Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate Pf6N2E2_359 Opine oxidase subunit B
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_359 Length = 424 Score = 170 bits (431), Expect = 7e-47 Identities = 130/404 (32%), Positives = 200/404 (49%), Gaps = 15/404 (3%) Query: 29 DVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIGFGASGRNGGQLVNSYSRDIDVIEKSY 88 DV +VGGG+TGL++A LA G V VLEA R+ ASGRNGG ++D + S Sbjct: 27 DVAIVGGGFTGLAAARALALKGASVAVLEAGRVIGEASGRNGGHCSTGVAQDYAALTASL 86 Query: 89 GMDTARMLGSMMFEGGEIIRERIKRYQIDCDY-RPGGLFVAMNDKQLATLEEQKENWERY 147 G D AR + +++ QI CD R G L +A L E + Sbjct: 87 GADKARAYYQAYENAVHSVVTLVEQEQIACDLKRNGKLKLAAKPMHYEGLARTCELIRKE 146 Query: 148 GNKQLELLDANAIRREVASDRYTGALLDHSGGHIHPLNLAIGEADAIRLNGGRVYELSAV 207 + ++ELL A R EV S ++ G LL +G +H +G A+A +G +++ AV Sbjct: 147 VDAEVELLSAQETRAEVNSAQFHGGLLQRNGVQMHVGRFGVGLAEAAARHGALIFQGVAV 206 Query: 208 TQIQHTTPAV-VRTAKGQVTAKYVIVA-GNAYLGDKVEPELAKRSMPCGTQVITTERLSE 265 + + V T+KG + A +++A G G +R +P G+ VI TE L + Sbjct: 207 QDWKASAGGYRVNTSKGALQASQILLATGTCQQGGL--GWYRRRIVPVGSFVIATEVLPQ 264 Query: 266 DLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGARDP-DDVE--RLVVPKLLK 322 L +L+P + +Y+RLT DNRLL+GG + D D + +++ +++ Sbjct: 265 VLIDNLLPARRSYVTSRMIGNYFRLTPDNRLLFGGRARFAMSDSVSDAKSGKVLQAAMVQ 324 Query: 323 TFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYMQGYSGHGVTCTHLAGRLIAELL 382 FPQL +IDY W G +T R+P+ G+ +Y+ GYSGHGV + G+++AE++ Sbjct: 325 MFPQLANTRIDYCWGGLVDMTSDRLPRAGQ-HGGVYHSMGYSGHGVQMSVHMGQVMAEVM 383 Query: 383 RGDAERFDAFANLPHYPFPG--GRTLRVPFTAMGAAYYSLRDRL 424 G E + + L PG G+ +P AYY L+D L Sbjct: 384 AGKVEA-NPWRELDWPAIPGHFGKPWFLPLV---GAYYRLQDYL 423 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: 502 Number of extensions: 38 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: 424 Length adjustment: 32 Effective length of query: 394 Effective length of database: 392 Effective search space: 154448 Effective search space used: 154448 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