Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_013450865.1 CALNI_RS03705 aspartate aminotransferase family protein
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000183405.1:WP_013450865.1 Length = 386 Score = 194 bits (492), Expect = 6e-54 Identities = 133/401 (33%), Positives = 195/401 (48%), Gaps = 40/401 (9%) Query: 69 LSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKR 128 +S M R + +V G YLFDE+G++Y+D GIAV N GH + ++ E + Q Sbjct: 1 MSAVMNTYNRYNITLVKGDYFYLFDENGKKYVDFATGIAVTNLGHSNKEIAEIICRQSAT 60 Query: 129 LQHPTVLYLNHAIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQD---- 184 L H + LY N + ++ + S L KV FF NSG EANE AL +A++Y + Sbjct: 61 LMHTSNLYKNPIQEEVAQII-SDLSFGCKV-FFCNSGAEANEAALKLARIYGNKKHNGKR 118 Query: 185 --IVAVRNGYHGNAAATMGATGQSMWK--FNVVQNSVHHALNPDPYRGVFGSDGEKYAKD 240 I+ + N +HG AT+ ATGQ K F + + H P+ + Sbjct: 119 YKIITMVNSFHGRTFATLAATGQEKVKKGFEPTLDFIKHI----PFNDI----------- 163 Query: 241 LQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFAR 300 D + + E IQG GG++ GYL A + L I DEVQ+G R Sbjct: 164 --DAFEKAIEPETVAVVMEVIQGEGGVIPAKEGYLDAVRRICFEKDILLIFDEVQTGIGR 221 Query: 301 TGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTA 360 TG +G++ ++V PDI T+AK +GNGFP+GA+V EIA L+ ++ +TFGGN + Sbjct: 222 TGEVFGYQLYDVKPDIFTLAKALGNGFPIGAMVAKTEIAEYLSPGTHASTFGGNYLGCAI 281 Query: 361 GLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKT 420 VL + ++ G+YLK K LK +G++RG G+M+GV L+ L Sbjct: 282 AKYVLETVSDRSFLDSVKEKGNYLKNK---LKTIFGDMGEIRGEGMMIGVRLIDSISLS- 337 Query: 421 PATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKD 461 +D+ + GVL G N RI P L + D Sbjct: 338 -------DFIDRAHKNGVLTVPAG--DNTVRIYPALNISYD 369 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: 450 Number of extensions: 19 Number of successful extensions: 5 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: 386 Length adjustment: 32 Effective length of query: 445 Effective length of database: 354 Effective search space: 157530 Effective search space used: 157530 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