Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate WP_038021942.1 HA49_RS08155 FAD-binding oxidoreductase
Query= SwissProt::P37906 (426 letters) >NCBI__GCF_000757425.2:WP_038021942.1 Length = 478 Score = 173 bits (439), Expect = 9e-48 Identities = 126/406 (31%), Positives = 199/406 (49%), Gaps = 6/406 (1%) Query: 6 SSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGA 65 ++YY ++ + F + C++ V+GGG G S+ALHLAE+G D ++LE + IG GA Sbjct: 48 ANYYESTLAPWMSFPAMETDKQCELVVIGGGLLGASTALHLAESGIDTILLEKNTIGSGA 107 Query: 66 SGRNGGQLVNSYSR-DIDVIEKSYGMDTARMLGSM-MFEGGEIIRERIKRYQIDCDYRPG 123 SGRNGGQL +R + + + ++ D AR L E +I E RY + D + G Sbjct: 108 SGRNGGQLTPGLARWEAESMLENLSTDEARRLWRFTSAEAMGLIDEIAGRYDLQLDRQYG 167 Query: 124 GLFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGHIHP 183 L A++ + L + + + G++Q+ +L ++ + SD Y G +LD+ GG IH Sbjct: 168 HLTAAVHPGHMNALVQAADARKFLGDEQVTILGNYQLQDHINSDIYYGGVLDNCGGQIHS 227 Query: 184 LNLAIGEADAIRLNGGRVYELSAVTQIQHT-TPAVVRTAKGQVTAKYVIVAGNAYLGDKV 242 L L G LNGG V+E S V +I+ + T V TA G +TA +V + Sbjct: 228 LALNRGLIYGFLLNGGCVHEHSEVIKIEESPTGTKVHTASGVITATRGVVIAVHDETHNL 287 Query: 243 EPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGV 302 E + ++P T V T + E +SL+P V D +DYYR + RLL+GG Sbjct: 288 LNENSSTTLPFYTYVGVTSPV-EGGHQSLLPTGKPVYDTQLQIDYYRPVRNQRLLFGGQG 346 Query: 303 VYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTN--IYYM 360 D + +L F Q +++D+ W+G LTL+ + + IY + Sbjct: 347 TGMRWDDTRTVDYLTSRLRTVFSQRDDIQLDFAWSGTTDLTLNGATDCRQNGAHGQIYSV 406 Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTL 406 G+SGHG+ T G+ I + + G + F ++ H GR L Sbjct: 407 HGWSGHGIAQTVRIGKAITDDITGRNDDFKMLTSIKHTSLLLGRQL 452 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: 544 Number of extensions: 32 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: 478 Length adjustment: 33 Effective length of query: 393 Effective length of database: 445 Effective search space: 174885 Effective search space used: 174885 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