Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate CCNA_03229 CCNA_03229 FAD dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Caulo:CCNA_03229 Length = 429 Score = 268 bits (684), Expect = 3e-76 Identities = 163/430 (37%), Positives = 227/430 (52%), Gaps = 17/430 (3%) Query: 5 PYPESY-----YAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLE 59 PYP Y YA + VP P L DV +VC+IGAG+TGL +AL L G + VLE Sbjct: 8 PYPSPYGRGNWYADTVTDVPASPPLDGDVAAEVCIIGAGFTGLGAALAL---GSRAVVLE 64 Query: 60 AAKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQ 119 A ++G ASGRNGGQ+ RD +E++VG A L +A E V I Sbjct: 65 AGRIGCAASGRNGGQVHTGQRRDQAWLEKTVGRDDALALWRLAEEARAHFASLVTA--ID 122 Query: 120 CDLKDGGVFAALTAKQMGHLESQKRLW---ERFGHTQLELLDQRRIREVVACEEYVGGML 176 CD + G + A K G E L +R+G+ QLEL+ + + + + Y GG+ Sbjct: 123 CDWRPGMIHAR--HKPGGEAEDADYLALMADRYGYDQLELIGETALAHELGTDVYHGGLA 180 Query: 177 DMSGGHIHPLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVA 235 D GGH+HPL LA G AA + G VI+E + A R G VV T G+V +I++ Sbjct: 181 DHGGGHVHPLKLAQGMAAQARAAGAVIHENTRADAWRREGGKIVVETGGGRVTCDQLILS 240 Query: 236 GNAYLGNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDK 295 G+ L + A+ MP + T PLG LA ++ + V D ++++Y+R T D Sbjct: 241 GDGLLNRMAGPAQARVMPINNFIAVTAPLG-ALADEIIRSNAAVSDSRFVVNYFRKTPDG 299 Query: 296 RLIFGGGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLG 355 RL+FGGG Y P +I ++R + K +P+L DV+I +AW G +T SR+P VG + Sbjct: 300 RLLFGGGENYRPGFPHDIAGLVRKNLAKIYPRLADVEITHAWGGTLGITFSRMPFVGEVA 359 Query: 356 DNIYYSQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMG 415 + + G SG GV GK+LAEA G+ D + LP PFPGG+LLR P G Sbjct: 360 QGVRVAAGYSGQGVMLAPYVGKLLAEAALGETGPVDLLSRLPTPPFPGGRLLRWPLTVAG 419 Query: 416 AWYYGLRDKL 425 +Y LRD+L Sbjct: 420 LSWYALRDRL 429 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: 614 Number of extensions: 34 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: 429 Length adjustment: 32 Effective length of query: 395 Effective length of database: 397 Effective search space: 156815 Effective search space used: 156815 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