Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_086509880.1 BZY95_RS10510 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_002151265.1:WP_086509880.1 Length = 431 Score = 361 bits (926), Expect = e-104 Identities = 185/425 (43%), Positives = 262/425 (61%), Gaps = 9/425 (2%) Query: 7 PESYYAASA-----NPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 P SYY S PP+ Q DVCV+G G TG S+AL L E G+ V +LEA Sbjct: 10 PASYYRDSVAVRLDRACPPQRGHQ---RVDVCVVGGGITGCSAALHLAERGYSVALLEAH 66 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 ++GFGASGR+GGQI+ DI +E+++G ++A+ + M+ E R+ E + ++ I CD Sbjct: 67 EIGFGASGRSGGQILPGLGTDIATVEQALGRERARQVWEMSREAVRLTAELIERHAIPCD 126 Query: 122 LKDGGVFAALTAKQMGHLES-QKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 L G + AA+ + + L Q+R+ +G+ L L+ +RE V + Y G + D G Sbjct: 127 LAWGYLHAAVKPRHVRELRQFQERMARDYGYEALAWLEGEALRERVVTDAYPGALFDSEG 186 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240 GH+HPLN LG A A + G I+E SPA+ + RG V T +G++ A F++V NAYL Sbjct: 187 GHLHPLNYTLGLARAAQQAGVAIHEHSPALDVRRGQPATVVTERGEITADFVVVGANAYL 246 Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300 G L+PEL M ++ATEPLG+ A +LP + + D N++LDYYRL+ DKRLI+G Sbjct: 247 GRLLPELDGHIMRAANYIVATEPLGEARASQVLPYNDAISDANFVLDYYRLSADKRLIYG 306 Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360 G V Y R+P ++ + K+ + FP L+ V+IDY W G+ +TL+R P GRLG N+YY Sbjct: 307 GEVSYDGREPRGLQRRMDAKIARLFPLLEGVRIDYRWGGDVAITLNRAPDFGRLGANVYY 366 Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420 +QG SGHG+ LAGK+LAEA+ GQ+E FD FA +PH FPGG+ LRTP + +Y Sbjct: 367 AQGYSGHGMALAGLAGKLLAEAIAGQSEGFDLFAAMPHRRFPGGERLRTPLLVLATTFYK 426 Query: 421 LRDKL 425 LRD+L Sbjct: 427 LRDRL 431 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: 27 Number of successful extensions: 2 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: 431 Length adjustment: 32 Effective length of query: 395 Effective length of database: 399 Effective search space: 157605 Effective search space used: 157605 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