Align Gamma-glutamylputrescine oxidoreductase; Gamma-Glu-Put oxidase; Gamma-glutamylputrescine oxidase; EC 1.4.3.- (characterized)
to candidate Pf1N1B4_4356 Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)
Query= SwissProt::P37906 (426 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4356 Length = 432 Score = 621 bits (1602), Expect = 0.0 Identities = 292/424 (68%), Positives = 348/424 (82%) Query: 3 EHTSSYYAASANKYAPFDTLNESITCDVCVVGGGYTGLSSALHLAEAGFDVVVLEASRIG 62 +H +SYYAA+ N F L +++ CDVCV+G GYTGLSSAL L+EAG+ V VLEA+++G Sbjct: 9 KHVNSYYAATRNFTGDFPVLEQAVDCDVCVIGAGYTGLSSALFLSEAGYSVTVLEAAKVG 68 Query: 63 FGASGRNGGQLVNSYSRDIDVIEKSYGMDTARMLGSMMFEGGEIIRERIKRYQIDCDYRP 122 FGASGRNGGQLVNSYSRD+DVIE+ YG TA +LGSM+FEG +IIR RIK Y I CDYRP Sbjct: 69 FGASGRNGGQLVNSYSRDVDVIEERYGDKTAEVLGSMIFEGADIIRSRIKEYDIQCDYRP 128 Query: 123 GGLFVAMNDKQLATLEEQKENWERYGNKQLELLDANAIRREVASDRYTGALLDHSGGHIH 182 GG+F A+N KQL L EQK +WERYGNK L +LDA I+REV D Y G LLD GGHIH Sbjct: 129 GGIFAALNKKQLNGLAEQKSSWERYGNKNLRMLDAADIKREVGCDNYVGGLLDMQGGHIH 188 Query: 183 PLNLAIGEADAIRLNGGRVYELSAVTQIQHTTPAVVRTAKGQVTAKYVIVAGNAYLGDKV 242 PLNLA+GEA AI GG++YE SA +I + P VRTAKG V AKY+++AGNAYL + Sbjct: 189 PLNLALGEAAAIIRLGGKIYEQSAAVEITYGEPITVRTAKGVVRAKYLLIAGNAYLPQDL 248 Query: 243 EPELAKRSMPCGTQVITTERLSEDLARSLIPKNYCVEDCNYLLDYYRLTADNRLLYGGGV 302 + + ++SMPCG+Q++ TE LSE +ARSLI NYCVEDCNYLLDYYRLTADNRLLYGGGV Sbjct: 249 DNRVTRKSMPCGSQIVVTEPLSEKVARSLIANNYCVEDCNYLLDYYRLTADNRLLYGGGV 308 Query: 303 VYGARDPDDVERLVVPKLLKTFPQLKGVKIDYRWTGNFLLTLSRMPQFGRLDTNIYYMQG 362 VYGAR+PDD+E+L+ PK+LKTFPQLK VKIDYRWTGNFLLT+SRMPQFGR++ N YYMQG Sbjct: 309 VYGAREPDDIEQLIRPKILKTFPQLKDVKIDYRWTGNFLLTMSRMPQFGRIEKNAYYMQG 368 Query: 363 YSGHGVTCTHLAGRLIAELLRGDAERFDAFANLPHYPFPGGRTLRVPFTAMGAAYYSLRD 422 YSGHGVTC+HLAG+LI+E++RGDAERFDAFA+LPH P GGRT + P TAMGAAYY+LRD Sbjct: 369 YSGHGVTCSHLAGKLISEMIRGDAERFDAFASLPHMPMLGGRTFQAPLTAMGAAYYALRD 428 Query: 423 RLGV 426 R G+ Sbjct: 429 RFGI 432 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: 684 Number of extensions: 23 Number of successful extensions: 1 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: 432 Length adjustment: 32 Effective length of query: 394 Effective length of database: 400 Effective search space: 157600 Effective search space used: 157600 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