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_012282232.1 HM1_RS05100 alanine--glyoxylate aminotransferase family protein
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000019165.1:WP_012282232.1 Length = 387 Score = 249 bits (635), Expect = 1e-70 Identities = 141/378 (37%), Positives = 216/378 (57%), Gaps = 5/378 (1%) Query: 9 RHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFPTT 68 + +L +PGP +P ++RA++ ++R P+ L + E ++ ++T + + P++ Sbjct: 4 KEYLMLPGPTPVPPRLLRALSEPLINHRGPSFKRLIDEVTEGIRYAYQTKNDV-LILPSS 62 Query: 69 GTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVLAS 128 GTG E+A+ N LSPGD++++ IG F + + VD V+ +WG +L V+ + Sbjct: 63 GTGGMEAAIVNFLSPGDKVLALSIGAFGDRFATIAQTYGCIVDKVDFEWGTAVDLNVVKA 122 Query: 129 KLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFRMD 188 KL+ D N KAI + HNET+TGV ND+ + + HPAL+LVD VS + ++ + D Sbjct: 123 KLAADVNKEYKAILVTHNETSTGVCNDLKGLSEIRGD--HPALILVDSVSGLGVMEVKTD 180 Query: 189 EWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTYWP 248 EWG+DV +T +QK +P G+ V SP+A A + S + K ++D KF + G P Sbjct: 181 EWGLDVIVTAAQKGFMIPPGVAFVSVSPRAWAAYEKSTAPKFYWDLGSAKKFLEKGQT-P 239 Query: 249 YTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISNTV 308 TP+I L GLR AL L E+G E + A+ L TR V+A GLK + S V Sbjct: 240 VTPAIPQLTGLREALQLFREKGREAVFAKQRYLRDITRAGVKALGLKLLAD-DAVASAAV 298 Query: 309 TAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGVEM 368 TAV P I+ I +R + +N+ L G K+ K+FRIGHLG L +L +A +EM Sbjct: 299 TAVWAPEGIEAKAINKRMREAHNVVLAGGQKKLENKIFRIGHLGYGQHLDVLATVAALEM 358 Query: 369 ILKDVGYPVVMGSGVAAA 386 LK++GYPV +G+GV AA Sbjct: 359 TLKELGYPVELGAGVKAA 376 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: 385 Number of extensions: 22 Number of successful extensions: 7 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: 387 Length adjustment: 31 Effective length of query: 370 Effective length of database: 356 Effective search space: 131720 Effective search space used: 131720 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