Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate RR42_RS34300 RR42_RS34300 FAD-dependent oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Cup4G11:RR42_RS34300 Length = 424 Score = 204 bits (520), Expect = 3e-57 Identities = 138/428 (32%), Positives = 208/428 (48%), Gaps = 12/428 (2%) Query: 5 PYPESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVG 64 P P S +AA+A P PP PAL++ + TDV VIG G+TGLS+AL L E G V VLEA + G Sbjct: 2 PLPSSLWAATAPPAPPTPALRESLATDVLVIGGGFTGLSTALHLAEGGAHVCVLEANEPG 61 Query: 65 FGASGRNGGQIVNSYSRDIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCD-LK 123 +GASGRNGGQ+ + D D + R G +A+ L + ++ + +A++ I C ++ Sbjct: 62 WGASGRNGGQVNPTLKHDPDELVRLFGAARAEPLLDAVSRSADLVFDLIARHGIDCQPVR 121 Query: 124 DGGVFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHI 183 G + + + + + ++ W R G +++LD+ + V + + GG LD G I Sbjct: 122 SGWLQLSYSPGAVPAMHARAEQWARRG-APVDVLDRAAVARRVGTQAFAGGWLDGRAGAI 180 Query: 184 HPLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQ--GKVRAKFIIVAGNAYLG 241 PL G A + G ++ + + R + V T V AK +++A N Y G Sbjct: 181 QPLAYTRGLVGAAQRAGATVHGGTAVTALARQGTHWVATTSLGATVTAKQVVIATNGYTG 240 Query: 242 NLVPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGG 301 L P LA + + ++AT+PL D AH +L Q LL Y+R RL+ GG Sbjct: 241 PLWPGLAQTVLSANSFIVATQPLRDAEAHGILTQGETASTSQRLLLYFRKDALGRLLMGG 300 Query: 302 -GVVYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYY 360 G R P + + R L FPQL + +Y W G +T +P V + Sbjct: 301 RGFFADPRGPQDFAHLERSLEL-LFPQLGPLSYEYRWAGRIAITRDFMPHVHEPAPGVIM 359 Query: 361 SQGCSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQL--LRTPFAAMGAWY 418 + GC+G G+ G+ +A L G+ F P P G L L+ + A G + Sbjct: 360 ALGCNGRGIALCTSLGQHIAARLAGKGGDF----PYPITPVAGIPLHGLQRFYIAAGVAW 415 Query: 419 YGLRDKLG 426 Y L DKLG Sbjct: 416 YSLLDKLG 423 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: 515 Number of extensions: 28 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: 424 Length adjustment: 32 Effective length of query: 395 Effective length of database: 392 Effective search space: 154840 Effective search space used: 154840 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