Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_046008544.1 OLEAN_RS06405 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000967895.1:WP_046008544.1 Length = 388 Score = 191 bits (486), Expect = 3e-53 Identities = 125/408 (30%), Positives = 198/408 (48%), Gaps = 40/408 (9%) Query: 69 LSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKR 128 + P M R P+ V G+ ++FD G++YLDA +GIAV GH HP V + + +Q Sbjct: 1 MQPIMNTYGRLPVTFVKGEGSWVFDTDGKKYLDALSGIAVCGLGHAHPAVTQAIRDQADN 60 Query: 129 LQHPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQ----- 183 L H + LY + +E L +++ G + VFF+NSG EANE A+ +A+ Y Q Sbjct: 61 LVHTSNLYGIGRQQELAERL-TRISG-MDNVFFSNSGAEANEAAIKIARKYGHDQGVPEP 118 Query: 184 DIVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQD 243 I+ + +HG AT+ ATG NP G QD Sbjct: 119 QIIVMTKAFHGRTMATLTATG-----------------NPAAQLGFAPLVSGFIRVPYQD 161 Query: 244 L----IQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFA 299 L +I + E IQG GG+ + Y+ + L + DEVQ+G Sbjct: 162 LDAAKAMVAANPNIVAILLEPIQGEGGLATASTDYIQGLRSLCDEHNLLMMLDEVQTGNG 221 Query: 300 RTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTT 359 RTG ++ F+ H + PD++T AKG+GNG P+GA + + A VL ++ +T+GGN ++ Sbjct: 222 RTGTYFNFQQHGITPDVLTTAKGLGNGVPIGACIAKGKAAHVLQPGNHGSTYGGNPLACA 281 Query: 360 AGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLK 419 A +AV++ IEKE + +N ++ T + + ++RG GLMLG+ + D Sbjct: 282 AAVAVIDSIEKENIYDNVKARSEQMRSAFTSRLVEKGLATELRGTGLMLGIVIKQD---- 337 Query: 420 TPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLV 467 ++ + ++G+LI NV R+ PP+ + DAD +V Sbjct: 338 ------CPQLIKEALDIGLLINVTS--NNVIRLLPPMNINQQDADQVV 377 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: 445 Number of extensions: 19 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 477 Length of database: 388 Length adjustment: 32 Effective length of query: 445 Effective length of database: 356 Effective search space: 158420 Effective search space used: 158420 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