Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate WP_053938621.1 WG78_RS14815 FAD-binding oxidoreductase
Query= SwissProt::P37906 (426 letters) >NCBI__GCF_001294205.1:WP_053938621.1 Length = 428 Score = 344 bits (882), Expect = 3e-99 Identities = 178/422 (42%), Positives = 265/422 (62%), Gaps = 2/422 (0%) Query: 2 TEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRI 61 TEH +S+YAA+AN L ++ CDV VVG G TGL +AL+LAE G+ VVVLEA+R+ Sbjct: 6 TEHIASWYAATANDSTRHAPLMGTLACDVLVVGAGLTGLHAALNLAERGYKVVVLEAARV 65 Query: 62 GFGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYR 121 G+ ASGRNGGQ++N ++ +D E + + + M E ++RERI ++ IDCDYR Sbjct: 66 GWAASGRNGGQVINGFACGMDTFESELPKEDLQRVFDMGIEANTLLRERIAKHNIDCDYR 125 Query: 122 PGGLFVAMNDKQLATLEEQK-ENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGH 180 G L A + L+ + E +R+G L ++ + + V S+RY G L D + GH Sbjct: 126 AGYLTAANKAAHVKDLQAWRDEAAQRWGYPDLSWVERSELPGYVQSERYAGGLFDPNSGH 185 Query: 181 IHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGD 240 +HPLN +G A A G +++E S VT++Q TP V++TA GQV A++V++A NA++ + Sbjct: 186 LHPLNYTLGLARAAVAAGVQIFEHSLVTEMQQGTPHVLKTAHGQVQAQFVVLACNAFI-E 244 Query: 241 KVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300 + P L ++ MP GT VITTE ++ ++L+P + D ++LDY+R T D R+L+GG Sbjct: 245 HLSPALNRKIMPVGTYVITTEPITPVRFKALMPAGAAICDSRFVLDYFRPTPDGRVLWGG 304 Query: 301 GVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYM 360 V Y P ++ + + +LKTFPQL +KI + W G +T++R P FGRL + +Y+ Sbjct: 305 KVSYSTLAPANLAQAMRADMLKTFPQLADIKIIHAWGGMVDITMNRAPHFGRLASTVYFA 364 Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSL 420 QG+SGHGV + LAG+L+AE + G AERFD F + H+ FPGG LR P + A+Y L Sbjct: 365 QGFSGHGVNVSGLAGKLMAEAIAGQAERFDIFTKIRHHDFPGGDLLRTPSLVLAMAWYRL 424 Query: 421 RD 422 +D Sbjct: 425 KD 426 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: 470 Number of extensions: 27 Number of successful extensions: 3 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: 428 Length adjustment: 32 Effective length of query: 394 Effective length of database: 396 Effective search space: 156024 Effective search space used: 156024 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 24 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