Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_053939623.1 WG78_RS20115 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_001294205.1:WP_053939623.1 Length = 428 Score = 319 bits (817), Expect = 1e-91 Identities = 171/418 (40%), Positives = 252/418 (60%), Gaps = 6/418 (1%) Query: 9 SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68 S+Y AS P ALQ ++ DVC++GAGY+GLS+AL L + GF V VLEA +V +GAS Sbjct: 12 SWYEASVTRPPADAALQGALDVDVCIVGAGYSGLSAALELRQRGFSVAVLEAEQVAWGAS 71 Query: 69 GRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVF 128 GRNGGQ++ ++ D D + R +GP A+ +++ G ++ RVA+Y I CDL G + Sbjct: 72 GRNGGQVLVGFAND-DTVLRQLGPAAARQAWDISVAGVHLLHARVARYGIDCDLVRGYLH 130 Query: 129 AALTAKQ---MGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHP 185 A +A++ + H +Q R + FG+ + + + +R + YVG D GHIHP Sbjct: 131 VATSARKAEGLRHWTAQMR--DTFGYDPISDIAPKDVRNWIDSPRYVGAAHDALSGHIHP 188 Query: 186 LNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVP 245 L ALG A A G ++ S RIE G +HT QG+VR++F ++A NAY+G L+ Sbjct: 189 LKYALGLADAARQAGVQLFAHSAVSRIEHGPLVTLHTAQGRVRSRFALIAANAYVGQLLG 248 Query: 246 ELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVY 305 + A+ MP + +IATEPL E A +L+ V D N+++DY+RL+ D R++FGG V Sbjct: 249 KTGARIMPVRSFIIATEPLPPEQAQALIRGRAAVCDTNFMIDYFRLSADGRVLFGGRVTS 308 Query: 306 GARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCS 365 G P + +R ++ FPQL V I +AW G +T++R P GR+ N+YY QG Sbjct: 309 GNAGPDALMPSLRARLAGVFPQLAHVAITHAWGGLVDVTMNRAPDFGRIAPNVYYLQGFC 368 Query: 366 GHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423 GHGV T +AG+++AEA+ GQAERFD FA L H+ +PGG L + + +G Y L++ Sbjct: 369 GHGVALTGMAGQLVAEAIAGQAERFDLFARLQHHRYPGGPGLHSTWLRLGVAYNQLKE 426 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: 491 Number of extensions: 18 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: 428 Length adjustment: 32 Effective length of query: 395 Effective length of database: 396 Effective search space: 156420 Effective search space used: 156420 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