Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_090448530.1 BLS63_RS25100 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_900100495.1:WP_090448530.1 Length = 437 Score = 341 bits (875), Expect = 2e-98 Identities = 182/421 (43%), Positives = 251/421 (59%), Gaps = 5/421 (1%) Query: 9 SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68 SYY+A+ + P LQ +V DV +IG G+TG++SA+ L E G KV ++EA K+G+GAS Sbjct: 17 SYYSATLDQETAYPPLQGEVSVDVVIIGGGFTGVASAVELAERGLKVAIVEANKIGWGAS 76 Query: 69 GRNGGQIVNSYSRDIDV---IERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GRNGGQ+ S S D + + +++G + + + + G II RV+KY I CDLK G Sbjct: 77 GRNGGQVTGSLSGDAAMRKQMRKTLGEEVDDFIWQLRWRGHAIIENRVSKYGIACDLKHG 136 Query: 126 GVFAALTAKQMGHLESQKRLWERFGH-TQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 + AA+ M LE+ R G L LLD+ +R +A E Y G + + H+H Sbjct: 137 HLHAAMKPAHMAELEASYAEAVRRGMGDSLTLLDRAGVRSHLASELYCGALKNRRNLHLH 196 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 PLNL +GEA A SLG +I+E SP + I GA P V T QG++ AK +++AG+ Y Sbjct: 197 PLNLCIGEAKAAASLGALIFEHSPVLDIIHGARPAVVTAQGRINAKQVLLAGDVYHKLEA 256 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 L P ++AT PLG LA L PQD V DC ++LDYYRLT DKRL+FGGG Sbjct: 257 NRLKGLIFPAMGGIVATAPLG-ALAEQLNPQDLAVYDCRFVLDYYRLTADKRLLFGGGCN 315 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364 Y RD +I +RP + + FPQLK V ID+ W+ + ++R+PQ+G+L DN++Y QG Sbjct: 316 YSGRDSRDIAGELRPGIERTFPQLKGVAIDFQWSCAMGIVINRIPQLGKLSDNVWYCQGY 375 Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDK 424 SGHG+ +H+ G+++A AL G ERFD FA P G L P A G WYY L +K Sbjct: 376 SGHGIATSHIMGEIMASALTGSLERFDTFAACKQIKVPLGDLFGNPMLAAGMWYYQLLEK 435 Query: 425 L 425 L Sbjct: 436 L 436 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: 574 Number of extensions: 19 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: 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 Sep 24 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