Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 3608835 Dshi_2227 FAD dependent oxidoreductase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Dino:3608835 Length = 434 Score = 304 bits (779), Expect = 3e-87 Identities = 170/424 (40%), Positives = 242/424 (57%), Gaps = 4/424 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YP SYYA++ P PA Q + TDVC++G GYTGLS+AL L E G+ V VLEA +VGF Sbjct: 13 YPPSYYASTVPARPALPAAQGPIHTDVCIVGGGYTGLSAALHLAERGYDVVVLEAQRVGF 72 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGGQ+ + D+ +E G + A +A E +++ E VA+ + CDL+ G Sbjct: 73 GASGRNGGQVASGPRLDLSTLEARYGRETAHAQWALAREARKLVDELVAR-GLDCDLRAG 131 Query: 126 GVFAALTAKQM-GHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 ++A A + G+ + G+ + LD+ RI +V Y GG+LD H++ Sbjct: 132 VIYATDRAGDVAGYHAEAAHVQAAVGYDGVTPLDRDRIAALVGSAVYAGGVLDAGAAHLN 191 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRI-ERGASPVVHTPQGKVRAKFIIVAGNAYLGNL 243 PL L LG A + G I+E S + + G VV T + A+ +I+AGN Y+G L Sbjct: 192 PLKLVLGLADLAQVAGAQIFEGSQVRSVADAGPHVVVTTDAATIAAEQVILAGNGYIGGL 251 Query: 244 VPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGV 303 AA MP + ++ATEPLG + A ++LP+ + V D ++++Y+R D RL+FGGG Sbjct: 252 DSATAAHVMPINSYMVATEPLGPD-ADAILPEGHAVADNKFVVNYFRRAPDGRLLFGGGE 310 Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQG 363 Y R +I +R + + FPQL+ + IDYAW G +T SRLP ++ ++ + G Sbjct: 311 SYRYRFTPDIAGKVRGPLERIFPQLRGIGIDYAWGGTLAITRSRLPFARKVSPRVFSAGG 370 Query: 364 CSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423 SGHGV + L GK +AEA G+ ERF+ A LPH PFPGG LR P GLRD Sbjct: 371 YSGHGVALSLLFGKAMAEAAAGEPERFNQLAALPHAPFPGGAALRAPLLLGAMSLAGLRD 430 Query: 424 KLGF 427 +L F Sbjct: 431 RLPF 434 Lambda K H 0.320 0.139 0.421 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: 557 Number of extensions: 28 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: 427 Length of database: 434 Length adjustment: 32 Effective length of query: 395 Effective length of database: 402 Effective search space: 158790 Effective search space used: 158790 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 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