Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PP_2448 PP_2448 gamma-glutamylputrescine oxidase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Putida:PP_2448 Length = 427 Score = 814 bits (2103), Expect = 0.0 Identities = 392/427 (91%), Positives = 417/427 (97%) Query: 1 MANTPYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEA 60 MANTPYP+SYYAASANPVPPRPALQ +VETDVC+IGAGYTGLSSALFLLENGFKV+++EA Sbjct: 1 MANTPYPQSYYAASANPVPPRPALQGEVETDVCIIGAGYTGLSSALFLLENGFKVSIVEA 60 Query: 61 AKVGFGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQC 120 AKVGFGASGRNGGQIVNSYSRDIDVIER+VGP+QAQLLG+MAFEGGRIIRERVAKY IQC Sbjct: 61 AKVGFGASGRNGGQIVNSYSRDIDVIERTVGPKQAQLLGHMAFEGGRIIRERVAKYNIQC 120 Query: 121 DLKDGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSG 180 DLKDGGVFAALT+KQMGHLESQKRLWERFGH QLEL+DQ+RIREVVAC+ Y+GGMLDMSG Sbjct: 121 DLKDGGVFAALTSKQMGHLESQKRLWERFGHNQLELMDQKRIREVVACDSYIGGMLDMSG 180 Query: 181 GHIHPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYL 240 GHIHPLNLALGEAAAVESLGG+IYEQ+PAVRIERGA+PVVHTPQGKVRAKFIIVAGNAYL Sbjct: 181 GHIHPLNLALGEAAAVESLGGIIYEQTPAVRIERGANPVVHTPQGKVRAKFIIVAGNAYL 240 Query: 241 GNLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFG 300 GNLVPELAAKSMPCGTQVI TEPLG+ELA +LLPQDYCVEDCNYLLDYYRLT DKRLIFG Sbjct: 241 GNLVPELAAKSMPCGTQVITTEPLGEELARTLLPQDYCVEDCNYLLDYYRLTSDKRLIFG 300 Query: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360 GGVVYGARDPANIEAIIRPKMLKAFPQLK+VKIDYAWTGNFLLTLSRLPQVGR+GDNIYY Sbjct: 301 GGVVYGARDPANIEAIIRPKMLKAFPQLKNVKIDYAWTGNFLLTLSRLPQVGRIGDNIYY 360 Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYG 420 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFA LPHYPFPGGQ+LR PF+A+GAWYY Sbjct: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFAGLPHYPFPGGQMLRVPFSAIGAWYYS 420 Query: 421 LRDKLGF 427 LRD+LGF Sbjct: 421 LRDRLGF 427 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: 850 Number of extensions: 18 Number of successful extensions: 1 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: 427 Length adjustment: 32 Effective length of query: 395 Effective length of database: 395 Effective search space: 156025 Effective search space used: 156025 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