Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AO353_24770 AO353_24770 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24770 Length = 436 Score = 355 bits (910), Expect = e-102 Identities = 183/425 (43%), Positives = 259/425 (60%), Gaps = 4/425 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 + SYY ASAN + P L D++ DVCVIG G+TG+++A+ L + G V +LE ++G+ Sbjct: 12 HARSYYNASANAMVQHPTLTSDLQADVCVIGGGFTGVNTAIELAQRGLSVILLEGRRIGW 71 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGGQ++ D+ R VG + + L E ++ R+ ++ I CDL+ G Sbjct: 72 GASGRNGGQLIRGIGHDVSGFARYVGQEGVRYLERAGIESVEVVGNRIREHGIDCDLRWG 131 Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQL-ELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 A T Q + ++ + G+ L+ +R+VV Y GG++DM GH+H Sbjct: 132 FCELANTPAQFAAFQVEQETLDAQGYAHATRLVRPEDMRQVVNSGVYAGGLVDMGSGHLH 191 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 PLNL LGEA ESLG I+EQSP + I G++ V G VRA +++ NA+L +L Sbjct: 192 PLNLVLGEARVAESLGVRIFEQSPVLEIIHGSTVQVRCAGGTVRAGSLVLGCNAHLEDLE 251 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 P L+ K +P G+ +IATEPL + A L+PQ+ + D LDYYRL+ D+RL+FGG Sbjct: 252 PRLSGKVLPAGSYIIATEPLSAQAAAELIPQNLALCDQKVGLDYYRLSADRRLLFGGACH 311 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYSQ 362 Y RDP +I A +RPKMLK FPQL DV+IDY W G +T +R PQVGRL N++Y+Q Sbjct: 312 YSGRDPTDIAAYMRPKMLKVFPQLTDVRIDYQWGGRIGITANRFPQVGRLSQYPNVFYAQ 371 Query: 363 GCSGHGVTYTHLAGKVLAEALR-GQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGL 421 G SGHG+ TH ++LAEA+ G + D F+ +PH FPGG+ LRTP A+G ++ L Sbjct: 372 GYSGHGLNVTHWTARLLAEAIHAGHSHGLDVFSAVPHMTFPGGRALRTPLLALGMLWHRL 431 Query: 422 RDKLG 426 R+ LG Sbjct: 432 REVLG 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: 622 Number of extensions: 28 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: 436 Length adjustment: 32 Effective length of query: 395 Effective length of database: 404 Effective search space: 159580 Effective search space used: 159580 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