Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate WP_025274361.1 HALAL_RS0112700 acetylornithine transaminase
Query= SwissProt::Q94AL9 (477 letters) >NCBI__GCF_000527155.1:WP_025274361.1 Length = 401 Score = 190 bits (483), Expect = 7e-53 Identities = 123/394 (31%), Positives = 187/394 (47%), Gaps = 34/394 (8%) Query: 80 PLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNH 139 P+ + G +++ D GR YLD GIAV GH HPD VE V+ Q + H + L+ + Sbjct: 25 PVALASGNGRHVTDVDGRTYLDMIGGIAVSTVGHRHPDYVEAVVRQTATIAHTSNLFFHP 84 Query: 140 AIADFSEALASKLPGDLKVVFFTNSGTEANELALMMAKLYT---GCQDIVAVRNGYHGNA 196 + +E L KL G VFF+NSGTEANE AL +A G IVA N +HG Sbjct: 85 TEVELAETLV-KLTGADGRVFFSNSGTEANEAALKLALKAGKPHGKTRIVAAENSFHGRT 143 Query: 197 AATMGATGQSMWKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGF 256 T+ TG++ S+ P F G+ A + +A Sbjct: 144 LGTLAVTGKA---------SIREPFAPFGIEATFVPYGDTAA------LTAAVDDTVAAV 188 Query: 257 ICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDI 316 I E QG G+V + +L A + G I DE+Q+GF RTG ++ A ++ PDI Sbjct: 189 ILEPTQGEAGVVPASTDFLHTARALTHEHGSALILDEIQAGFGRTGRWFAHHAADITPDI 248 Query: 317 VTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQEN 376 +T+AKG+ G P+GA + + V + +TFGGN ++ A LAV+++IE+E L +N Sbjct: 249 ITLAKGLAGGIPMGATIGVGDWGNVFQAGDHGSTFGGNPIAGAAALAVIDIIEREDLFDN 308 Query: 377 AAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKEL 436 +G L+ +L + G+ RG++L ++ +D + Q++ Sbjct: 309 VNTLGRKLENRLHNHPAVIAVRGEALWRGIVLDTDIAAD-------------VCGQLRNA 355 Query: 437 GVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAM 470 G+L NV RI PPL T + + A+ Sbjct: 356 GILANP--VRPNVIRIAPPLSITAAELEQFTSAL 387 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: 458 Number of extensions: 15 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: 401 Length adjustment: 32 Effective length of query: 445 Effective length of database: 369 Effective search space: 164205 Effective search space used: 164205 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