Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate 7025943 Shewana3_3091 4-aminobutyrate aminotransferase (RefSeq)
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__ANA3:7025943 Length = 425 Score = 195 bits (496), Expect = 2e-54 Identities = 127/372 (34%), Positives = 184/372 (49%), Gaps = 12/372 (3%) Query: 91 LFDESGRRYLDAFAGIAVVNCGHCHPDVVEPVINQIKRLQHPTVLYLNH-AIADFSEALA 149 ++D GR ++D GIAV+N GH HP V V Q++ H + L + + E L Sbjct: 36 VWDVEGREFIDFAGGIAVLNTGHLHPKVKAAVAAQLEDFSHTCFMVLGYESYIQVCEKLN 95 Query: 150 SKLPGDL--KVVFFTNSGTEANELALMMAKLYTGCQDIVAVRNGYHGNAAATMGATGQSM 207 +PGD K FT SG+EA E A+ +A+ YT ++A +GYHG A + TG+ Sbjct: 96 QLVPGDFAKKTALFT-SGSEAVENAVKVARAYTKRAGVIAFTSGYHGRTMAALALTGKVA 154 Query: 208 ---WKFNVVQNSVHHALNPDPYRGVFGSDGEKYAKDLQDLIQYGTTGHIAGFICEAIQGV 264 ++ +V A P GV SD + A + +IA I E +QG Sbjct: 155 PYSKGMGLMSANVFRAEFPCALHGV--SDDDAMASIERIFKNDAEPSNIAAIILEPVQGE 212 Query: 265 GGIVELAPGYLSAAYDTVKKAGGLFIADEVQSGFARTGNFWGFEAHNVVPDIVTMAKGIG 324 GG +P ++ + G + IADEVQ+G RTG F+ E V DI T AK I Sbjct: 213 GGFYAASPEFMQRLRALCDREGIMLIADEVQTGAGRTGTFFAMEQMGVSADITTFAKSIA 272 Query: 325 NGFPLGAVVTTPEIAGVLTRRSYFNTFGGNSVSTTAGLAVLNVIEKEKLQENAAMVGSYL 384 GFPL + E+ + T+GGN ++ A LAVL V E+EKL E A +G + Sbjct: 273 GGFPLSGITGKAEVMDAIGPGGLGGTYGGNPLACAAALAVLEVFEEEKLLERANAIGERI 332 Query: 385 KEKLTQLKEKHEIIGDVRGRGLMLGVELVSDRKLKTPATAETLHIMDQMKELGVLIGKGG 444 K L ++ +H I DVRG G M+ +EL+ + K PA I+ + + G+++ G Sbjct: 333 KSALNTMQVEHPQIADVRGLGAMIAIELMEEGK---PAPQYCAQILAEARNRGLILLSCG 389 Query: 445 YFGNVFRITPPL 456 +GNV RI PL Sbjct: 390 TYGNVLRILVPL 401 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: 490 Number of extensions: 26 Number of successful extensions: 3 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: 425 Length adjustment: 33 Effective length of query: 444 Effective length of database: 392 Effective search space: 174048 Effective search space used: 174048 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