Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate GFF3817 PGA1_262p02210 FAD dependent oxidoreductase
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__Phaeo:GFF3817 Length = 433 Score = 134 bits (337), Expect = 5e-36 Identities = 125/421 (29%), Positives = 179/421 (42%), Gaps = 19/421 (4%) Query: 3 EHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIG 62 + S + A+ + L++ ++ D+ VVGGGYTG S+AL AE G DV +LEA G Sbjct: 4 DRNRSLWQATCREDLDAAALHDDVSADLVVVGGGYTGCSAALRAAELGADVRLLEAETFG 63 Query: 63 FGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCD-YR 121 G SGRN G + I G L +++ + E IK +QIDC+ + Sbjct: 64 AGGSGRNVGLVNAGLWLPPKKINSVLGEVNGTRLSTLLAAAPAAVFELIKTHQIDCEPIQ 123 Query: 122 PGGLFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGHI 181 G L A L L ++ + G L +AI R V SD GAL D G I Sbjct: 124 TGTLHCAHARSGLKDLRKRHQQLTAIGAPVTLLSRGDAIAR-VGSDAVYGALFDPRAGTI 182 Query: 182 HPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPA-VVRTAKGQVTAKYVIVAGNAYLGD 240 PL AIG A A G R++ S V + T V T G V A+++I+A NAY Sbjct: 183 QPLAYAIGLARAAASQGARLHASSPVVGLTRETDGWRVSTPGGTVRARHLIMATNAY-PL 241 Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYG- 299 + A ++P T L LA ++P+ D ++ +R RL+ G Sbjct: 242 PITGYTAPATIPVSYFQAATAPLPAGLAGRILPQAEGCWDTGLIMSSWRRDRAGRLIIGG 301 Query: 300 -GGVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIY 358 G + + AR + KL FP L + W G +T +P+ L + Sbjct: 302 MGDLSHPARSVH--TNWLRRKLAVMFPALADHPFEAEWAGKIAMTTEHIPKIIDLGQG-F 358 Query: 359 YMQGYSGHGVTCTHLAGRLIAE-LLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAY 417 GYSG G+ + GR +AE L+ GD P P R+PF + Y Sbjct: 359 ACFGYSGRGIGPGTVFGRRMAEALMHGDRSLL---------PIPVSDDHRLPFAGVRGTY 409 Query: 418 Y 418 Y Sbjct: 410 Y 410 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: 464 Number of extensions: 23 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: 426 Length of database: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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