Align Alanine--glyoxylate aminotransferase 2 homolog 1, mitochondrial; Beta-alanine-pyruvate aminotransferase 1; EC 2.6.1.44 (characterized)
to candidate GFF179 PS417_00900 4-aminobutyrate aminotransferase
Query= SwissProt::Q940M2 (476 letters) >FitnessBrowser__WCS417:GFF179 Length = 425 Score = 194 bits (494), Expect = 4e-54 Identities = 125/391 (31%), Positives = 188/391 (48%), Gaps = 8/391 (2%) Query: 78 PLNIVEGKMQYLYDESGRRYLDAFAGIVTVSCGHCHPDILNAITEQSKLLQHAT-TIYLH 136 P+ K + D GR ++D GI ++ GH HP I+ A+TEQ L H + + Sbjct: 25 PIFAESAKNATVTDVEGREFIDFAGGIAVLNTGHVHPKIIAAVTEQLNKLTHTCFQVLAY 84 Query: 137 HAIGDFAEALAAKMPGNL-KVVYFVNSGSEANELAMMMARLYTGSLEMISLRNAYHGGSS 195 + E + AK+PG+ K V +GSEA E A+ +AR TG +I+ AYHG + Sbjct: 85 EPYVELCEKINAKVPGDFAKKTLLVTTGSEAVENAVKIARAATGRAGVIAFTGAYHGRTM 144 Query: 196 NTIGLTAL---NTWKYPLPQGEIHHVVNPDPYRGVFGSDGSLYAKDVHDHIEYGTSGKVA 252 T+GLT + L G + + P+ GV SD A +A Sbjct: 145 MTLGLTGKVVPYSAGMGLMPGGVFRALFPNELHGV--SDDDAIASIERIFKNDAEPRDIA 202 Query: 253 GFIAETIQGVGGAVELAPGYLKSVYEIVRNAGGVCIADEVQTGFGRTGSHYWGFQTQDVV 312 I E +QG GG ++K + E+ G + IADEVQTG GRTG+ ++ + V Sbjct: 203 AIIIEPVQGEGGFYVAPKSFMKRLRELCDKHGILLIADEVQTGAGRTGT-FFAMEQMGVA 261 Query: 313 PDIVTMAKGIGNGLPLGAVVTTPEIASVLASKILFNTFGGNPVCSAGGLAVLNVIDKEKR 372 D+ T AK I G PL V E +A L T+ G+P+ A LAV+ V ++E Sbjct: 262 ADLTTFAKSIAGGFPLAGVCGKAEYMDAIAPGGLGGTYAGSPIACAAALAVMEVFEEEHL 321 Query: 373 QEHCAEVGSHLIQRLKDVQKRHDIIGDVRGRGLMVGIELVSDRKDKTPAKAETSVLFEQL 432 + C VG L+ LK +Q ++ +IG+VR G M+ +EL D P A + + + Sbjct: 322 LDRCKAVGERLVTGLKAIQAKYPVIGEVRALGAMIAVELFDDGDTHKPNAAAVASVVAKA 381 Query: 433 RELGILVGKGGLHGNVFRIKPPMCFTKDDAD 463 RE G+++ G +GNV R+ P+ + D Sbjct: 382 REKGLILLSCGTYGNVLRVLVPLTSPDEQLD 412 Lambda K H 0.320 0.138 0.412 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: 484 Number of extensions: 31 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: 476 Length of database: 425 Length adjustment: 33 Effective length of query: 443 Effective length of database: 392 Effective search space: 173656 Effective search space used: 173656 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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