Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate 15422 b1302 GABA aminotransferase, PLP-dependent (NCBI)
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__Keio:15422 Length = 421 Score = 184 bits (468), Expect = 4e-51 Identities = 137/388 (35%), Positives = 189/388 (48%), Gaps = 26/388 (6%) Query: 91 LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNH----AIADFSE 146 L D G Y+D AGIAV+N GH HPD+V V Q+++ H + + +A+ Sbjct: 34 LKDVEGNEYIDFAAGIAVLNTGHRHPDLVAAVEQQLQQFTHTAYQIVPYESYVTLAEKIN 93 Query: 147 ALASKLPGDLKVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQ- 205 ALA + G K FFT +G EA E A+ +A+ +TG ++A G+HG TM TG+ Sbjct: 94 ALAP-VSGQAKTAFFT-TGAEAVENAVKIARAHTGRPGVIAFSGGFHGRTYMTMALTGKV 151 Query: 206 SMWK--FNVVQNSVHHALNPDPYRGVFGSDG-----EKYAKDLQDLIQYGTTGHIAGFIC 258 + +K F SV+H P G+ D + D++ +A I Sbjct: 152 APYKIGFGPFPGSVYHVPYPSDLHGISTQDSLDAIERLFKSDIE-------AKQVAAIIF 204 Query: 259 EAIQGVGGIVELAPGYLSAAYDTVKKAGGL-FIADEVQSGFARTGNFWGFEAHNVVPDIV 317 E +QG GG +AP L AA + G+ IADEVQSGFARTG + + + PD++ Sbjct: 205 EPVQGEGGF-NVAPKELVAAIRRLCDEHGIVMIADEVQSGFARTGKLFAMDHYADKPDLM 263 Query: 318 TMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENA 377 TMAK + G PL VV I T+ GN ++ A AVLN+I+KE L E A Sbjct: 264 TMAKSLAGGMPLSGVVGNANIMDAPAPGGLGGTYAGNPLAVAAAHAVLNIIDKESLCERA 323 Query: 378 AMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELG 437 +G LK L KE I VRG G M+ VE +D + P+ A I + G Sbjct: 324 NQLGQRLKNTLIDAKESVPAIAAVRGLGSMIAVEF-NDPQTGEPSAAIAQKIQQRALAQG 382 Query: 438 VLIGKGGYFGNVFRITPPLCFTKDDADF 465 +L+ G +GNV R PL T DA F Sbjct: 383 LLLLTCGAYGNVIRFLYPL--TIPDAQF 408 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: 495 Number of extensions: 28 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 477 Length of database: 421 Length adjustment: 33 Effective length of query: 444 Effective length of database: 388 Effective search space: 172272 Effective search space used: 172272 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