Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate GFF3491 PS417_17875 FAD-dependent oxidoreductase
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__WCS417:GFF3491 Length = 432 Score = 251 bits (642), Expect = 2e-71 Identities = 143/420 (34%), Positives = 238/420 (56%), Gaps = 5/420 (1%) Query: 5 TSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGF-DVVVLEASRIGF 63 T +YY A+ F TL + I DV V+GGG++G+++AL LAE G ++VVLEA +GF Sbjct: 6 TPTYYTATKKYNLSFPTLEQDIDADVVVIGGGFSGINTALELAEKGITNIVVLEARYLGF 65 Query: 64 GASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYRPG 123 G +GRNGGQ++ D++ I+K G D R + + G +II+ RI +Y ID D+ G Sbjct: 66 GGTGRNGGQIMAGIGHDLEKIKKDVGEDGLRQVFEISDLGADIIKNRIAKYNIDADFCHG 125 Query: 124 GLFVAMNDKQLATLEEQKENWERYGNK-QLELLDANAIRREVASDRYTGALLDHSGGHIH 182 ++ N +Q TL +++++ ++ ++ L + +++ + S Y+ ALL GGH+H Sbjct: 126 YGYMGFNARQEKTLRAWEKDFKSVNSQHEIRFLGGSDVQQIIGSKAYSSALLHMGGGHVH 185 Query: 183 PLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGDKV 242 LNL +GEA A+ +G R++E S ++ + VRT +G V A ++ A +++L +K+ Sbjct: 186 SLNLLLGEATALASHGVRIFENSPALEVSYGERITVRTGRGSVRASKLLWACDSFL-NKL 244 Query: 243 EPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGV 302 EPEL + ++ + TE LSE+L + + P D ++DYYR+T +NRLL+G Sbjct: 245 EPELHRSTINTYAFQMMTEPLSEELIQRISPIRGAYSDIRPVIDYYRVTHENRLLFGAAT 304 Query: 303 VYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD--TNIYYM 360 P D++ +LK FP LK VKID W G + + PQ G L +N +++ Sbjct: 305 PLVEHIPGDLKAWNRTLMLKIFPYLKDVKIDLAWGGPMACSPNLFPQVGTLPGRSNAFFV 364 Query: 361 QGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSL 420 QGYSG GVT +H+ +++AE + + R+D +++ G +R G +++ L Sbjct: 365 QGYSGFGVTPSHIICKVLAEGMSEGSARYDLVSSIHRPTIIGKDAIRPLLLTAGKSWHQL 424 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: 499 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: 432 Length adjustment: 32 Effective length of query: 394 Effective length of database: 400 Effective search space: 157600 Effective search space used: 157600 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