Align Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial; Beta-alanine-pyruvate aminotransferase 2; EC 2.6.1.44 (characterized)
to candidate AO353_28215 AO353_28215 4-aminobutyrate aminotransferase
Query= SwissProt::Q94AL9 (477 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28215 Length = 430 Score = 219 bits (557), Expect = 2e-61 Identities = 139/424 (32%), Positives = 217/424 (51%), Gaps = 13/424 (3%) Query: 61 ILSKRKEFLSPSMFCLYRKPLNIVDGKMQYLFDESGRRYLDAFAGIAVVNCGHCHPDVVE 120 +L +R +F+ + + PL I + L+D G+RYLD GI V+N GH HP VV Sbjct: 11 LLRQRDQFVPRGLVTAH--PLVIDRAQGAELWDVDGKRYLDFVGGIGVLNIGHNHPKVVA 68 Query: 121 PVINQIKRLQHPTVLYLNHA-IADFSEALASKLPGD--LKVVFFTNSGTEANELALMMAK 177 V Q++++ H + + D ++ L + G+ K FFT SG EA E A+ +A+ Sbjct: 69 AVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGNEAYKAAFFT-SGAEAVENAVKIAR 127 Query: 178 LYTGCQDIVAVRNGYHGNAAATMGATGQSM---WKFNVVQNSVHHALNPDPYRGVFGSDG 234 +T ++A R G+HG TG S F V H P+ YRGV Sbjct: 128 AHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGV---SS 184 Query: 235 EKYAKDLQDLIQYGTTGH-IAGFICEAIQGVGGIVELAPGYLSAAYDTVKKAGGLFIADE 293 E K L +L+ +A I E +QG GG + +L A +K G + I DE Sbjct: 185 EMALKALDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQALRALTEKHGIVLILDE 244 Query: 294 VQSGFARTGNFWGFEAHNVVPDIVTMAKGIGNGFPLGAVVTTPEIAGVLTRRSYFNTFGG 353 +Q+GF RTG ++GF+ + PD+VT+AK + G PL VV I T+GG Sbjct: 245 IQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAGIMDAPLPGGLGGTYGG 304 Query: 354 NSVSTTAGLAVLNVIEKEKLQENAAMVGSYLKEKLTQLKEKHEIIGDVRGRGLMLGVELV 413 N++S A LAV++ E+E+L +G L++ L +L+ +H IGDVRG G ML +EL+ Sbjct: 305 NALSCAAALAVIDAYEQEQLLARGDALGERLRQGLLRLQARHRQIGDVRGSGFMLAIELI 364 Query: 414 SDRKLKTPATAETLHIMDQMKELGVLIGKGGYFGNVFRITPPLCFTKDDADFLVEAMDYS 473 D +TP ++D+ + G+L+ K G + NV R PL T+D D ++ ++ + Sbjct: 365 KDDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTTEDQIDEALQILEAA 424 Query: 474 MSKM 477 ++++ Sbjct: 425 LARV 428 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: 511 Number of extensions: 30 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: 430 Length adjustment: 33 Effective length of query: 444 Effective length of database: 397 Effective search space: 176268 Effective search space used: 176268 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