Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PfGW456L13_3223 Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3223 Length = 433 Score = 357 bits (915), Expect = e-103 Identities = 185/426 (43%), Positives = 267/426 (62%), Gaps = 5/426 (1%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 + SYYAASA + RPAL D+ DVCV+GAG+TG+++A+ L + G V +LEA ++G+ Sbjct: 8 HTHSYYAASAKGMRQRPALASDLVADVCVVGAGFTGINTAIELAQRGLSVVLLEARRIGW 67 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGGQ++ D+ + +G Q L + E +++ R+ ++ I CDL G Sbjct: 68 GASGRNGGQLIRGIGHDVSGFAKHIGADGVQYLEHAGNESVQVVANRIREHGIDCDLSWG 127 Query: 126 GVFAALTAKQMGHLESQKRLWERFGHT-QLELLDQRRIRE-VVACEEYVGGMLDMSGGHI 183 A T Q L++++ G+ + L+ +IRE VV Y GG++DM GH+ Sbjct: 128 FCELANTPAQFKALKAEQVQLIESGYAFETRLVAPEQIREQVVNSGVYAGGLVDMGSGHL 187 Query: 184 HPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNL 243 HPLNL LGEA ESLG I+EQSP + + G++ V G V A +++A NA+L L Sbjct: 188 HPLNLVLGEAQVAESLGVRIFEQSPVLELIHGSTVQVRCAGGTVSAGTLVLACNAHLEEL 247 Query: 244 VPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGV 303 P+L+ K +P G+ +IATEPL E A L+P + + D LDYYRL+ D+RL+FGG Sbjct: 248 EPKLSGKVLPAGSYIIATEPLSQEAAAKLIPHNVALCDQKVGLDYYRLSADRRLLFGGAC 307 Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGD--NIYYS 361 Y RDP++I A +RP+MLK FPQL DV+IDY W G ++ +R PQVGRL N++Y+ Sbjct: 308 HYSGRDPSDISAYMRPQMLKVFPQLADVRIDYQWGGKIGISANRFPQVGRLSQHPNVFYA 367 Query: 362 QGCSGHGVTYTHLAGKVLAEALR-GQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420 QG SGHG+ TH K+L EA+ G ++ FD F+ +PH FPGG+ LR+P A+G ++Y Sbjct: 368 QGYSGHGLNVTHWCAKLLGEAIHAGHSKGFDVFSAVPHMTFPGGRALRSPLLALGMFWYR 427 Query: 421 LRDKLG 426 +R+ LG Sbjct: 428 MREMLG 433 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: 610 Number of extensions: 34 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: 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