 Query: 131 SQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEW 190 + E+ IKA+ I HNET+TG+TND+ ++ +++ LL+VD +SS+ ++D +DEW Sbjct: 122 A--EHPEIKAVLITHNETSTGITNDLKSLASVVKGAGK--LLMVDAISSLSSIDLPVDEW 177 Query: 191 GVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYT 250 G DV ++GSQK +P GL + SP A +A SK + ++D + + G P+T Sbjct: 178 GCDVVVSGSQKGWMVPPGLAFISVSPDAWKANAESKMPRFYWDLAKHKASIEKG-QTPWT 236 Query: 251 PSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNTVTA 310 P + ++ L AL ++ +EG++NI RH ++ TR V+ GL +E++ SNTVTA Sbjct: 237 PCVSVIVALHKALAMMEKEGMQNIFKRHQKIADFTRKGVKELGL-TLLAEEKYASNTVTA 295 Query: 311 VMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVEMIL 370 V+ +D ++++ + YN L G + GK+FRIGHLG V E + L +++ L Sbjct: 296 VLATEGLDPKKLLKVMREEYNTVLAGGQGPLEGKIFRIGHLGWVTENDIKVTLDNLKLAL 355 Query: 371 KDVGY 375 G+ Sbjct: 356 PKAGF 360 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: 323 Number of extensions: 9 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: 401 Length of database: 362 Length adjustment: 30 Effective length of query: 371 Effective length of database: 332 Effective search space: 123172 Effective search space used: 123172 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