Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AO356_00055 AO356_00055 oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00055 Length = 433 Score = 205 bits (521), Expect = 3e-57 Identities = 141/442 (31%), Positives = 220/442 (49%), Gaps = 26/442 (5%) Query: 1 MANTPYPE---SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTV 57 MA +P+ S + ++A P PAL+ D DV V+G GYTGLS+A +L + G V Sbjct: 1 MAVSPFAADIASLWQSTAVDAPSFPALEGDRSYDVVVVGGGYTGLSTAHYLAKKGLATVV 60 Query: 58 LEAAKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQ 117 LEA+++G+GASGRNGG + Y + + G + AQ + ++ E + E VA Y Sbjct: 61 LEASRIGWGASGRNGGVVSAKYRISLSKVAARYGLEMAQTMRRLSLESVEHLEELVAVYS 120 Query: 118 IQCD--LKDGGVFAALTAKQMGH-LESQKRLWERFGHTQLELLDQRRIREVVACEEYVGG 174 ++ + G + A + + + + L E G + E+L +++E ++VGG Sbjct: 121 LEAAQYRRSGSLHCAHNEATLDYCVREAQWLHEHLGDSSFEVLCAGQMQEETGSGDFVGG 180 Query: 175 MLDMSGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFII 233 +LD GG +HPLN G A V + G I+E +P + I R G V TP G VRAK ++ Sbjct: 181 VLDRGGGLLHPLNFVRGLADGVSAAGVSIHEGAPVMGIRRMGTGVRVETPTGTVRAKQVV 240 Query: 234 VAGNAYLGNLVPELA---AKSMPCGTQVIATEPL-GDELAHSLLPQDYCVEDCNYLLDYY 289 +A N Y +L P A +P + ++ATEPL G +L LL + ++ ++ Sbjct: 241 LATNGY-SSLTPATAPVRKSVVPFRSAMLATEPLTGPQL--ELLRHGRSYTETRRMMRWF 297 Query: 290 RLTGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLP 349 R+ D RL++GG +G D + M+K FP L I + W+G LT+ +P Sbjct: 298 RMAED-RLLYGGRGAFGTDDSEAAFNALHEAMVKQFPLLARATITHRWSGLVALTIDSVP 356 Query: 350 QVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERF-----DAFADLPHYPFPGG 404 VGR+ D + Y+ G +G GV + GK +A+ + G+ D +P Y Sbjct: 357 HVGRIDDRVVYAMGYNGTGVAMSSYIGKHVADVIVGRKPELGLMWADKIRRIPFYS---- 412 Query: 405 QLLRTPFAAMGAWYYGLRDKLG 426 LR P M A +Y D +G Sbjct: 413 --LRVPVVRMVAGWYQFLDAIG 432 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: 458 Number of extensions: 20 Number of successful extensions: 5 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: 433 Length adjustment: 32 Effective length of query: 395 Effective length of database: 401 Effective search space: 158395 Effective search space used: 158395 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