Align [LysW]-aminoadipate semialdehyde transaminase; EC 2.6.1.- (uncharacterized)
to candidate AO353_28215 AO353_28215 4-aminobutyrate aminotransferase
Query= curated2:Q5SHH5 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_28215 Length = 430 Score = 231 bits (588), Expect = 4e-65 Identities = 155/426 (36%), Positives = 224/426 (52%), Gaps = 31/426 (7%) Query: 1 METRTLEDWRALLEAEKTLDSGVYNKHDLLIVRGQGARVWDAEGNEYIDCVGGYGVANLG 60 M ++ E L + ++ + G+ H L+I R QGA +WD +G Y+D VGG GV N+G Sbjct: 1 MNSKVDETPHLLRQRDQFVPRGLVTAHPLVIDRAQGAELWDVDGKRYLDFVGGIGVLNIG 60 Query: 61 HGNPEVVEAVKRQAETLM--AMPQTLPTPMRGEFYRTLTAILPPELNRVFPVNSGTEANE 118 H +P+VV AV+ Q + + P R I E + SG EA E Sbjct: 61 HNHPKVVAAVQAQLQKVSHACFQVVAYKPYLDLAQRLCEMIGGNEAYKAAFFTSGAEAVE 120 Query: 119 AALKFARAHTGRKKFVAAMRGFSGRTMGSLSVT-WEPKYREPFLPLVEPVEFIPYNDV-- 175 A+K ARAHT R +A GF GRT+ ++T Y++ F P V PY + Sbjct: 121 NAVKIARAHTNRSAVIAFRGGFHGRTLLGTTLTGMSQPYKQNFGPFAPEVFHTPYPNAYR 180 Query: 176 ----EALKRAVDE---------ETAAVILEPVQGEGGVRPATPEFLRAAREITQEKGALL 222 E +A+DE AA+I+EPVQG+GG A EFL+A R +T++ G +L Sbjct: 181 GVSSEMALKALDELLATQVAPERVAAIIIEPVQGDGGFLSAPAEFLQALRALTEKHGIVL 240 Query: 223 ILDEIQTGMGRTGKRFAFEHFGIVPDILTLAKALGGGVPLGAAVMREEVARSMPKGGHGT 282 ILDEIQTG GRTGK F F+H GI PD++T+AK+L GG+PL V + + + GG G Sbjct: 241 ILDEIQTGFGRTGKWFGFQHAGIQPDLVTVAKSLAGGLPLSGVVGKAGIMDAPLPGGLGG 300 Query: 283 TFGGNPLAMAAGVAAIRYLERTRLWERAAELGPWFMEKLRAIPS--PKIREVRGMGLMVG 340 T+GGN L+ AA +A I E+ +L R LG + L + + +I +VRG G M+ Sbjct: 301 TYGGNALSCAAALAVIDAYEQEQLLARGDALGERLRQGLLRLQARHRQIGDVRGSGFMLA 360 Query: 341 LEL------KEKAAPYIARLEKEHR---VLALQAG--PTVIRFLPPLVIEKEDLERVVEA 389 +EL + A RL E R +L ++ G V+RFL PLV ++ ++ ++ Sbjct: 361 IELIKDDDARTPDADLNQRLIDEARAGGLLVIKCGVYRNVLRFLAPLVTTEDQIDEALQI 420 Query: 390 VRAVLA 395 + A LA Sbjct: 421 LEAALA 426 Lambda K H 0.319 0.137 0.402 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: 21 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 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