Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate GFF2313 PS417_11795 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__WCS417:GFF2313 Length = 430 Score = 345 bits (885), Expect = 2e-99 Identities = 177/425 (41%), Positives = 262/425 (61%), Gaps = 4/425 (0%) Query: 3 NTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAK 62 +T + SYY A+AN + RPAL D+ DVCVIG G+TG+++A+ L + G V +LEA + Sbjct: 4 STDHARSYYRATANALTERPALGTDLTADVCVIGGGFTGVNTAIELAQRGLSVVLLEARR 63 Query: 63 VGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDL 122 +G+GASGRNGGQ++ D+ + VG + + L + ++ ER+ ++I CDL Sbjct: 64 IGWGASGRNGGQLIRGIGHDVSGFGKYVGEEGVRYLERAGIDSVALVGERIRTHRIDCDL 123 Query: 123 KDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMSGG 181 + G A T Q + ++ G+ + L+ + I++VV Y GG++DM G Sbjct: 124 RWGFCELANTPAQFAAFKGEQAHLAALGYAHETRLVGPQDIQQVVGSPVYAGGLVDMGSG 183 Query: 182 HIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLG 241 H+HPLNL LGEA ESLG I+E + + + G + V G VRA +++A NA+L Sbjct: 184 HLHPLNLVLGEARLAESLGVRIFEHTEVLELIHGDTVHVRCAGGTVRAASLVLACNAHLE 243 Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301 L P L+ K +P G+ +IATEPL +LA+ L+PQ+ + D LDYYRL+ D+RL+FGG Sbjct: 244 ELEPRLSGKVLPAGSYIIATEPLSADLANQLIPQNLALCDQKVGLDYYRLSADRRLLFGG 303 Query: 302 GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIY 359 Y RDPA+I A ++PKMLK FPQL + I++ W G +T +R PQVGRL N++ Sbjct: 304 ACHYSGRDPADIAAYMQPKMLKVFPQLANTAIEFQWGGKIGITANRFPQVGRLKQYPNVF 363 Query: 360 YSQGCSGHGVTYTHLAGKVLAEALR-GQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWY 418 Y+QG SGHG+ TH ++LAEA++ G + D F+ +PH FPGG+ LR+P A+G + Sbjct: 364 YAQGYSGHGLNVTHWCARLLAEAIQAGHSTGLDIFSQVPHMTFPGGKALRSPLLALGMLW 423 Query: 419 YGLRD 423 Y LR+ Sbjct: 424 YRLRE 428 Lambda K H 0.320 0.139 0.421 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: 616 Number of extensions: 36 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: 427 Length of database: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 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