Align beta-alanine-pyruvate transaminase (EC 2.6.1.18); alanine-glyoxylate transaminase (EC 2.6.1.44) (characterized)
to candidate Pf6N2E2_373 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= BRENDA::Q9SR86 (481 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_373 Length = 430 Score = 213 bits (541), Expect = 1e-59 Identities = 141/427 (33%), Positives = 218/427 (51%), Gaps = 12/427 (2%) Query: 61 TAEIIAKRREFLSPALFHFYNTPLNIVEAKMQYVFDENGRRYLDAFGGIATVSCGHCHPE 120 T ++ +R +F+ L + PL I A+ ++D +G+RYLD GGI ++ GH HP+ Sbjct: 8 TPSLLRQRDQFVPRGLVTAH--PLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIGHNHPK 65 Query: 121 VVNSVVKQLKLINHSTILYLNHT-ISDFAEALVSTLPGD--LKVVFFTNSGTEANELAMM 177 VV +V QL+ I+H+ + + D A+ L + G K FFT SG EA E A+ Sbjct: 66 VVAAVQAQLQKISHACFQVVAYKPYLDLAQRLCEMIGGQHAYKAAFFT-SGAEAVENAVK 124 Query: 178 MARLYTGCNDIVSLRNSYHGNAAATMGATAQSN---WKFNVVQSGVHHAINPDPYRGIFG 234 +AR +T + +++ R +HG T S F V H P+ YRG+ Sbjct: 125 IARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYRGVTS 184 Query: 235 SDGEKYASDVHDLIQFGTSGQVAGFIGESIQGVGGIVELAPGYLPAAYDIVRKAGGVCIA 294 + + ++ L +VA I E +QG GG + +L + +K G V I Sbjct: 185 AMALQALDEL--LATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQGLRALTQKHGIVLIL 242 Query: 295 DEVQSGFARTGTHFWGFQSHGVIPDIVTMAKGIGNGIPLGAVVTTPEIAGVLSRRSYFNT 354 DE+Q+GF RTG F GFQ G+ PD+VT+AK + G+PL VV EI T Sbjct: 243 DEIQTGFGRTGKWF-GFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGGT 301 Query: 355 FGGNPMCTAAGHAVLRVLHEEKLQENANLVGSHLKRRLTLLKNKYELIGDVRGRGLMLGV 414 +GGN + AA AV+ +E+L ++G L++ L L+ +Y IGDVRG G ML + Sbjct: 302 YGGNALSCAAALAVIEAYEQEQLLARGEVLGERLRQGLLHLQTRYPQIGDVRGSGFMLAI 361 Query: 415 EFVKDRDLKTPAKAETLHLMDQMKEMGVLVGKGGFYGNVFRITPPLCFTLSDADFLVDVM 474 E +K + +TP L+D+ + G+LV K G Y NV R PL + + D + ++ Sbjct: 362 ELIKHDEARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQIDEALQIL 421 Query: 475 DHAMSKM 481 D A++++ Sbjct: 422 DGALARV 428 Lambda K H 0.320 0.136 0.406 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: 521 Number of extensions: 35 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: 481 Length of database: 430 Length adjustment: 33 Effective length of query: 448 Effective length of database: 397 Effective search space: 177856 Effective search space used: 177856 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