Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate GFF3726 Psest_3795 Glycine/D-amino acid oxidases (deaminating)
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__psRCH2:GFF3726 Length = 444 Score = 362 bits (928), Expect = e-104 Identities = 191/426 (44%), Positives = 266/426 (62%), Gaps = 5/426 (1%) Query: 2 TEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRI 61 ++H SYYAAS N+ F+ L DVC+VGGG++GL++A+ LAE G V++LEA RI Sbjct: 19 SDHAPSYYAASVNRELSFEPLQGEQRADVCIVGGGFSGLNTAIELAERGLSVILLEAHRI 78 Query: 62 GFGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYR 121 G+GASGRNGGQL+ D++ G + L M FE +I+R+RI+RY IDCD Sbjct: 79 GWGASGRNGGQLIRGVGHDVEQFTNILGEEGVDELKRMGFEAVDIVRQRIERYAIDCDLT 138 Query: 122 PGGLFVAMNDKQLATLEEQKENWERYGNKQ-LELLDANAIRREVASDRYTGALLDHSGGH 180 G +A + L +E+ + R G L+ + + V S RY G LLD GH Sbjct: 139 WGYCDLATKPRHLKGFDEEYSDLLRLGYPHPLQRVSRPNLATVVGSQRYLGGLLDMGSGH 198 Query: 181 IHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGD 240 +HPLNLA+GEA A + G R++E SAV +I++ + TA+G V A +++A NAYL + Sbjct: 199 LHPLNLALGEAAAAQSLGVRLFEQSAVERIEYGPQVALHTAQGVVHADNLVLACNAYL-N 257 Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300 ++P+LA + +P G+ +I TERL E L R L+P+N V D LDY+RL+AD RLL+GG Sbjct: 258 GLQPKLAGKVLPAGSYIIATERLPEPLQRELLPQNMAVCDQRVALDYFRLSADGRLLFGG 317 Query: 301 GVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRL--DTNIY 358 Y RDP D+ + PK+L+ FPQL G+ IDY+W G + +R+PQ GRL N++ Sbjct: 318 ACHYSGRDPKDIAAYMQPKMLEVFPQLIGIGIDYQWGGMIGIGANRLPQIGRLPEQPNVF 377 Query: 359 YMQGYSGHGVTCTHLAGRLIAE-LLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAY 417 Y Q YSGHG+ THLAG L+AE + ++ FD FA +PH FPGGR LR P A+G + Sbjct: 378 YAQAYSGHGLNATHLAGHLLAEAIATQESHGFDLFAQVPHPTFPGGRALRSPLLALGMLW 437 Query: 418 YSLRDR 423 Y L+DR Sbjct: 438 YRLKDR 443 Lambda K H 0.320 0.138 0.411 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: 556 Number of extensions: 29 Number of successful extensions: 6 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: 426 Length of database: 444 Length adjustment: 32 Effective length of query: 394 Effective length of database: 412 Effective search space: 162328 Effective search space used: 162328 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