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_012334105.1 M446_RS20920 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000019365.1:WP_012334105.1 Length = 397 Score = 315 bits (808), Expect = 1e-90 Identities = 165/384 (42%), Positives = 227/384 (59%), Gaps = 3/384 (0%) Query: 7 PGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFP 66 PGRH L +PGP N+P P++ A R D+RS L + +L +K IFKT + ++ Sbjct: 5 PGRHFLQIPGPTNVPLPILAATARPVIDHRSAEFGQLGREVLAGIKTIFKTENPV-LIYA 63 Query: 67 TTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVL 126 +GTG WESAL NTL GDR++ + G F+ LW ++L+ + + DW G ++ + Sbjct: 64 ASGTGGWESALVNTLQAGDRVLMYETGHFAALWERMARKLSLKPEFIRGDWRSGVDVAAI 123 Query: 127 ASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFR 186 + L+ D H IKA+CIVHNETATG +D+ VR LD HPALL+VD +SS+ + D+R Sbjct: 124 EAHLAGDRQHGIKAVCIVHNETATGTLSDVQGVRAALDRTGHPALLMVDTISSLGSTDYR 183 Query: 187 MDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTY 246 D WGVDV + GSQK L LP GL S KAL A++ + + ++DW D L + G Y Sbjct: 184 HDAWGVDVTVGGSQKGLMLPPGLAFNAVSDKALAASRQATLPRAYWDWEDMLAANRTG-Y 242 Query: 247 WPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISN 306 +P TP+I LLYGL+ A++ + EGL+ + ARHAR ATR AV WG + S Sbjct: 243 FPQTPAINLLYGLKVAIETLHAEGLDAVFARHARAAAATRAAVRHWGFETQCAVPAQASP 302 Query: 307 TVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGV 366 TVT V +P +R+N++LG GL +A +VFRIGH+G+ N+L + G LAGV Sbjct: 303 TVTTVRMPEGHSADAFRALVLERFNMALGSGLGPLADRVFRIGHIGDFNDLTIAGALAGV 362 Query: 367 EMILKDVGYPVVMGSGVAAASTYL 390 EM L G P G G A A L Sbjct: 363 EMGLAAAGIPHRAG-GAAVAQAIL 385 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: 433 Number of extensions: 16 Number of successful extensions: 3 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: 397 Length adjustment: 31 Effective length of query: 370 Effective length of database: 366 Effective search space: 135420 Effective search space used: 135420 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