Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate WP_086509629.1 BZY95_RS09110 FAD-binding oxidoreductase
Query= SwissProt::P37906 (426 letters) >NCBI__GCF_002151265.1:WP_086509629.1 Length = 426 Score = 137 bits (345), Expect = 6e-37 Identities = 108/357 (30%), Positives = 170/357 (47%), Gaps = 6/357 (1%) Query: 29 DVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQLVNSYSRDIDVIEKSY 88 DV V+GGG TG+++ALHLAEAG DV ++EA + GASGRN G + D I + Sbjct: 28 DVLVIGGGITGINTALHLAEAGVDVTLIEAGDVPSGASGRNVGLVNAGMWIPPDDIREVL 87 Query: 89 GMDTARMLGSMMFEGGEIIRERIKRYQIDCD-YRPGGLFVAMNDKQLATLEEQKENWERY 147 G + +++ + ++ I+R+ I C R G L +A N + L + E +R Sbjct: 88 GEEIGERANTILGDAPAVVFSLIERHGIACQATRTGTLHLAHNGRGEQELARRAEQLQRR 147 Query: 148 GNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEADAIRLNGGRVYELSAV 207 G +ELL+A A + + + R ALLDH G ++P G A A + G R++ SA Sbjct: 148 G-APVELLEAAACQERLGTRRIHRALLDHRAGTLNPSAYTRGLARAAKAAGARLHTHSAA 206 Query: 208 TQIQHTTPA-VVRTAKGQVTAKYVIVAGNAYLGDKVEPELAKRSMPCGTQVITTERLSED 266 T + V TA G V A+ +++A NAY D+ E+ + + + LS + Sbjct: 207 TGVARAGDGWRVTTAHGSVQAQRLVLATNAYTEDRWN-EVRRHFFVGHFYQVASRPLSGE 265 Query: 267 LARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGARDPDDVERLVVPKLLK-TFP 325 A ++P + D +L R A+ RL+ G + G P R ++ + FP Sbjct: 266 AADEILPGHQGAWDTRMVLSSIRRDAEGRLIL-GSLGKGEGKPAAFLRCWANRIQRHYFP 324 Query: 326 QLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYMQGYSGHGVTCTHLAGRLIAELL 382 QL V+ + WTG T + L + + GY+G G+T + G+ A L Sbjct: 325 QLGSVEWECSWTGRIGFTPDHTLRLFELAPGVLGVSGYNGRGITTGTVVGKGFARYL 381 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: 421 Number of extensions: 22 Number of successful extensions: 4 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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