Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_164924450.1 NGR_RS23860 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_000018545.1:WP_164924450.1 Length = 437 Score = 486 bits (1252), Expect = e-142 Identities = 224/423 (52%), Positives = 308/423 (72%), Gaps = 1/423 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YPESYYAAS N + L+ VETD+CV+GAGYTGL++A+ L E G+KV V+E A+VG+ Sbjct: 15 YPESYYAASRNVIRTPVKLKGRVETDICVVGAGYTGLATAIHLAEKGYKVAVIEGAQVGW 74 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGGQ+VN + + I+R G A+ +G + EGGRI+R V+ Y+I CDLK G Sbjct: 75 GASGRNGGQVVNGLNASLSTIQRRFGEDAARFIGGLVQEGGRILRRIVSHYRIDCDLKSG 134 Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHP 185 ++AA T M LE+++ LW ++G +LD+ +R++V E Y GGMLD++GGH+HP Sbjct: 135 NIYAAYTGAHMKDLEAKQALWRKYGMDDHLMLDRDALRKLVNSEAYCGGMLDITGGHMHP 194 Query: 186 LNLALGEAAAVESLGGVIYEQSPAVRIE-RGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 LNL LGEA A ESLGG+I+E SP R++ R A P V+T +G+V A+ +++ GNAYLG+ V Sbjct: 195 LNLVLGEARAFESLGGIIHEMSPVTRVDHRAARPTVYTREGEVSARIVVLCGNAYLGDAV 254 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 PEL ++ MP TQ+I T PLG+ELA L+P D CVED Y+LDY+RL+ DKR++FGGG V Sbjct: 255 PELVSRVMPVSTQMITTAPLGEELADMLIPSDMCVEDVRYILDYFRLSADKRMVFGGGTV 314 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364 YG DPA++ A +RP + K FP+LK VKIDYAW+GNF L+ +R+PQ+GR+G N Y++ G Sbjct: 315 YGGTDPADVVAKLRPNLEKVFPRLKGVKIDYAWSGNFALSFTRVPQMGRIGANTYFAHGY 374 Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDK 424 SGHGVT +HL G+ LAEA+ G RFD F LP YPFPGG++ R ++ +G+W+Y +D Sbjct: 375 SGHGVTGSHLFGRTLAEAIDGDQSRFDMFEKLPWYPFPGGRIFRAQYSTIGSWWYSFKDA 434 Query: 425 LGF 427 +G+ Sbjct: 435 VGW 437 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: 685 Number of extensions: 33 Number of successful extensions: 2 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: 437 Length adjustment: 32 Effective length of query: 395 Effective length of database: 405 Effective search space: 159975 Effective search space used: 159975 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 Apr 09 2024. 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