Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate 5208465 Shew_0977 FAD dependent oxidoreductase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__PV4:5208465 Length = 428 Score = 681 bits (1757), Expect = 0.0 Identities = 330/427 (77%), Positives = 371/427 (86%), Gaps = 1/427 (0%) Query: 1 MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60 M TP+ SYYAASAN R L D++ETDVC+IGAGYTGLSSA+ LLE GFKVTVLEA Sbjct: 1 MTCTPHANSYYAASANTKALRDKLSDNIETDVCIIGAGYTGLSSAIHLLEAGFKVTVLEA 60 Query: 61 AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120 A+VGFGASGRNGGQIVNS+SRDID IE+ VG +QA+L G MAFEGGRI++ VAKY IQC Sbjct: 61 ARVGFGASGRNGGQIVNSFSRDIDTIEKVVGTEQAKLFGQMAFEGGRILKGLVAKYNIQC 120 Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIREVVACEEYVGGMLDMS 179 DLKDGGVFAAL KQMGHLE+QK LWE+ GH LELLD++ IR+VV E YVGG+LD S Sbjct: 121 DLKDGGVFAALNKKQMGHLEAQKALWEKHGHLGHLELLDEQGIRDVVDTERYVGGLLDKS 180 Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAY 239 GGHIHPLNLALGEA AVESLGG I+E S VR+++G +PVVHT +G V+ KF+IVAGNAY Sbjct: 181 GGHIHPLNLALGEADAVESLGGQIFEDSAVVRVDQGENPVVHTQEGSVKCKFVIVAGNAY 240 Query: 240 LGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIF 299 L L+PEL AKSMPCGTQVI TEPLG+ELAHSLLPQDYCVEDCNYLLDY+RL+GDKRLI+ Sbjct: 241 LKGLLPELQAKSMPCGTQVITTEPLGEELAHSLLPQDYCVEDCNYLLDYFRLSGDKRLIY 300 Query: 300 GGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIY 359 GGGVVYGARDPANIEAIIRPKML FPQLKDVKID+ WTGNFLLTLSRLPQVGR+G NIY Sbjct: 301 GGGVVYGARDPANIEAIIRPKMLATFPQLKDVKIDFTWTGNFLLTLSRLPQVGRIGGNIY 360 Query: 360 YSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYY 419 YSQGCSGHGVTYTHLAG++LAE + GQA+RFDAFA LPHYPFPGG LL+ PF+A+GAWYY Sbjct: 361 YSQGCSGHGVTYTHLAGQILAETINGQAKRFDAFAQLPHYPFPGGHLLQVPFSAIGAWYY 420 Query: 420 GLRDKLG 426 +RDKLG Sbjct: 421 TMRDKLG 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: 748 Number of extensions: 26 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: 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 17 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