Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AZOBR_RS08855 AZOBR_RS08855 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__azobra:AZOBR_RS08855 Length = 426 Score = 391 bits (1004), Expect = e-113 Identities = 195/426 (45%), Positives = 275/426 (64%), Gaps = 1/426 (0%) Query: 1 MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60 M + + S+YA +A P P P L+D + DVCV+G GYTGL +AL L E G+ V +LEA Sbjct: 1 MPPSSHIRSWYADTATPYPQHPVLEDSLSCDVCVVGGGYTGLMTALELAEQGYDVVLLEA 60 Query: 61 AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120 +VG+GASGRNGGQI+ Y++ + IER VG + A+ L ++ E ++ ERVA++ I C Sbjct: 61 NRVGWGASGRNGGQIITGYNKSMSTIERWVGKEDARRLWDLGEESKALLAERVARHAIPC 120 Query: 121 DLKDGGVFAALTAKQMGHLESQKR-LWERFGHTQLELLDQRRIREVVACEEYVGGMLDMS 179 DL G AA+ + M + + +R + + +G+ ++ LD+ +R VV + YVGG+ D Sbjct: 121 DLTWGFAHAAVKPRHMDDVAAMEREMRDDYGYNKVRALDREAMRAVVGSDAYVGGLADDG 180 Query: 180 GGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAY 239 GH+HPLN ALG A+A G I+E S I+ G PV T G+V A+F+++AGNAY Sbjct: 181 SGHLHPLNYALGLASAAARAGVRIFEDSRVTAIDTGDRPVASTAMGRVTARFLVLAGNAY 240 Query: 240 LGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIF 299 LG L P L+A MP T +IATEPLG+ A SLLP + V D N++L+Y+R + D RL+F Sbjct: 241 LGALAPRLSAVVMPVATYMIATEPLGEATAASLLPTNIAVSDMNFVLNYFRRSADHRLLF 300 Query: 300 GGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIY 359 GGGV Y D ++ +R KML FPQL+ +D+ W G+ +T++R+PQVGRL Y Sbjct: 301 GGGVSYSGLDAPGLKIAMRSKMLAVFPQLRGSAVDHFWGGHVAITMNRMPQVGRLTPTTY 360 Query: 360 YSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYY 419 ++ G SGHGV +AG+V+AEA+RG AERFD FA +PH PFPGG+ RTP + ++ Sbjct: 361 FAHGYSGHGVALAGMAGRVMAEAIRGTAERFDVFARVPHLPFPGGRRFRTPALVLAMLWF 420 Query: 420 GLRDKL 425 LRD L Sbjct: 421 RLRDLL 426 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: 560 Number of extensions: 23 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: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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