Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate N515DRAFT_2697 N515DRAFT_2697 gamma-glutamylputrescine oxidase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Dyella79:N515DRAFT_2697 Length = 429 Score = 228 bits (582), Expect = 2e-64 Identities = 148/427 (34%), Positives = 221/427 (51%), Gaps = 10/427 (2%) Query: 1 MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFK-VTVLE 59 M P P SYY A+A+ P AL+ E V ++G G+ GL +AL L E G + V +LE Sbjct: 1 MKQPPAP-SYYRATASAYEPYAALRGRAEAKVVIVGGGFAGLHTALGLAERGVRDVVLLE 59 Query: 60 AAKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQ 119 +VGFGASGRNGG + YS + +G ++A+ L + IR +V +Y I Sbjct: 60 REQVGFGASGRNGGFVFAGYSLGEQSLLDQLGEERARALFGLTTAAVERIRAQVLRYGIA 119 Query: 120 CDLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMS 179 CDL D GV A + L ++ L E+ Q E + Q +RE V Y G+ + + Sbjct: 120 CDLVDEGVLWANWFRDPAVLRRRQALLEKHYGVQWEWVAQDALRERVHTRRYFDGLYERN 179 Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVAGNA 238 H+HPLN A+G AAA G I+E + A ++ R G V T QG V A+ +++A Sbjct: 180 AFHLHPLNFAIGLAAAAAGQGVRIHEHTDAWQLRRDGLRWRVETDQGTVLAEHVVLACGG 239 Query: 239 YLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLI 298 YL L + +P T V+ TEPLGD L + L + D + DYYR D RL+ Sbjct: 240 YLAGLRRAIDRAILPIATYVMTTEPLGDRL-RACLDTRAAIYDTRFAFDYYRPLPDTRLL 298 Query: 299 FGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNI 358 +GG + R P + ++ +L+ FP L+ V+ID+AW+G ++PQ+G + + Sbjct: 299 WGGRISIRNRSPQAVRRLLTRDLLRVFPALQGVRIDHAWSGLMSYARHQMPQIGGGDEGL 358 Query: 359 YYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFAD--LPHYPFPGGQLLRTPFAAMGA 416 +++Q GHG+ T AG++LA A+ + +R+ FAD L P G L A Sbjct: 359 WWAQAFGGHGLAPTCAAGELLAAAIAERDQRWKQFADYGLASAHRPAGYLA----AQASY 414 Query: 417 WYYGLRD 423 W++ RD Sbjct: 415 WWHQGRD 421 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: 545 Number of extensions: 32 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