Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate 5209538 Shew_2005 FAD dependent oxidoreductase (RefSeq)
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__PV4:5209538 Length = 443 Score = 163 bits (413), Expect = 9e-45 Identities = 134/430 (31%), Positives = 211/430 (49%), Gaps = 20/430 (4%) Query: 7 SYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLA-EAGFDVVVLEASRIGFGA 65 SY+A + ++ A L+ + DV +VGGG+TGL +A +LA E + VLEA++IGFGA Sbjct: 19 SYWATTVSRPARLPALSGRMQTDVAIVGGGFTGLLTAYYLASEFNIEARVLEANQIGFGA 78 Query: 66 SGRNGGQLVNSYSR-DIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYRPGG 124 SGRN G ++ R + K +GM+T + + + + I++++I CD +P G Sbjct: 79 SGRNAGFVLKGSGRMGYSQMAKKWGMETTKGIYGEFTSAVRRVEQLIEQHEIACDAQPKG 138 Query: 125 -LFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYT-GALLDHSGGHIH 182 L +A N K +TL+ + + + L + ++ + GAL + G ++ Sbjct: 139 YLKIAHNAKAYSTLKGAADFIAEHLGDDAQFLTPSELKESYMDNHQAYGALRLNDGFGVN 198 Query: 183 PLNLAIGEADAIRLNGGRVYELSAVTQ-IQHTTPAVVRTAKGQVTAKYVIVAGNAYLGDK 241 PL L +G ++ G ++E S V + ++ + T KG++ AK V+ AGNAY + Sbjct: 199 PLKLCLGYKRVVQSLGVHLHEESCVREWLKEGPHHRLITDKGELIAKQVVSAGNAYTPKR 258 Query: 242 VEPELAKRSMPCGTQVITTERLSE-DLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGG 300 + R +P + +I T L++ L + + + V D L YYRL +DNRLL+GG Sbjct: 259 FNQAVDNRYLPILSNIIVTAPLTDAQLEATGLKTHQVVMDTRRLKYYYRLLSDNRLLFGG 318 Query: 301 -GVVYG--ARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNI 357 G + G A DP ERL + FP L V +D+ WTG L MP N+ Sbjct: 319 RGAISGADAGDPRYGERL-KSAMADCFPALAEVTVDHNWTGWIAAALDDMPHVFS-QGNM 376 Query: 358 YYMQGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMG-AA 416 Y GY G GV + A +A+ + G + LP Y P + +G +A Sbjct: 377 GYSLGYCGSGVAFSAQAAYRLAQHIAG-----ERLPELPLYQSPLPKFHFARLRRLGQSA 431 Query: 417 YYS---LRDR 423 YY LRDR Sbjct: 432 YYQYAWLRDR 441 Lambda K H 0.320 0.138 0.411 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: 514 Number of extensions: 35 Number of successful extensions: 8 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: 426 Length of database: 443 Length adjustment: 32 Effective length of query: 394 Effective length of database: 411 Effective search space: 161934 Effective search space used: 161934 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