Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_025272511.1 HALAL_RS0102620 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000527155.1:WP_025272511.1 Length = 417 Score = 220 bits (561), Expect = 6e-62 Identities = 146/394 (37%), Positives = 209/394 (53%), Gaps = 14/394 (3%) Query: 86 GKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNHA-IADF 144 G+ YL+D GRRYLD AGI V + GHCHP VV+ Q+ +L H + H + + Sbjct: 19 GEGVYLYDADGRRYLDFTAGIGVTSTGHCHPHVVQAAQEQVGKLIHGQYTTVMHQPLLEL 78 Query: 145 SEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATG 204 + L LP L +FF+NSG+EA E AL +++ TG +IV + G+HG AT T Sbjct: 79 TRRLGDVLPAGLDSLFFSNSGSEAVEAALRLSRQATGRPNIVVFQGGFHGRTVATATLT- 137 Query: 205 QSMWKFNV----VQNSVHHALNPDPYR-GVFGSDGEKYA-KDLQDLIQYGTT-GHIAGFI 257 S +F+ + + VH A P YR G S ++A ++L L T+ A F Sbjct: 138 TSGTRFSAGISPLMSGVHMAPFPYAYRYGWDESTATEFALRELDYLFATVTSPAETAAFF 197 Query: 258 CEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIV 317 E + G GG V P +L+ + G L + DE+Q+GF RTG FWG + V PD+V Sbjct: 198 IEPVLGEGGYVPANPEFLAGLRQRADEHGILLVLDEIQTGFGRTGKFWGHDHFGVHPDVV 257 Query: 318 TMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENA 377 +AKG+ +GFPL + T+ E+ S T+GGN+V+ A +A L+VI++E L +NA Sbjct: 258 LIAKGLASGFPLSGMATSEELMSQAWPGSQGGTYGGNAVACAAAVATLDVIQREGLVDNA 317 Query: 378 AMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELG 437 A G L E + EK +IGDVRG GLM+G E + ATA+ + G Sbjct: 318 ADRGRQLLEGARHIGEKTPLIGDVRGLGLMVGSEFTTPDGQPDTATAQA--AQKEAAARG 375 Query: 438 VLIGKGGYFGNVFRITPPLCFTKDDADFLVEAMD 471 +++ G NV R+ PPL DA + EA+D Sbjct: 376 LMLLTCGAHMNVVRMIPPLVV---DAAQVDEALD 406 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: 509 Number of extensions: 30 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: 477 Length of database: 417 Length adjustment: 32 Effective length of query: 445 Effective length of database: 385 Effective search space: 171325 Effective search space used: 171325 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