Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate GFF1136 PGA1_c11510 gamma-glutamylputrescine oxidoreductase PuuB
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Phaeo:GFF1136 Length = 436 Score = 335 bits (860), Expect = 1e-96 Identities = 182/423 (43%), Positives = 257/423 (60%), Gaps = 4/423 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YP S+YAA+A P+ P LQ + DVC++G GYTGLS+AL L E G V +LEA +VGF Sbjct: 15 YPNSWYAATATPLAPFAPLQGEARADVCIVGGGYTGLSAALHLAEAGRSVILLEANRVGF 74 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGGQ+ + + D +E +G A L ++A + +++ +A++ I C LK G Sbjct: 75 GASGRNGGQLGSGQRMEQDGLESLMGEPDAAKLWHLAEDAKDLVKSLIARHDIDCHLKPG 134 Query: 126 GVFAALTAKQMGHLESQ-KRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 A + + H + L R+G+ + LD+ ++ + YVGG LDM GH+H Sbjct: 135 IAHACFSKSDVSHEHRYVEHLQTRYGYGDITALDKAALQAICPSPAYVGGSLDMGAGHLH 194 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 PL ALG A A + G I E S + IE GA + T +G+V A +I+A N YLG L Sbjct: 195 PLAYALGLARAAAAAGVQICEGSEVLDIEDGAQIRLRTAEGQVTADHLILACNGYLGGLN 254 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 ++AA+ MP + ATEPLG + A +L +D V D ++++Y+RL+ D RL+FGGG Sbjct: 255 RQVAARVMPINNFIAATEPLGADAAQ-VLARDVAVADSKFVVNYFRLSHDGRLLFGGGES 313 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364 YG R P++I A +R M + FP L+DVKIDYAW G +TL R+P + RLG NI + G Sbjct: 314 YGYRFPSDIAATVRKPMTEIFPHLRDVKIDYAWGGTLAITLKRMPYLARLGPNILSASGY 373 Query: 365 SGHGV-TYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRD 423 SGHGV T TH AG+++A A+ G + FD A +P FPGG +R+P A+ +Y LRD Sbjct: 374 SGHGVGTATH-AGQLMALAVAGDGDGFDTMARVPAPAFPGGAAMRSPLLALAMTWYALRD 432 Query: 424 KLG 426 +LG Sbjct: 433 RLG 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: 549 Number of extensions: 32 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: 436 Length adjustment: 32 Effective length of query: 395 Effective length of database: 404 Effective search space: 159580 Effective search space used: 159580 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