Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 5209059 Shew_1537 FAD dependent oxidoreductase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__PV4:5209059 Length = 429 Score = 297 bits (760), Expect = 5e-85 Identities = 159/419 (37%), Positives = 243/419 (57%), Gaps = 4/419 (0%) Query: 9 SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68 SYY A+ P+L+ +++ DV +IGAG+TG+++AL L E G KV V+EA KVG+GA+ Sbjct: 8 SYYNATIKQETYYPSLEGELDVDVVIIGAGFTGVATALELAERGVKVAVVEANKVGWGAT 67 Query: 69 GRNGGQIVNSYSRD---IDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GRNGGQ+ S S D + + +G + + N+ + G II++RV KYQI CDLK G Sbjct: 68 GRNGGQVTGSLSGDNAMVKQLRNCIGHDAEEFVWNLRWRGHEIIKKRVEKYQIDCDLKFG 127 Query: 126 GVFAALTAKQMGHLESQKRLWERFGH-TQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 + A M +++ R G +L LL + I + + Y GG+L+ H+H Sbjct: 128 HLHTAYKPAHMAEMQTTYEEGLRRGMGDELTLLSKADIPDYLDTPLYHGGLLNRRNMHLH 187 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 +NL +GEA A E+ G +I+E S + I V T +G++ A ++AGNAY Sbjct: 188 SVNLCIGEARAAEAYGALIFEGSQVLDISDDKRVTVTTDKGRITANCAVLAGNAYHRLAR 247 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 +L P AT L +LA L P D V D ++LDYYR+T D RL+FGGG Sbjct: 248 HKLRGMLFPASLGNCATVRLDPQLAKQLNPHDLAVYDSRFVLDYYRMTADNRLMFGGGTN 307 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364 Y RD N+ A +RP + + FP+LK V+I++ WTG + ++R+PQ+G++ ++++Y QG Sbjct: 308 YSGRDSKNVAAELRPAIERTFPRLKGVEIEFDWTGMAGIVVNRIPQLGKVSEHLFYCQGY 367 Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423 SGHGV +H+ G+++++A++GQ E FD FA + P G L A+G YY + + Sbjct: 368 SGHGVATSHIMGEIMSQAVQGQLEEFDLFAQMKQIRLPVGDWLGNQGMALGMLYYRMME 426 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: 555 Number of extensions: 28 Number of successful extensions: 3 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: 429 Length adjustment: 32 Effective length of query: 395 Effective length of database: 397 Effective search space: 156815 Effective search space used: 156815 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