Align [amino group carrier protein]-gamma-(L-lysyl)-L-glutamate aminotransferase (EC 2.6.1.118) (characterized)
to candidate Pf1N1B4_4910 Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19)
Query= BRENDA::Q93R93 (395 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4910 Length = 430 Score = 233 bits (594), Expect = 8e-66 Identities = 157/426 (36%), Positives = 223/426 (52%), Gaps = 31/426 (7%) Query: 1 METRTLEDWRALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLG 60 M ++ E L + ++ + G+ H L+I R QG+ +WD +G Y+D VGG GV N+G Sbjct: 1 MNSKVDETPHLLRQRDQFVPRGLVTAHPLVIDRAQGSELWDVDGKRYLDFVGGIGVLNIG 60 Query: 61 HGNPEVVEAVKRQAETLM--AMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANE 118 H +P+VV AV+ Q + + P R I E + SG EA E Sbjct: 61 HNHPKVVAAVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGQESYKAAFFTSGAEAVE 120 Query: 119 AALKFARAHTGRKKFVAAMRGFSGRTMGSLSVT-WEPKYREPFLPLVEPVEFIPYNDVE- 176 A+K ARAHT R +A GF GRT+ ++T Y++ F P V PY + Sbjct: 121 NAVKIARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYR 180 Query: 177 ------ALK--------RAVDEETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALL 222 ALK + E AA+I+EPVQG+GG A EFL+A R +T + G +L Sbjct: 181 GVTSDMALKALDELLATQVAPERVAAIIIEPVQGDGGFLSAPTEFLQALRALTAKHGIVL 240 Query: 223 ILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGVAVMREEVARSMPKGGHGT 282 ILDEIQTG GRTGK F F+H GI PD++T+AK+L GG+PL V + E+ + GG G Sbjct: 241 ILDEIQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAEIMDAPLPGGLGG 300 Query: 283 TFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVG 340 T+GGN L+ AA +A I E+ +L R LG E L + + P+I +VRG G M+ Sbjct: 301 TYGGNALSCAAALAVIEAYEQEQLLARGEALGERLREGLLRLQARYPRIGDVRGSGFMLA 360 Query: 341 LEL------KEKAAPYIARLEKEHR---VLALQAG--PTVIRFLPPLVIEKEDLERVVEA 389 +EL + A RL E R +L ++ G V+RFL PLV + ++ ++ Sbjct: 361 IELIKDDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTSEAQVDEALQI 420 Query: 390 VRAVLA 395 + A LA Sbjct: 421 LDAALA 426 Lambda K H 0.319 0.137 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: 420 Number of extensions: 18 Number of successful extensions: 5 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: 395 Length of database: 430 Length adjustment: 31 Effective length of query: 364 Effective length of database: 399 Effective search space: 145236 Effective search space used: 145236 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 (21.7 bits) S2: 50 (23.9 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