Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_090448545.1 BLS63_RS25175 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_900100495.1:WP_090448545.1 Length = 429 Score = 284 bits (727), Expect = 3e-81 Identities = 158/418 (37%), Positives = 249/418 (59%), Gaps = 4/418 (0%) Query: 9 SYYAAS-ANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGA 67 SYYA + P+P RP L ET+V ++GAG++GL +AL L G +V +LE ++V + A Sbjct: 11 SYYARTYPGPIPLRPTLAGREETEVLIVGAGFSGLHTALRLALAGKRVCLLEVSRVAWAA 70 Query: 68 SGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGV 127 SGRNGGQ + +S D+ +E+++G ++++ L + +RE ++ + D + G + Sbjct: 71 SGRNGGQALLGWSCDMPPLEKALGLERSRRLWDSMRWAAAELRELPQRHGFEVDYRRGSL 130 Query: 128 FAALTAKQMGHL-ESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPL 186 + A+ +++ L E+Q ++G+ L L+ + + E +A Y+ + D H++PL Sbjct: 131 WTAVLPRRVRLLQEAQADALAKWGYAALRLIGRDELPEWIASPRYLAALYDPEAAHLNPL 190 Query: 187 NLALGEAAAVESLGGVIYEQSPAVRI-ERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVP 245 LA G AAA+E GG IYEQS + E A + T +G+VR + +++A NAY+ L Sbjct: 191 KLAQGLAAAIERAGGRIYEQSQVLDYRESAAGYIARTAKGEVRGEVLVLACNAYIDRLDR 250 Query: 246 ELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVY 305 +L+++ +P G+ +AT PL ELAHSLLPQD CV D ++ DY+RLT D+RL+FGGG Y Sbjct: 251 QLSSRLLPVGSYQVATVPLDPELAHSLLPQDSCVIDNQFVPDYFRLTPDRRLLFGGGCTY 310 Query: 306 GARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCS 365 P +I A RP + + FPQL+ V++++AW G+ ++L R P +GR G Y+ QG S Sbjct: 311 LGGIPRDIAAATRPHLERVFPQLRGVELEFAWGGHIDVSLKRTPDIGRQGQR-YWLQGFS 369 Query: 366 GHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423 GHGV T + ++EA+ G + + + FPGG LL P A G +Y LRD Sbjct: 370 GHGVLPTLAGARAVSEAILGDDALLALYQAIGNPRFPGGTLLAAPLEAAGKAWYRLRD 427 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: 561 Number of extensions: 31 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 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