Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_085636469.1 MGEO_RS08635 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_002115805.1:WP_085636469.1 Length = 434 Score = 352 bits (904), Expect = e-101 Identities = 180/426 (42%), Positives = 264/426 (61%), Gaps = 2/426 (0%) Query: 2 ANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAA 61 A YP+S+YAA+A P+PP LQ + DVC+IGAGYTGLS+AL L E G V +L+A Sbjct: 9 ARGSYPDSWYAATATPLPPFAPLQGETRADVCIIGAGYTGLSAALHLAEMGADVVLLDAH 68 Query: 62 KVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD 121 +VGFGASGRNGGQ+ + +D +E+ VG A+ L ++ + ++R+ VA++ + C Sbjct: 69 RVGFGASGRNGGQLGSGQRQDQITLEKLVGSDAARALWDLGEDSKTLVRDLVARHGLDCY 128 Query: 122 LKDGGVFAALTAKQMGHLESQ-KRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 L+DG +AA L + L R+G+ ++E LD+ + +Y+GG LDM Sbjct: 129 LRDGVAWAASRPADADDLHQYAEHLQTRYGYDRIEALDRDAFHALCPSPDYIGGTLDMGA 188 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240 GH+HPL LALG A A G I+E+S I G+ V T G V A +I+AGN YL Sbjct: 189 GHLHPLRLALGLADAAAKAGARIHERSHVHDIRHGSKITVRTDAGHVIADQVILAGNGYL 248 Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300 G L ++ A+ MP ++ATEPLG++ +L +D V D ++++Y+RL+ D RL+FG Sbjct: 249 GGLDRQVIARVMPINNYIVATEPLGEDRM-KVLTRDVAVADSRFVVNYFRLSHDGRLLFG 307 Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360 GG YG R PA+I A++R +M +P L+DV+IDYAW G +T+ R+P + R+ N+ Sbjct: 308 GGETYGYRFPADIPALVRKRMAVIYPHLRDVRIDYAWGGTLAITIRRMPYLARVRPNMLS 367 Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420 + G SGHGV AGK+LAEA RG ++ F+ + +PH PFPGG + RTP + ++ Sbjct: 368 ASGYSGHGVGTAIQAGKLLAEATRGTSDGFETYNAIPHTPFPGGGMFRTPLLTLAMTWFA 427 Query: 421 LRDKLG 426 +RD+LG Sbjct: 428 MRDRLG 433 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: 573 Number of extensions: 30 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: 434 Length adjustment: 32 Effective length of query: 395 Effective length of database: 402 Effective search space: 158790 Effective search space used: 158790 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