Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate Ga0059261_3205 Ga0059261_3205 transaminase, acetylornithine/succinylornithine family
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Korea:Ga0059261_3205 Length = 398 Score = 189 bits (481), Expect = 1e-52 Identities = 136/400 (34%), Positives = 197/400 (49%), Gaps = 43/400 (10%) Query: 69 LSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKR 128 ++P M R + V G+ YL E G RYLD AGIAV GH HP + + Q Sbjct: 3 ITPLMPVYPRCEVRPVRGEGCYLIGERGERYLDFAAGIAVNALGHGHPQFTKAIAEQAAT 62 Query: 129 LQHPTVLYLNHAIADFSEALASKLPGD--LKVVFFTNSGTEANELALMMAKLYTGCQD-- 184 L H + LY + EALA ++ + VFFTNSG EA E A+ A+ Y Sbjct: 63 LMHVSNLYGSPQ----GEALAQRIVDNSFADTVFFTNSGVEAIECAIKTARRYHYVNGNP 118 Query: 185 ----IVAVRNGYHGNAAATMGATGQSMWKFNVVQNSVHHALNPDPYRGVF-GSDGEKYAK 239 ++ +N +HG + + AT Q + D + + G D K+ Sbjct: 119 QRHKLITFKNAFHGRSIGAISATDQPKMR--------------DGFEPLLPGFDYVKF-N 163 Query: 240 DLQDLIQYGTTGHIAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFA 299 DL+ I AGF+ E +QG GG+ ++ + G L I DE+Q G+ Sbjct: 164 DLEGAIAK-IDDETAGFLVETVQGEGGMTAGTVEFIQGLRKACDEHGLLLILDEIQCGYG 222 Query: 300 RTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTT 359 RTG W +E + + PDI+T AKGIGNGFPLGA + T E A +T ++ +T+GGN ++ Sbjct: 223 RTGKMWAYEHYGITPDILTAAKGIGNGFPLGACLATEEAAKGMTFGTHGSTYGGNPLAMA 282 Query: 360 AGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHE-IIGDVRGRGLMLGVELVSDRKL 418 AG AVL+V+ + E+ +G L+ QL H+ + ++RG+GLMLG+ KL Sbjct: 283 AGQAVLDVMLEPGFFEHVEKMGERLRAGFEQLIPNHDHLFDEIRGKGLMLGI------KL 336 Query: 419 KTPATAE--TLHIMDQMKELGVLIGKGGYFGNVFRITPPL 456 K PA + H+ + L V G+ NVFR+ PPL Sbjct: 337 KEPAVSRDFVAHLRENHGLLTVAAGE-----NVFRVLPPL 371 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: 483 Number of extensions: 25 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: 398 Length adjustment: 32 Effective length of query: 445 Effective length of database: 366 Effective search space: 162870 Effective search space used: 162870 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 09 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