Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PfGW456L13_3923 Nucleoside-diphosphate-sugar epimerases
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3923 Length = 400 Score = 779 bits (2011), Expect = 0.0 Identities = 380/400 (95%), Positives = 394/400 (98%) Query: 28 VETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGASGRNGGQIVNSYSRDIDVIE 87 VETDVCVIGAGYTGLS+ALFLLENGFKVTVLEAA+VGFGASGRNGGQIVNSYSRDIDVIE Sbjct: 1 VETDVCVIGAGYTGLSAALFLLENGFKVTVLEAARVGFGASGRNGGQIVNSYSRDIDVIE 60 Query: 88 RSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGGVFAALTAKQMGHLESQKRLWE 147 R+VGP+QAQLLG MAFEGGRIIRERVA+Y IQCDLKDGGVFAA+TAKQMGHLESQKRLWE Sbjct: 61 RTVGPKQAQLLGQMAFEGGRIIRERVARYNIQCDLKDGGVFAAMTAKQMGHLESQKRLWE 120 Query: 148 RFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNLALGEAAAVESLGGVIYEQS 207 RFGHTQLEL+DQRRIREVVAC++YVGGMLDMSGGHIHPLNLALGEAAAVESLGG IYEQS Sbjct: 121 RFGHTQLELMDQRRIREVVACDQYVGGMLDMSGGHIHPLNLALGEAAAVESLGGTIYEQS 180 Query: 208 PAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVIATEPLGDE 267 PAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVI TEPLG+E Sbjct: 181 PAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLVPELAAKSMPCGTQVITTEPLGEE 240 Query: 268 LAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFPQ 327 LA +LLPQDYCVEDCNYLLDYYRL+GDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFPQ Sbjct: 241 LAKTLLPQDYCVEDCNYLLDYYRLSGDKRLIFGGGVVYGARDPANIEAIIRPKMLKAFPQ 300 Query: 328 LKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQA 387 LKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQA Sbjct: 301 LKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGHGVTYTHLAGKVLAEALRGQA 360 Query: 388 ERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDKLGF 427 ERFDAFADLPHYPFPGGQLLRTPFAA+GAWYYGLRDK G+ Sbjct: 361 ERFDAFADLPHYPFPGGQLLRTPFAALGAWYYGLRDKFGY 400 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: 797 Number of extensions: 19 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: 400 Length adjustment: 31 Effective length of query: 396 Effective length of database: 369 Effective search space: 146124 Effective search space used: 146124 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: 50 (23.9 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