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_012966670.1 FERP_RS11050 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000025505.1:WP_012966670.1 Length = 374 Score = 177 bits (449), Expect = 5e-49 Identities = 122/369 (33%), Positives = 194/369 (52%), Gaps = 16/369 (4%) Query: 12 LFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTTGTG 71 L +PGPV + E +I+A+ +RS + + E +K +F T G + +GT Sbjct: 7 LMIPGPVQLHERIIKALGSQMISHRSKDFEEVYEYCREALKPLFGT-KGDVVIISGSGTA 65 Query: 72 AWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLASKLS 131 E+A+ + S +I G+F + + R VD V+ +WG +L + L Sbjct: 66 GMEAAVAS-FSKVRKITCVSNGKFGERFAEIAWRYA-EVDHVKFEWGDSIDLDKVRESLE 123 Query: 132 QDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMDEWG 191 + + VHNET+TG+ N + + Y AL+++DG++S+ + RMDEWG Sbjct: 124 NGS----EMVTFVHNETSTGILNPAREICKIAKEYD--ALVVMDGITSVGGDEVRMDEWG 177 Query: 192 VDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWPYTP 251 VDV + GSQK L P GL V + KA E ++ + + D Y+K + PYTP Sbjct: 178 VDVCIVGSQKCLGAPPGLAAVAINEKAWEF--YNERVPYYLDLKAYVKKAE-KNQTPYTP 234 Query: 252 SIQLLYGLRAALDLIFEEGLENIIARHARLGKATR-LAVEAWGLKNCTQKEEW--ISNTV 308 ++ L L+ AL +I EEGLEN I RH RL KA R A+EA GL+ + E+ SNTV Sbjct: 235 AVPLFLALKEALKIIEEEGLENRIERHRRLAKAVREWAIEA-GLELFPRLNEYSSYSNTV 293 Query: 309 TAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVEM 368 TA+ +P I SE+ + +++ G + GK+FRIG++GNV++ +++ LA +E Sbjct: 294 TAIKMPKGITDSELRGTLRNEFGITISGGQEHLKGKIFRIGNMGNVSKREIVATLAAIES 353 Query: 369 ILKDVGYPV 377 ++ G + Sbjct: 354 VMLRKGVEI 362 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: 335 Number of extensions: 13 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: 374 Length adjustment: 30 Effective length of query: 371 Effective length of database: 344 Effective search space: 127624 Effective search space used: 127624 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