Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AO356_12605 AO356_12605 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_12605 Length = 437 Score = 379 bits (973), Expect = e-109 Identities = 199/425 (46%), Positives = 265/425 (62%), Gaps = 4/425 (0%) Query: 3 NTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAK 62 N + SYYAAS+ P P P L ++ DVCV+G G++GL++A+ L E G V +LEA + Sbjct: 11 NHAHAASYYAASSLPQPDHPLLLGELRADVCVVGGGFSGLNTAIELAERGMSVVLLEAHR 70 Query: 63 VGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDL 122 +G+GASGRNGGQ++ +D +G + + M E I+R+RV ++QI CDL Sbjct: 71 IGWGASGRNGGQLIRGVGHGLDQFAPIIGTDGVRQMKLMGLEAVEIVRQRVERFQIPCDL 130 Query: 123 KDGGVFAALTAKQM-GHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGG 181 G A + G E + L LL + VV + YVGG++DM G Sbjct: 131 TWGYCDLANKPSDLEGFAEDAEELRSLGYRHPTRLLQADEMHSVVGSDRYVGGLIDMGSG 190 Query: 182 HIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLG 241 H+HPLNLALGEAAA + LG ++EQS RI+ G VHT +G VRAK +++ NAYL Sbjct: 191 HLHPLNLALGEAAAAQQLGVRLFEQSAVTRIDYGPEVNVHTQRGSVRAKTLVLGCNAYLN 250 Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301 L P+L K +P G+ +IATEPL A +LLPQ+ V D LDYYRL+ D+RL+FGG Sbjct: 251 GLNPQLGGKVLPAGSYIIATEPLSQAQAQALLPQNMAVCDQRVALDYYRLSADRRLLFGG 310 Query: 302 GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIY 359 Y RDP +I A +RPKMLK FPQL DVKIDY W G + +RLPQ+GRL D N+Y Sbjct: 311 ACHYSGRDPQDIGAYMRPKMLKVFPQLADVKIDYQWGGMIGIGANRLPQIGRLKDQPNVY 370 Query: 360 YSQGCSGHGVTYTHLAGKVLAEALRGQ-AERFDAFADLPHYPFPGGQLLRTPFAAMGAWY 418 Y+Q SGHGV THLAGK+LAEA+ GQ + FD FA +PH FPGG+ LR+P A+G + Sbjct: 371 YAQAYSGHGVNATHLAGKLLAEAISGQHSSGFDLFAQVPHMTFPGGKHLRSPLLALGMLW 430 Query: 419 YGLRD 423 + L++ Sbjct: 431 HRLKE 435 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: 621 Number of extensions: 33 Number of successful extensions: 4 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: 437 Length adjustment: 32 Effective length of query: 395 Effective length of database: 405 Effective search space: 159975 Effective search space used: 159975 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