Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 5208457 Shew_0969 FAD dependent oxidoreductase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__PV4:5208457 Length = 434 Score = 361 bits (927), Expect = e-104 Identities = 174/421 (41%), Positives = 265/421 (62%), Gaps = 3/421 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YP+S+Y A+AN + P L++ + DVC++G G++G+++A+ L E GF+V +LEA ++G+ Sbjct: 12 YPDSFYHATANALEALPQLKERISADVCIVGGGFSGINTAIELAERGFEVVLLEAKRIGW 71 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGG+++ +++ +G + + + M FE I+R RVAK+ I C+L+ G Sbjct: 72 GASGRNGGELIRGIGHNVEQFRNEIGSEGVEAIERMGFEAVEIVRNRVAKHNIDCNLQMG 131 Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHP 185 A + M L + + G +LL++ ++ EV+ + Y G ++DM+ GH+HP Sbjct: 132 YCDLATKPRHMKELAADYQEMLHQGREGFKLLEKHQLGEVIGSDLYCGALVDMNSGHLHP 191 Query: 186 LNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGN-LV 244 LNLALGEA SLG ++E S A +I +G P VHT G+V +++++AGNAY+G+ L Sbjct: 192 LNLALGEAKVARSLGVKMFEYSAATKIVKGERPCVHTEHGRVDCRYLVLAGNAYIGHELN 251 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 + K +P G+ ++ATEPL E+ ++PQ+ D LDY+ L+ D RL+FGG Sbjct: 252 GYIGGKVLPAGSYLLATEPLSQEMCDEIIPQNMAFADMRIDLDYFHLSQDNRLLFGGLCT 311 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYSQ 362 Y +DP +I+A +RP + K FPQLK VKI+Y W G + +RLPQ+GRL D NI Y+Q Sbjct: 312 YSGKDPKDIDAALRPNLEKVFPQLKGVKIEYEWGGMIGIGANRLPQIGRLPDCPNILYAQ 371 Query: 363 GCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLR 422 +GHGV TH+A +++ EAL QAERFD F + H FPGG R+P A G Y+ L+ Sbjct: 372 AYAGHGVNATHMAARLIGEALTAQAERFDIFDRVQHMTFPGGPRFRSPMLAAGMLYHRLK 431 Query: 423 D 423 D Sbjct: 432 D 432 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: 593 Number of extensions: 30 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: 434 Length adjustment: 32 Effective length of query: 395 Effective length of database: 402 Effective search space: 158790 Effective search space used: 158790 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