Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate WP_011841395.1 RSPH17029_RS10235 FAD-binding oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >NCBI__GCF_000015985.1:WP_011841395.1 Length = 433 Score = 344 bits (883), Expect = 3e-99 Identities = 177/422 (41%), Positives = 263/422 (62%), Gaps = 3/422 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YP S+YA +A + P PAL +V DVCV+G GYTGLS+AL L E G+ V +LEA ++GF Sbjct: 13 YPGSWYAETAAELAPFPALAGEVRADVCVVGGGYTGLSTALHLAERGYSVVLLEAHRMGF 72 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGGQ+ + + + +E VG + A+ L + E ++R +A++ + + G Sbjct: 73 GASGRNGGQVGSGQRLEQEELEAMVGLEDARKLWELGEEAKALVRGLIARHDMPVTFQAG 132 Query: 126 GVFAALTAKQMGHLESQ-KRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 A ++ H + ++L +G+ ++E LD+ IR ++ + YVGG +D GH+H Sbjct: 133 IAHACRKVSEVAHSHAYAEKLARDYGYDRIEPLDRDGIRRLIGSDAYVGGDIDRGAGHLH 192 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 PLN A+G A A ++ G ++EQS RI GA PVV T +G+VRA+++++ N YLG L Sbjct: 193 PLNFAIGLARACDAAGVRLHEQSLVTRIVHGAEPVVETDRGRVRARWVVLGANGYLGGLE 252 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 P +AA+ MP ++ATEPLG A +L + V D ++++Y+RL+ D RL+FGGG Sbjct: 253 PSVAARVMPINNFILATEPLGARAA-DVLSEPVAVADTRFVVNYWRLSEDGRLLFGGGES 311 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364 YG R P +I +R ML+ +PQL+DV I +AW G +T++R+P R+ N+ + G Sbjct: 312 YGYRFP-DIARTVRKPMLEVYPQLRDVAITHAWGGTLAITMNRMPCFARVAPNVLSASGY 370 Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDK 424 SGHGV LAG+++AEA+ GQAERFD A LP FPGG LR P + +Y +RD+ Sbjct: 371 SGHGVAMATLAGRLMAEAVAGQAERFDLMAALPQPRFPGGAALRWPMLVLAMSWYAMRDR 430 Query: 425 LG 426 LG Sbjct: 431 LG 432 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: 554 Number of extensions: 29 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 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