Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_086509874.1 BZY95_RS10480 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_002151265.1:WP_086509874.1 Length = 430 Score = 560 bits (1442), Expect = e-164 Identities = 263/426 (61%), Positives = 332/426 (77%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 AN + SYYAA+AN P RPAL+ D+E +VCV+GAG+TG+SSAL L E G V VLEAA Sbjct: 5 ANAEHVASYYAATANFSPERPALEGDIECEVCVVGAGFTGISSALHLAEQGHDVVVLEAA 64 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 +VGFGASGRNGGQIVNSYSRD+DVIE G + A+ LG+MAFEG RIIRER+ +Y I CD Sbjct: 65 RVGFGASGRNGGQIVNSYSRDMDVIEAKYGTETARALGDMAFEGNRIIRERIRQYAIACD 124 Query: 122 LKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGG 181 LK+G +FAA KQ+ L K LWERFG+ +LELL+ + + E Y G ++D SGG Sbjct: 125 LKNGNLFAACNRKQLEGLREHKALWERFGNHELELLEGEAYKREIGSERYTGALVDHSGG 184 Query: 182 HIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLG 241 H+HPLNL LG+AAA ESLGGVI+E++P + G + + TP+G VRA+ +++AGNAYL Sbjct: 185 HLHPLNLVLGQAAAFESLGGVIHERTPVSGVRHGETVTLTTPRGSVRARRVVMAGNAYLQ 244 Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301 ++PEL +KSMPCGTQV+ TEPL L L+P D VEDCNYLLDYYR T D RL++GG Sbjct: 245 GVLPELESKSMPCGTQVVTTEPLPQALRRELIPNDMAVEDCNYLLDYYRFTADGRLLYGG 304 Query: 302 GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYS 361 GV YG +DPA+I A+IRPK+LK FPQL +V+ID+AW+GNFL+TL+RLPQ GRL DN+YY+ Sbjct: 305 GVNYGGQDPADIAAVIRPKILKTFPQLAEVRIDFAWSGNFLMTLNRLPQFGRLNDNVYYA 364 Query: 362 QGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGL 421 QG SGHGVT +HLAG+++AE +RG++ RFDAFA LPH PFPGG+LLR P +A+GAWYY Sbjct: 365 QGYSGHGVTCSHLAGRLIAEVMRGESARFDAFAGLPHLPFPGGRLLRVPLSALGAWYYAT 424 Query: 422 RDKLGF 427 RD+LG+ Sbjct: 425 RDRLGW 430 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: 682 Number of extensions: 21 Number of successful extensions: 1 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: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 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