Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate AZOBR_RS25655 AZOBR_RS25655 oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__azobra:AZOBR_RS25655 Length = 426 Score = 208 bits (529), Expect = 3e-58 Identities = 127/405 (31%), Positives = 205/405 (50%), Gaps = 4/405 (0%) Query: 7 PESYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFG 66 P+S + A+A P P P L+D VE D+ VIG G+TGLS+AL E+G + VLEA+++G G Sbjct: 5 PDSLWEATAPPPPALPVLKDSVEADLLVIGGGFTGLSAALHAAESGKRAVVLEASEIGRG 64 Query: 67 ASGRNGGQIVNSYSR-DIDVIERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 ASGRN GQ++ + +R D + + G ++ + + + + + + I C + Sbjct: 65 ASGRNNGQVIPTLTRPDPEDLIAKFGQERGERFVALIRDSAETLFALIRRLNIDCAAEQT 124 Query: 126 G-VFAALTAKQMGHLESQKRLWERFGHTQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 G V + ++ E + + W G +ELLD+ I ++ + Y GG ++ SGGHI+ Sbjct: 125 GWVQPVHSPGRIAIAERRAKQWGSRG-APVELLDRAGISALLGTDAYYGGWMNRSGGHIN 183 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIER-GASPVVHTPQGKVRAKFIIVAGNAYLGNL 243 PL LA G A G ++ SP + +ER G V TP G V +++ N Y + Sbjct: 184 PLALARGLAGKAVEAGASVFINSPVLSVERRGDRWVARTPDGTVTTHALVLGTNGYAAAV 243 Query: 244 VPELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGV 303 PE+ + +P + +AT+PL + S+LP + D + L + R T D RL+ GG + Sbjct: 244 FPEIRTEVVPVLSWQMATQPLDEAQRRSILPGRQAMSDTHGDLRFMRYTADHRLVSGGAL 303 Query: 304 VYGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQG 363 + + I+ ++ FP L+ ++ DY W G +T P+V +LG N + G Sbjct: 304 LVPVDGADRLRRIVGLRLASMFPTLRGLRFDYVWNGRIAMTTDYTPRVHQLGPNAFTWAG 363 Query: 364 CSGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLR 408 C+G GV + G+ LA A G+ A P P LL+ Sbjct: 364 CNGRGVALSVSLGRELAYAALGRDPAELALPLTEPRPLPFNDLLQ 408 Lambda K H 0.320 0.139 0.421 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: 516 Number of extensions: 23 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: 427 Length of database: 426 Length adjustment: 32 Effective length of query: 395 Effective length of database: 394 Effective search space: 155630 Effective search space used: 155630 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