Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate BPHYT_RS30200 BPHYT_RS30200 FAD-dependent oxidoreductase
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__BFirm:BPHYT_RS30200 Length = 424 Score = 199 bits (507), Expect = 1e-55 Identities = 133/400 (33%), Positives = 207/400 (51%), Gaps = 11/400 (2%) Query: 29 DVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQLVNSYSRDIDVIEKSY 88 DV V+GGG+TGLS+A L + G V VL+A RIG GASGRNGGQ+ ++D + Sbjct: 27 DVVVIGGGFTGLSAAQALGKRGAAVTVLDAGRIGGGASGRNGGQVNTGVAQDFVALVAQL 86 Query: 89 GMDTARMLGSMMFEGGEIIRERIKRYQIDCDY-RPGGLFVAMNDKQLATLEEQKENWERY 147 G++ A + + + I+ IDC+Y G L +A LA LE+ E R Sbjct: 87 GVERASACYRAFSDAVDTVERLIREENIDCNYIATGKLKLASKPHHLAHLEKTAEAIRRE 146 Query: 148 GNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEADAIRLNGGRVYELSAV 207 + +EL+D + IR E+ SD + G LL GG +H +G A+A G ++YE +AV Sbjct: 147 VDTDIELIDRSRIRSEIQSDSFHGGLLQRHGGQMHMGKFTVGLAEAAVRRGAKLYENAAV 206 Query: 208 TQIQHTTPAV-VRTAKGQVTAKYVIVA-GNAYLGDKVEPELAKRSMPCGTQVITTERLSE 265 T I + TA+G+V AK V++A G + G +R P G+ ++ TE LS Sbjct: 207 TAIAKDGNGYRITTARGEVRAKQVLIATGPSRHGP--FGWYRRRLAPVGSFIVVTEPLSP 264 Query: 266 DLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGARD-PDDVE--RLVVPKLLK 322 +L + P + +Y+R+T D+RLL+GG + A + P D + R++ L Sbjct: 265 ELLAQVFPNRRAYTTTRLMHNYFRVTPDSRLLFGGRARFTASERPSDAKSGRILQEGLAA 324 Query: 323 TFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYMQGYSGHGVTCTHLAGRLIAELL 382 FP L +IDY W G ++ R+P G+ D IY+ GYSGHG + G+++A+++ Sbjct: 325 MFPTLASARIDYCWGGLVDMSADRLPHAGQHD-GIYFSMGYSGHGTQMSTHMGQVMADVM 383 Query: 383 RGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSLRD 422 G ++ + +P G T + F + YY ++D Sbjct: 384 DGHEDKNPWRES--EWPAIPGHTGKPWFLPLVGTYYRIKD 421 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: 503 Number of extensions: 32 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: 424 Length adjustment: 32 Effective length of query: 394 Effective length of database: 392 Effective search space: 154448 Effective search space used: 154448 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