Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_011880937.1 4-aminobutyrate transaminase
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000016205.1:WP_011880937.1 Length = 427 Score = 193 bits (490), Expect = 1e-53 Identities = 130/379 (34%), Positives = 194/379 (51%), Gaps = 24/379 (6%) Query: 91 LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHA-IADFSEALA 149 L+D GRR++D AGIAV+N GH HP +V+ + +Q+ H + +A + +E + Sbjct: 34 LWDVEGRRFIDFAAGIAVLNTGHRHPKIVKAIADQLNCFTHTAYQIVPYASYVELAEKIN 93 Query: 150 SKLPGDL--KVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQ-S 206 ++ PGD K FFT +G EA E A+ +A+ TG ++A G+HG M TG+ + Sbjct: 94 ARAPGDYPKKTAFFT-TGAEAVENAIKIARAATGRPGVIAFAGGFHGRTMMGMALTGKVA 152 Query: 207 MWKFNV--VQNSVHHALNPDPYRGVFGSDGEKYAKDL--QDLIQYGTTGHIAGFICEAIQ 262 +K N V HA P+P GV +D K + L D+ +A I E +Q Sbjct: 153 PYKLNFGPFPGDVFHAPYPNPLHGVTTADSIKAIEMLFKADI----DPKRVAAIIFEPVQ 208 Query: 263 GVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKG 322 G GG ++ A + G + IADEVQ+GFARTG + + ++V+ D++TMAK Sbjct: 209 GEGGFNPAPADFVRALRKICNEHGIMLIADEVQTGFARTGKLFAMQQYDVLADLITMAKS 268 Query: 323 IGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGS 382 + G PL VV ++ T+ GN ++ + AVL++I++EKL E A +G Sbjct: 269 LAGGMPLSGVVGRADVMDAAAPGGLGGTYAGNPLAVASAHAVLDIIDEEKLCERATQLGD 328 Query: 383 YLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAE-----TLHIMDQMKELG 437 LK KL L+ I DVRG G M+ VE V+ PAT E T + + E G Sbjct: 329 ALKAKLNALRADIAPIADVRGPGAMVAVEFVN------PATGEPDADFTKRVQARALERG 382 Query: 438 VLIGKGGYFGNVFRITPPL 456 +L+ G + NV R PL Sbjct: 383 LLLLVCGVYSNVVRFLFPL 401 Lambda K H 0.320 0.136 0.403 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: 523 Number of extensions: 29 Number of successful extensions: 4 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: 477 Length of database: 427 Length adjustment: 33 Effective length of query: 444 Effective length of database: 394 Effective search space: 174936 Effective search space used: 174936 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: 51 (24.3 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