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_010960683.1 MCA_RS06920 aminotransferase class V-fold PLP-dependent enzyme
Query= BRENDA::Q56YA5 (401 letters) >NCBI__GCF_000008325.1:WP_010960683.1 Length = 395 Score = 444 bits (1141), Expect = e-129 Identities = 216/395 (54%), Positives = 282/395 (71%), Gaps = 1/395 (0%) Query: 7 PGRHHLFVPGPVNIPEPVIRAMNRNNEDYRSPAIPALTKTLLEDVKKIFKTTSGTPFLFP 66 PGR+HL+VPGP NIP+ V+ AM+ ED+R P PAL LLE++KK+F+T +G F+FP Sbjct: 2 PGRNHLYVPGPTNIPDAVLSAMHVPMEDHRRPDFPALVTPLLENLKKVFRTEAGQCFIFP 61 Query: 67 TTGTGAWESALTNTLSPGDRIVSFLIGQFSLLWIDQQKRLNFNVDVVESDWGQGANLQVL 126 TGT WE AL+NTLSPGD+++S+ GQFS LWID +RL V+ E WGQG L L Sbjct: 62 ATGTAGWEIALSNTLSPGDKVLSYRFGQFSHLWIDLARRLGLEVEYEEVPWGQGVPLDRL 121 Query: 127 ASKLSQDENHTIKAICIVHNETATGVTNDISAVRTLLDHYKHPALLLVDGVSSICALDFR 186 ++L D H IKA+ I HNETATGVTND+ AVR +D HPAL VDGVSSI +LDFR Sbjct: 122 EARLKADTAHEIKAVLICHNETATGVTNDLPAVRKAIDAAGHPALFYVDGVSSIGSLDFR 181 Query: 187 MDEWGVDVALTGSQKALSLPTGLGIVCASPKALEATKTSKSLKVFFDWNDYLKFYKLGTY 246 MDEWG+D+ + GSQK LP GL ++ S KAL+A +++K + F D ND++ + G + Sbjct: 182 MDEWGIDIGVAGSQKGFMLPAGLALLGFSQKALKARESAKCKRAFLDINDHI-LHNAGGF 240 Query: 247 WPYTPSIQLLYGLRAALDLIFEEGLENIIARHARLGKATRLAVEAWGLKNCTQKEEWISN 306 +PYTPSI LLYGLR +L+L+ EEGLEN+ ARHARL + R AV AWGL+ C Q +W SN Sbjct: 241 FPYTPSIPLLYGLRKSLELLLEEGLENVYARHARLAEGVRRAVAAWGLQLCAQDPKWYSN 300 Query: 307 TVTAVMVPPHIDGSEIVRRAWQRYNLSLGLGLNKVAGKVFRIGHLGNVNELQLLGCLAGV 366 TV+AV+VPP D +++ A+ RYNLSLG GL++V+GKVFRIGHLG++NEL L + G Sbjct: 301 TVSAVVVPPEFDARDVIHTAYFRYNLSLGAGLSEVSGKVFRIGHLGDLNELSLASAIVGS 360 Query: 367 EMILKDVGYPVVMGSGVAAASTYLQHHIPLIPSRI 401 EM + DVG P+ GSG+AAAS + + P+I R+ Sbjct: 361 EMAMLDVGIPLTPGSGIAAASAHWRETAPVIQPRV 395 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: 474 Number of extensions: 15 Number of successful extensions: 2 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: 395 Length adjustment: 31 Effective length of query: 370 Effective length of database: 364 Effective search space: 134680 Effective search space used: 134680 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