Align glycine C-acetyltransferase (EC 2.3.1.29) (characterized)
to candidate Ga0059261_3508 Ga0059261_3508 7-keto-8-aminopelargonate synthetase and related enzymes
Query= BRENDA::P0AB77 (398 letters) >FitnessBrowser__Korea:Ga0059261_3508 Length = 417 Score = 212 bits (540), Expect = 1e-59 Identities = 134/363 (36%), Positives = 191/363 (52%), Gaps = 7/363 (1%) Query: 38 VADGSHVINFCANNYLGLANHPDLIAAAKAGMDSHGFGMASVRFICGTQDSHKELEQKLA 97 V G I NY+G+ PD+I A K +D G G R + GT H E+EQ L Sbjct: 58 VIKGKDTILLGTYNYMGMTFDPDVIQAGKDALDQFGSGTNGSRMLNGTFRDHMEVEQALR 117 Query: 98 AFLGMEDAILYSSCFDANGGLFETLLGAEDAIISDALNHASIIDGVRLCKAKRYRYANND 157 F G AI++S+ + AN G+ TL G D II DA +HASI DG + A+ R+ +N Sbjct: 118 DFYGTTGAIVFSTGYMANLGMISTLAGKGDYIILDADSHASIYDGCKQGYAEIVRFRHNS 177 Query: 158 MQELEARL-KEAREAGARHVLIATDGVFSMDGVIANLKGVCDLADKYDALVMVDDSHAVG 216 +++L+ RL + EAG L+ +GV+SM G IA LK + +A K+ A+V+ D++H++G Sbjct: 178 VEDLDKRLGRLPAEAGK---LVVLEGVYSMLGDIAPLKEMVAVAKKHGAMVLSDEAHSMG 234 Query: 217 FVGENGRGSHEYCDVMGRVDIITGTLGKALGGASGGYTAARKEVVEWLRQRSRPYLFSNS 276 F G NGRG +E G VD I GT K++ G GG+ + E +R R Y+F+ S Sbjct: 235 FFGPNGRGVYEAQGCEGDVDFIVGTFSKSV-GTVGGFCVSNHPKFEAIRLACRQYIFTAS 293 Query: 277 LAPAIVAASIKVLEMVEAGSELRDRLWANARQFREQMSAAGFTLA--GADHAIIPVMLGD 334 L P++VA + + ++ R LW NAR + GF L D AII V+L D Sbjct: 294 LPPSVVATAATSIRKLQHAHNKRQHLWENARAVHSGLKEMGFKLGTETCDSAIIAVILTD 353 Query: 335 AVVAQKFARELQKEGIYVTGFFYPVVPKGQARIRTQMSAAHTPEQITRAVEAFTRIGKQL 394 A + L G+YV P P G +R + A HTPEQ+ R + F G+ + Sbjct: 354 QEQAVTMWQALLDNGLYVNMARPPATPAGTFLLRCSLCAEHTPEQVQRILAMFRAAGQAV 413 Query: 395 GVI 397 GVI Sbjct: 414 GVI 416 Lambda K H 0.320 0.135 0.388 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: 387 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: 398 Length of database: 417 Length adjustment: 31 Effective length of query: 367 Effective length of database: 386 Effective search space: 141662 Effective search space used: 141662 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: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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