Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PfGW456L13_3806 Nucleoside-diphosphate-sugar epimerases
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3806 Length = 429 Score = 309 bits (792), Expect = 9e-89 Identities = 171/426 (40%), Positives = 265/426 (62%), Gaps = 4/426 (0%) Query: 3 NTPYPESYYAAS-ANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 +T + SYYA + A+ + R L+ + +T+V +IGAG++GL +AL L G +VT+LEA+ Sbjct: 5 STRHVASYYAHTCADRLVDRAVLEGEQDTEVLIIGAGFSGLHTALRLALAGKRVTLLEAS 64 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 +V + ASGRNGGQ + +S D+ +E ++G ++A+ L + R +R+ +++ CD Sbjct: 65 RVAWAASGRNGGQAILGWSCDMPPLEAALGYERARRLWDGMRWAARELRDLPGRHEFDCD 124 Query: 122 LKDGGVFAALTAKQMGHL-ESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 + G ++ ++ +++G L E Q ++GH +L+ +++ + + VA E Y G+ D G Sbjct: 125 YRAGHLWTSVMPRRVGLLTEWQHEASHKWGHDKLQFIERSDLPQWVASERYQAGLFDPEG 184 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRI-ERGASPVVHTPQGKVRAKFIIVAGNAY 239 GH++PL LALG A A+E GG I+EQS A+ E G VV T +G++RA +++A NAY Sbjct: 185 GHLNPLKLALGLADAIERAGGRIHEQSKALSYGEEGDGFVVTTERGRIRADVLVLACNAY 244 Query: 240 LGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIF 299 L L P+LA+ +P GT +AT PL ELA +LLP + CV D ++LDY+R T D RL+F Sbjct: 245 LDRLDPQLASCVLPVGTYQVATAPLTKELATALLPSNVCVTDNQFVLDYFRRTPDNRLLF 304 Query: 300 GGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIY 359 GGG Y P +I A RP + + FPQL V +++AW G+ LTL R P +GR GD +Y Sbjct: 305 GGGCTYLGGMPKDIAAATRPFLERVFPQLTGVDLEFAWGGHIDLTLKRTPDIGRRGD-LY 363 Query: 360 YSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYY 419 + QG SGHGV T A + +++A+ GQ + + L + FPGG+ L P A+G +Y Sbjct: 364 WMQGYSGHGVLPTLAAARAVSDAVLGQPDELSLYQGLNNGSFPGGKYLAAPLEAIGKAWY 423 Query: 420 GLRDKL 425 LRD + Sbjct: 424 RLRDSI 429 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: 556 Number of extensions: 30 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: 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