Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_011765919.1 AZO_RS11060 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000061505.1:WP_011765919.1 Length = 396 Score = 191 bits (484), Expect = 5e-53 Identities = 139/401 (34%), Positives = 202/401 (50%), Gaps = 38/401 (9%) Query: 78 RKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLY- 136 R P+ G+ +L+D++G+RYLDA +GIAV GH HP +V + Q + H + LY Sbjct: 10 RLPVAFERGEGVWLYDDAGKRYLDALSGIAVSTLGHNHPRLVRAIAEQAAAVLHTSNLYR 69 Query: 137 --LNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLY-----TGCQDIVAVR 189 L +AD A++ + VFF NSG EANE A+ +A+ Y I+ + Sbjct: 70 IPLQEKLADRLGAISG-----MDEVFFCNSGCEANEAAIKLARFYGHKRGVAQPTIIVME 124 Query: 190 NGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGT 249 N +HG AT+ ATG K + PYR + + A+ QD++ Sbjct: 125 NAFHGRTLATLSATGNR--KAQAGFEPLVSGFIRVPYRDIQAI--RQVAEHNQDVV---- 176 Query: 250 TGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEA 309 + E IQG GGI G+ + G L I DEVQ G RTG ++G++ Sbjct: 177 -----AVMLEMIQGEGGINLAEAGFQRELRELCDARGWLLICDEVQCGVGRTGKWFGWQH 231 Query: 310 HNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIE 369 +V PD+VT+AKG+G+G P+GA +T+ AG+ ++ +TFGGN ++ A L L VIE Sbjct: 232 ADVRPDVVTLAKGLGSGVPIGACLTSGAAAGLFGPGNHGSTFGGNPLACAAALTTLEVIE 291 Query: 370 KEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHI 429 + L A VG + L + E + ++RGRGLM+GVEL DR P A + Sbjct: 292 ESGLMAQAEAVGETICSGLREALAGCEGVVEIRGRGLMIGVEL--DR----PCGA----L 341 Query: 430 MDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAM 470 + + E G+LI V R+ P L FT DA LV A+ Sbjct: 342 VTKALENGLLINVTA--ERVVRLLPALVFTAADAQALVGAL 380 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: 439 Number of extensions: 18 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: 396 Length adjustment: 32 Effective length of query: 445 Effective length of database: 364 Effective search space: 161980 Effective search space used: 161980 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