Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate 6937936 Sama_2077 oxidoreductase (RefSeq)
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__SB2B:6937936 Length = 429 Score = 307 bits (787), Expect = 4e-88 Identities = 167/430 (38%), Positives = 248/430 (57%), Gaps = 9/430 (2%) Query: 1 MTEHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASR 60 M SYY A+ + L E+I DV V+GGG+TG+++AL LAE G+ VV+LEA++ Sbjct: 1 MQARCGSYYNATIKHETDYPRLTEAIQADVAVIGGGFTGVNTALELAEQGYKVVLLEANK 60 Query: 61 IGFGASGRNGGQLVNSYSRDIDV---IEKSYGMDTARMLGSMMFEGGEIIRERIKRYQID 117 I +GA+GRNGGQ+ S S D + + G + + ++ + G +II+ R+ +Y ID Sbjct: 61 IAWGATGRNGGQVTGSLSGDQAMTKQLRNRIGAEAEDYVWALRWRGHDIIKNRVAKYNID 120 Query: 118 CDYRPGGLFVAMNDKQLATLEEQKENWERYGNKQL-ELLDANAIRREVASDRYTGALLDH 176 CD R G L A + L+ + +R G L L++ + + + + S Y G LL+ Sbjct: 121 CDLRHGHLHTAYKPAHMNELKSMLDEAQRKGMGDLVSLVEKDEMPQYLESPLYHGGLLNK 180 Query: 177 SGGHIHPLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNA 236 H+H +NL IGEA A G R++E + V I VV+TA G VTA V++AGNA Sbjct: 181 KNMHLHSVNLCIGEARAAESLGVRIFEDTQVLDIVEGPRPVVKTAFGSVTANKVLIAGNA 240 Query: 237 Y--LGDKVEPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADN 294 Y LG P+L P T RLS+++A ++ P N V DC ++LDYYRLTADN Sbjct: 241 YHKLG---RPKLRGMLFPASLGNCATVRLSDEVASAINPHNLAVYDCRFVLDYYRLTADN 297 Query: 295 RLLYGGGVVYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLD 354 RL++GGG Y RDP +V + P + +TFP+LKGV+I++ W G + ++R+PQ G++ Sbjct: 298 RLMFGGGTNYSGRDPKNVAEELRPAIERTFPRLKGVEIEFAWAGMAGIVINRIPQLGKVS 357 Query: 355 TNIYYMQGYSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMG 414 ++YY QGYSGHGV +H+ ++A+ + GD F FA + H+ P A+G Sbjct: 358 EHVYYCQGYSGHGVATSHIMSEIMAKAIDGDLREFGLFAGMKHWRIPLNEWFGNQALAIG 417 Query: 415 AAYYSLRDRL 424 YY LR+ L Sbjct: 418 MLYYQLRESL 427 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: 519 Number of extensions: 26 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: 426 Length of database: 429 Length adjustment: 32 Effective length of query: 394 Effective length of database: 397 Effective search space: 156418 Effective search space used: 156418 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