Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_011841574.1 RSPH17029_RS11565 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_000015985.1:WP_011841574.1 Length = 430 Score = 196 bits (498), Expect = 1e-54 Identities = 128/420 (30%), Positives = 204/420 (48%), Gaps = 6/420 (1%) Query: 10 YYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGASG 69 ++ AS P P L+ ETDV ++G G+TGL AL L E G VLEA VGFGASG Sbjct: 13 WWGASDEPALAAPPLRGTTETDVAIVGGGFTGLVIALHLAEAGLAPLVLEARHVGFGASG 72 Query: 70 RNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDGG-VF 128 RNGGQ++ D + + + GP + + L ++ + + + +++I+C + G + Sbjct: 73 RNGGQVIPGLKYDPEALLQKFGPDRGRALIDLVGGAADAVFDLIERHRIRCAPRRAGWIQ 132 Query: 129 AALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHPLNL 188 AA + + + + ++ R W+ G + +L + I Y GG D G ++PL Sbjct: 133 AAHSERALPAVLNRARQWQERG-VGVSILSRDEIAARTGTSLYHGGWHDPRAGGLNPLAY 191 Query: 189 ALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVAGNAYLGNLVPEL 247 A G A + G + E+SPA+ + R GA + TP+G VRA +++A NAY L+P L Sbjct: 192 ARGLGRAAIAAGAHLIEESPALSLTRKGAGWEIRTPEGLVRANRVLIATNAYGEGLLPGL 251 Query: 248 AAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVVYGA 307 A +P + ++AT PL ++L L+P + + L Y R + D RL+ GG G Sbjct: 252 AQSILPVQSMLVATAPLPEDLRARLMPGGVVLSETRKLAFYMRQSDDGRLVLGGRGAVGP 311 Query: 308 RDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGCSGH 367 + + A + + + FP+ I W+G LTL LP + + G +G Sbjct: 312 MEDGRLMAALEAGLARIFPEAARFGIAQRWSGQLALTLDGLPHLHAPEPGLQVLLGYNGR 371 Query: 368 GVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDKLGF 427 G+ G+++A L E F P P LR P G +Y L+D++GF Sbjct: 372 GIALATALGRMVANHLAHGEE--PVFPVTPIRPL-AWHRLREPVMNAGIRWYWLKDRMGF 428 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: 499 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: 430 Length adjustment: 32 Effective length of query: 395 Effective length of database: 398 Effective search space: 157210 Effective search space used: 157210 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 Apr 10 2024. 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