Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate 200442 SO1264 hypothetical oxidoreductase (NCBI ptt file)
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__MR1:200442 Length = 435 Score = 348 bits (894), Expect = e-100 Identities = 175/423 (41%), Positives = 259/423 (61%), Gaps = 3/423 (0%) Query: 3 EHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIG 62 ++ SYY +A + L SIT DVC+VGGG++G+++A+ L + G VV+LEA R+G Sbjct: 11 QYPHSYYLDTAKEIYAHPQLEGSITADVCIVGGGFSGINTAIELRQRGLSVVLLEAKRMG 70 Query: 63 FGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYRP 122 +GASGRNGG+L+ D G + + M FE +I+R RI+ +QIDCD + Sbjct: 71 WGASGRNGGELIRGIGHDPAQFINEIGQEGVSAIQQMGFEAVDIVRNRIQTHQIDCDLQM 130 Query: 123 GGLFVAMNDKQLATLEEQKENWERYGNK-QLELLDANAIRREVASDRYTGALLDHSGGHI 181 G +A+ + + L+E+ E+ + G K +++LL + + + SD Y GAL+D GH+ Sbjct: 131 GYCDLAVKPRHMIELQEEFESLKSLGYKHEIKLLAQSQLGNVIGSDFYQGALVDMGSGHL 190 Query: 182 HPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGDK 241 HPLNLA+GEA R G +++E SA +I V TAKG+VT +Y+++AGNAY+G K Sbjct: 191 HPLNLALGEARVARELGAQLFEYSAAEKIIQGDKPKVLTAKGEVTCQYLVLAGNAYIGHK 250 Query: 242 VEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGG 301 + + + +P G+ ++ TE L++ +++IP+N D LDY+ L+AD RLL+GG Sbjct: 251 LNSYIGGKVLPAGSYLLATEPLTQQQCKNIIPQNMAFADMRIALDYFHLSADRRLLFGGL 310 Query: 302 VVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD--TNIYY 359 Y +DP D+E + P L K FPQLKGV+IDY W G + +RMPQ GRL +NI++ Sbjct: 311 CTYSGKDPKDIEAALRPNLEKVFPQLKGVRIDYEWGGMIGIGANRMPQIGRLPDASNIFF 370 Query: 360 MQGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYS 419 Q Y+GHGV TH+A +L+AE + A FD FA + H FPGG T R P A G Y+ Sbjct: 371 AQAYAGHGVNATHMAAKLLAEAICQQAGHFDVFAKIKHMTFPGGPTFRSPMLAAGMLYHR 430 Query: 420 LRD 422 +D Sbjct: 431 FKD 433 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: 510 Number of extensions: 22 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: 426 Length of database: 435 Length adjustment: 32 Effective length of query: 394 Effective length of database: 403 Effective search space: 158782 Effective search space used: 158782 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