Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate SMc03132 SMc03132 oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Smeli:SMc03132 Length = 426 Score = 219 bits (558), Expect = 1e-61 Identities = 131/390 (33%), Positives = 194/390 (49%), Gaps = 3/390 (0%) Query: 6 YPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGF 65 YP +YY + RP L VE D +IG G GL++AL L G V VLEA VGF Sbjct: 3 YPNTYYKQTIAETNVRPPLSGTVECDTVIIGGGLAGLTTALQLARAGQSVVVLEAESVGF 62 Query: 66 GASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GASGRNGG + ++ D I R G + A+ + ++ EG +RE + +I Sbjct: 63 GASGRNGGFVSPGFATGSDNIARMAGTEAARQIHRLSIEGVEFVRETIEALKIDGARPQP 122 Query: 126 GVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIHP 185 G+ + L G L++ R +L+ L +R V+ Y + D H+HP Sbjct: 123 GITSVLRYDDGGSLKAHADEMRRIYGYELDYLSTGEVRSVLKSNRYFHALRDPKAFHMHP 182 Query: 186 LNLALGEAAAVESLGGVIYEQSPAV-RIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 LN G A +E LGG IYE S A + GA V T G+VRA+ ++ Y G L Sbjct: 183 LNYLRGLAREIERLGGRIYEGSAATGSVLDGAEKTVSTSGGRVRARHVVFTTGGYTGPLN 242 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLT-GDKRLIFGGGV 303 L +P T V+ +E EL + + + D DYYRL G KRL++GG + Sbjct: 243 GRLKRSFLPIATYVMLSEE-APELIRTAIATTDAIGDNRRAGDYYRLVEGGKRLLWGGRI 301 Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQG 363 A PA + +R +M+ +PQLKD+K + AW+G +PQ+G + +++ Sbjct: 302 TTRAASPAALAGELRREMVGTYPQLKDLKTELAWSGLMSYARHLMPQIGEMQPGVWHCTA 361 Query: 364 CSGHGVTYTHLAGKVLAEALRGQAERFDAF 393 GHG+ T + GK++AE + GQ++R+ F Sbjct: 362 FGGHGLNTTAIGGKLVAEGILGQSDRYKLF 391 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: 553 Number of extensions: 30 Number of successful extensions: 3 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: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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