Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_027457970.1 K420_RS0110205 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000519045.1:WP_027457970.1 Length = 390 Score = 180 bits (457), Expect = 7e-50 Identities = 128/397 (32%), Positives = 196/397 (49%), Gaps = 36/397 (9%) Query: 78 RKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYL 137 R P+ GK + D G+ YLDA +GIAV GH HP +V+ + Q R+ H + LY Sbjct: 10 RLPVTFSHGKGCRITDTEGKEYLDALSGIAVSTLGHAHPRLVDAIAAQAGRMLHTSNLYR 69 Query: 138 NHAIADFSEALASKLP--GDLKVVFFTNSGTEANELALMMAKLY-----TGCQDIVAVRN 190 E LA KL ++ VFF NSG EANE A+ +A+ Y IV + Sbjct: 70 IRE----QEQLADKLCELSGMQEVFFGNSGAEANEAAIKLARFYGHKKGVELPTIVVMEK 125 Query: 191 GYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTT 250 +HG AT+ ATG N + L R +G ++ + ++ Sbjct: 126 AFHGRTMATLSATG------NRKTQAGFEPLVSGFVRVPYGD-----LNAIRAVAEHNK- 173 Query: 251 GHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAH 310 +I + E IQG GGI P Y + + I DEVQ G RTG ++G++ Sbjct: 174 -NIVAVMLEIIQGEGGIHLADPVYYRGVRELCDAHDWMMICDEVQCGMGRTGKWFGYQQA 232 Query: 311 NVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEK 370 V+PD+ T+AKG+ +G +GA + + + AG+ ++ +TFGGN +++TA L + V+E+ Sbjct: 233 GVLPDVATLAKGLASGVAIGACMASGKAAGLFGPGNHGSTFGGNPLASTAALTTIAVMEE 292 Query: 371 EKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIM 430 E L +NAA +GS +++ + + D+RG GLM+G+EL DR ++ Sbjct: 293 EGLLDNAARIGSLIRQLFGEALAGVAGVVDIRGHGLMIGIEL--DRPCG--------ELV 342 Query: 431 DQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLV 467 + G+LI + R+ PPL F+ DDA LV Sbjct: 343 GKALSEGLLINVTS--EKIIRLLPPLIFSDDDARELV 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: 449 Number of extensions: 27 Number of successful extensions: 6 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: 390 Length adjustment: 32 Effective length of query: 445 Effective length of database: 358 Effective search space: 159310 Effective search space used: 159310 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