Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate GFF3871 PGA1_78p00350 FAD dependent oxidoreductase
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__Phaeo:GFF3871 Length = 445 Score = 152 bits (384), Expect = 2e-41 Identities = 134/430 (31%), Positives = 203/430 (47%), Gaps = 36/430 (8%) Query: 16 YAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQL-V 74 YAP L + +T + V+GGGYTGLS+AL LAEAG DVV+L+A R G+GASGRNGG + V Sbjct: 31 YAP---LQDEVTAEFAVIGGGYTGLSAALTLAEAGADVVLLDAQRPGWGASGRNGGLVSV 87 Query: 75 NSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCD-YRPGGLFVAMNDKQ 133 S D I + YG A + +++ ++R ++ D + G FVA + Sbjct: 88 GSAKLADDAILRRYGQADAEQFFAAERAAVDLVETYVERLALEVDRHSRGYTFVAHRPDR 147 Query: 134 LATLEEQ-KENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEAD 192 L L + +E RYG + + S + GA+ G ++P+ +G Sbjct: 148 LTELHDYGQEYTRRYGLSYEFIPKEEMAAHGLNSPEFHGAVNLPVGFALNPMKFVLGLTR 207 Query: 193 AIRLNGGRVYELSAVTQIQHTTPA----VVRTAKGQVTAKYVIVAGNAYLGDKVEPELAK 248 A+ G R++ + T +Q TPA +++ GQV A+++++A N Y D + LA Sbjct: 208 AVEAAGVRMF---SDTPVQAITPAAGGYLLQGPAGQVRARHLLIATNGYSSDDLPQALAG 264 Query: 249 RSMPCGTQVITTERLSE-DLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYG--GGV--- 302 R +P + ++ T LSE ++A V D LL Y RL D RLL G G V Sbjct: 265 RYLPVQSNIMVTRPLSEAEIADQGWWSEQMVCDSRTLLHYLRLLPDRRLLLGLRGSVRVS 324 Query: 303 -----VYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD--T 355 V AR D +R+ FP + V+ + W+G +T + +P G + Sbjct: 325 EENIAVTKARARADFDRM--------FPAWRAVETAHFWSGLICMTRNLVPFAGAIPGMK 376 Query: 356 NIYYMQGYSGHGVTCTHLAGRLIAELLRGDAER-FDAFANLPHYPFPGGRTLRVPFTAMG 414 N + GY G GV AG LIA+ G +R P F GR R+ + Sbjct: 377 NAWAALGYHGSGVCMAPYAGALIADQALGRHQRPHPDLMQRPLRRFELGRWRRLSL-PLA 435 Query: 415 AAYYSLRDRL 424 +Y ++DR+ Sbjct: 436 FGWYHIKDRI 445 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: 447 Number of extensions: 20 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: 445 Length adjustment: 32 Effective length of query: 394 Effective length of database: 413 Effective search space: 162722 Effective search space used: 162722 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